From b2b4f345fe1733316d5368c0057b62307f4ecc45 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Sun, 18 Sep 2016 11:30:50 +1200 Subject: [PATCH 01/28] Added missing CMake files for Classical Field Laplace example --- .../Laplace/Laplace/C/CMakeLists.txt | 24 +++++ ClassicalField/Laplace/Laplace/CMakeLists.txt | 38 ++++++++ .../Laplace/Laplace/Fortran/CMakeLists.txt | 50 ++++++++++ .../Laplace/Laplace/OpenCMISS.cmake | 95 +++++++++++++++++++ 4 files changed, 207 insertions(+) create mode 100644 ClassicalField/Laplace/Laplace/C/CMakeLists.txt create mode 100644 ClassicalField/Laplace/Laplace/CMakeLists.txt create mode 100644 ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt create mode 100644 ClassicalField/Laplace/Laplace/OpenCMISS.cmake diff --git a/ClassicalField/Laplace/Laplace/C/CMakeLists.txt b/ClassicalField/Laplace/Laplace/C/CMakeLists.txt new file mode 100644 index 00000000..441045e2 --- /dev/null +++ b/ClassicalField/Laplace/Laplace/C/CMakeLists.txt @@ -0,0 +1,24 @@ +# Add example executable +add_executable(laplace_c src/CExample.f90) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(fsi_fortran PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Laplace_C COMMAND laplace_c) +add_opencmiss_environment(Laplace_C) + diff --git a/ClassicalField/Laplace/Laplace/CMakeLists.txt b/ClassicalField/Laplace/Laplace/CMakeLists.txt new file mode 100644 index 00000000..8ed2810c --- /dev/null +++ b/ClassicalField/Laplace/Laplace/CMakeLists.txt @@ -0,0 +1,38 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(./OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran) +enable_language(C OPTIONAL) +enable_testing() + +message(STATUS "C Compiler: ${CMAKE_C_COMPILER}") +message(STATUS "MPI: ${MPI}") + + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(Fortran) +endif() diff --git a/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt b/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt new file mode 100644 index 00000000..b65b1c1d --- /dev/null +++ b/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(laplace_fortran src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(laplace_fortran PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(laplace_fortran PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Fsi_Fortran COMMAND laplace_fortran) +add_opencmiss_environment(Fsi_Fortran) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Laplace/Laplace/OpenCMISS.cmake b/ClassicalField/Laplace/Laplace/OpenCMISS.cmake new file mode 100644 index 00000000..d1798862 --- /dev/null +++ b/ClassicalField/Laplace/Laplace/OpenCMISS.cmake @@ -0,0 +1,95 @@ +########################### +# *DO NOT CHANGE THIS FILE* +########################### +# +# Prepares the use of OpenCMISS by scanning at various path locations for OpenCMISS (SDK) installations. +# +# Search order: +# - OPENCMISS_INSTALL_DIR variable +# - OPENCMISS_INSTALL_DIR environment variable +# - OPENCMISS_SDK_DIR variable +# - OPENCMISS_SDK_DIR environment variable +# - [Windows only] The Registry is searched additionally for installed SDKs. +# +# If found +# - Includes the toolchain config script of the found opencmiss installation to enable toolchain selection logic (non-windows) + +# Convenience: The OPENCMISS_INSTALL_DIR may also be defined in the environment and various other places +if (DEFINED OPENCMISS_INSTALL_DIR) + get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE) + if (EXISTS "${OPENCMISS_INSTALL_DIR}") + message(STATUS "Using specified installation directory '${OPENCMISS_INSTALL_DIR}'") + else() + message(WARNING "The specified OPENCMISS_INSTALL_DIR '${OPENCMISS_INSTALL_DIR}' does not exist. Skipping.") + unset(OPENCMISS_INSTALL_DIR) + endif() +endif() +if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_INSTALL_DIR}" STREQUAL "") + file(TO_CMAKE_PATH "$ENV{OPENCMISS_INSTALL_DIR}" OPENCMISS_INSTALL_DIR) + get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE) + if (EXISTS "${OPENCMISS_INSTALL_DIR}") + message(STATUS "Using environment installation directory '${OPENCMISS_INSTALL_DIR}'") + else() + message(WARNING "The environment variable OPENCMISS_INSTALL_DIR='${OPENCMISS_INSTALL_DIR}' contains an invalid path. Skipping.") + unset(OPENCMISS_INSTALL_DIR) + endif() +endif() +if (NOT OPENCMISS_INSTALL_DIR AND DEFINED OPENCMISS_SDK_DIR) + get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE) + if (EXISTS "${OPENCMISS_SDK_DIR}") + message(STATUS "Using SDK installation directory: ${OPENCMISS_SDK_DIR}") + set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}") + else() + message(WARNING "The specified OPENCMISS_SDK_DIR '${OPENCMISS_SDK_DIR}' does not exist. Skipping.") + endif() +endif() +if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_SDK_DIR}" STREQUAL "") + file(TO_CMAKE_PATH "$ENV{OPENCMISS_SDK_DIR}" OPENCMISS_SDK_DIR) + get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE) + if (EXISTS "${OPENCMISS_SDK_DIR}") + message(STATUS "Using environment SDK installation directory: ${OPENCMISS_SDK_DIR}") + set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}") + else() + message(WARNING "The environment variable OPENCMISS_SDK_DIR='${OPENCMISS_SDK_DIR}' contains an invalid path. Skipping.") + unset(OPENCMISS_SDK_DIR) + endif() +endif() +# On windows: check the registry for installed OpenCMISS SDKs +if(NOT OPENCMISS_INSTALL_DIR AND WIN32) + foreach(ROOT HKEY_CURRENT_USER HKEY_LOCAL_MACHINE) + foreach(PACKAGE OpenCMISSUserSDK OpenCMISSDeveloperSDK) + set(_REG_KEY "[${ROOT}\\Software\\Auckland Bioengineering Institute\\${PACKAGE}]") + get_filename_component(OPENCMISS_INSTALL_DIR "${_REG_KEY}" ABSOLUTE) + #message(STATUS "Trying registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}") + if (EXISTS "${OPENCMISS_INSTALL_DIR}") + message(STATUS "Found ${PACKAGE} in Windows registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}") + break() + else() + unset(OPENCMISS_INSTALL_DIR) + endif() + endforeach() + if (EXISTS "${OPENCMISS_INSTALL_DIR}") + break() + endif() + endforeach() +endif() + +if(OPENCMISS_INSTALL_DIR) + message(STATUS "OPENCMISS_INSTALL_DIR=${OPENCMISS_INSTALL_DIR}") + # Use the OpenCMISS scripts to also allow choosing a separate toolchain + # This file is located at the opencmiss installation rather than the local example + # as it avoids file replication and makes maintenance much easier + if (TOOLCHAIN) + set(_OCTC ${OPENCMISS_INSTALL_DIR}/cmake/OCToolchainCompilers.cmake) + if (EXISTS "${_OCTC}") + include(${_OCTC}) + else() + message(WARNING "TOOLCHAIN specified but OpenCMISS config script could not be found at ${_OCTC}. Trying CMake defaults.") + endif() + unset(_OCTC) + endif() + set(OpenCMISS_DIR "${OPENCMISS_INSTALL_DIR}" CACHE PATH "Path to the found OpenCMISS (SDK) installation") +else() + message(WARNING "No OpenCMISS (SDK) installation directory detected. Using default system environment.") +endif() + From 93553a87ca2534e3f8d6e748a11686502d2426f0 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Sun, 18 Sep 2016 15:49:15 +1200 Subject: [PATCH 02/28] Fortran Classical Field Laplace example modified to work with MPI decomposition by default --- .../Laplace/Laplace/Fortran/src/FortranExample.f90 | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/ClassicalField/Laplace/Laplace/Fortran/src/FortranExample.f90 b/ClassicalField/Laplace/Laplace/Fortran/src/FortranExample.f90 index c4ff1b80..32673c14 100644 --- a/ClassicalField/Laplace/Laplace/Fortran/src/FortranExample.f90 +++ b/ClassicalField/Laplace/Laplace/Fortran/src/FortranExample.f90 @@ -186,6 +186,16 @@ PROGRAM LAPLACEEXAMPLE !Get the computational nodes information CALL cmfe_ComputationalNumberOfNodesGet(NumberOfComputationalNodes,Err) CALL cmfe_ComputationalNodeNumberGet(ComputationalNodeNumber,Err) + + !If MPI is being used, check that global number of elements is sufficient enough to run + IF ( NumberOfComputationalNodes>1 ) THEN + IF ( NUMBER_GLOBAL_X_ELEMENTS==1 ) THEN + NUMBER_GLOBAL_X_ELEMENTS = 3 + ENDIF + ! IF ( NUMBER_GLOBAL_Z_ELEMENTS==1 ) THEN + ! NUMBER_GLOBAL_Z_ELEMENTS = 3 + ! ENDIF + ENDIF !Start the creation of a new RC coordinate system CALL cmfe_CoordinateSystem_Initialise(CoordinateSystem,Err) From 1cc1df986b90aceba6c6249af855aef0b5308713 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Sun, 18 Sep 2016 16:07:04 +1200 Subject: [PATCH 03/28] C version of Classical Field Laplace example enabled --- ClassicalField/Laplace/Laplace/C/CMakeLists.txt | 4 ++-- ClassicalField/Laplace/Laplace/CMakeLists.txt | 8 ++++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/ClassicalField/Laplace/Laplace/C/CMakeLists.txt b/ClassicalField/Laplace/Laplace/C/CMakeLists.txt index 441045e2..e6e04ed5 100644 --- a/ClassicalField/Laplace/Laplace/C/CMakeLists.txt +++ b/ClassicalField/Laplace/Laplace/C/CMakeLists.txt @@ -1,5 +1,5 @@ # Add example executable -add_executable(laplace_c src/CExample.f90) +add_executable(laplace_c src/CExample.c) # Link to opencmiss # ----------------- @@ -16,7 +16,7 @@ add_executable(laplace_c src/CExample.f90) # target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) # # All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. -target_link_libraries(fsi_fortran PRIVATE opencmiss) +target_link_libraries(laplace_c PRIVATE opencmiss) # Add a simple test that runs the executable add_test(NAME Laplace_C COMMAND laplace_c) diff --git a/ClassicalField/Laplace/Laplace/CMakeLists.txt b/ClassicalField/Laplace/Laplace/CMakeLists.txt index 8ed2810c..a57d23ef 100644 --- a/ClassicalField/Laplace/Laplace/CMakeLists.txt +++ b/ClassicalField/Laplace/Laplace/CMakeLists.txt @@ -11,11 +11,12 @@ include(./OpenCMISS.cmake) # Project setup # ------------- cmake_minimum_required(VERSION 3.3 FATAL_ERROR) -project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran) -enable_language(C OPTIONAL) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +#enable_language(C OPTIONAL) enable_testing() message(STATUS "C Compiler: ${CMAKE_C_COMPILER}") +message(STATUS "FORTRAN Compiler: ${CMAKE_Fortran_COMPILER}") message(STATUS "MPI: ${MPI}") @@ -36,3 +37,6 @@ find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) if (CMAKE_Fortran_COMPILER) add_subdirectory(Fortran) endif() +if (CMAKE_C_COMPILER) + add_subdirectory(C) +endif() From d90c3860ffe8f989a5dc153127734f44ab6d9bf4 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Sun, 18 Sep 2016 16:11:23 +1200 Subject: [PATCH 04/28] renamed Fsi_Fortran environment variable to Laplace_Fortran --- ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt b/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt index b65b1c1d..d447c38b 100644 --- a/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt +++ b/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt @@ -27,8 +27,8 @@ target_compile_options(laplace_fortran PRIVATE ${PROC_OPT}) target_link_libraries(laplace_fortran PRIVATE opencmiss) # Add a simple test that runs the executable -add_test(NAME Fsi_Fortran COMMAND laplace_fortran) -add_opencmiss_environment(Fsi_Fortran) +add_test(NAME Laplace_Fortran COMMAND laplace_fortran) +add_opencmiss_environment(Laplace_Fortran) ################### # Developer notice! From aa8f744cfb325479619cf1476fd88d6b03de19d8 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Tue, 11 Oct 2016 11:20:21 +1300 Subject: [PATCH 05/28] fixed import opencmiss.iron call --- .../NavierStokes/LidDrivenCavity/LidDriven.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py b/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py index fcc3877f..a036d3f9 100644 --- a/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py +++ b/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py @@ -49,13 +49,16 @@ # Add Python bindings directory to PATH import sys, os -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append(os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/intel-C16.0-intel-F16.0/intel_release/release', + 'python', + 'RELEASE'))) import math import time # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron # Get the computational nodes information numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet() @@ -459,7 +462,3 @@ def LidDriven(numberOfElements,cavityDimensions,lidVelocity,viscosity,density, iron.Finalise() - - - - From 9b2b8c4509f9a80b806bd38a52770981058e4476 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Fri, 14 Oct 2016 14:51:38 +1300 Subject: [PATCH 06/28] Cmake build added for Bioelectrics/Monodomain example. Python example fixed --- Bioelectrics/Monodomain/CMakeLists.txt | 37 + Bioelectrics/Monodomain/Fortran/FHN.xml | 355 -- Bioelectrics/Monodomain/Fortran/LRd.xml | 4320 ------------- Bioelectrics/Monodomain/Fortran/Makefile | 71 - .../Monodomain/Fortran/{ => input}/n98.xml | 0 Bioelectrics/Monodomain/Fortran/jrw-1998.xml | 5332 ----------------- .../Monodomain/Fortran/src/FortranExample.f90 | 4 +- Bioelectrics/Monodomain/OpenCMISS.cmake | 95 + .../Monodomain/Python/Monodomain2DSquare.py | 7 +- 9 files changed, 139 insertions(+), 10082 deletions(-) create mode 100644 Bioelectrics/Monodomain/CMakeLists.txt delete mode 100644 Bioelectrics/Monodomain/Fortran/FHN.xml delete mode 100644 Bioelectrics/Monodomain/Fortran/LRd.xml delete mode 100644 Bioelectrics/Monodomain/Fortran/Makefile rename Bioelectrics/Monodomain/Fortran/{ => input}/n98.xml (100%) delete mode 100644 Bioelectrics/Monodomain/Fortran/jrw-1998.xml create mode 100644 Bioelectrics/Monodomain/OpenCMISS.cmake diff --git a/Bioelectrics/Monodomain/CMakeLists.txt b/Bioelectrics/Monodomain/CMakeLists.txt new file mode 100644 index 00000000..4c514945 --- /dev/null +++ b/Bioelectrics/Monodomain/CMakeLists.txt @@ -0,0 +1,37 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(./OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +message(STATUS "FORTRAN Compiler: ${CMAKE_Fortran_COMPILER}") +message(STATUS "MPI: ${MPI}") + + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(Fortran) +endif() diff --git a/Bioelectrics/Monodomain/Fortran/FHN.xml b/Bioelectrics/Monodomain/Fortran/FHN.xml deleted file mode 100644 index c01c9d20..00000000 --- a/Bioelectrics/Monodomain/Fortran/FHN.xml +++ /dev/null @@ -1,355 +0,0 @@ - - - - -
- - The FitzHugh-Nagumo Simplified Cardiac Myocyte Model - - Catherine - Lloyd - - Bioengineering Institute, University of Auckland - - - -
- Model Status - - This version of the model has been curated by Penny Noble using - COR and is also known to read in to JSim and PCEnv. There is also a PCEnv session file associated with this model. - -
- -Model Structure - - -Often it is not necessary to model the ionic currents of a cell with the accuracy and complexity inherent in the biophysically based models. With a view to investigating phenomena on a larger spatial and temporal scale, several ionic current models have been developed that do not seek to model subcellular processes but only to provide an action potential at a minimal computational cost. - - - -The FitzHugh-Nagumo model (1961) is based on the cubic excitation model (see The Polynomial Model, 1975), but it also includes a recovery variable so both depolarisation and repolarisation can be modelled. In 1994, Rogers and McCulloch modified the original model to generate a more realistic action potential. The velocity of the upstroke was increased and the large hyperpolarisation at the end of the recovery phase was removed. The model parameters were also updated. In 1996, this form of the already modified FitzHugh_Nagumo model was further updated by Aliev and Panfilov. They altered the equation which modelled the change of the recovery variable to provide a more realistic restitution period and to allow for reentrant phenomena. - - - -The complete original paper references are cited below: - - - -Impulses and physiological states in theoretical models of nerve membrane, FitzHugh, R.A., 1961, - Biophys. J. - , 1, 445-466. - - - -An active pulse transmission line simulating nerve axon, Nagumo, J., Animoto, S., Yoshizawa, S., 1962, Proc. Inst. Radio Engineers, 50, 2061-2070. - - - -A collocation-Galerkin finite element model of cardiac action potential propagation, Rogers, J.M., McCulloch, A.D., 1994a, - IEEE Trans. Biomed. Eng. - , 41, 743-757. - - - -A simple two-variable model of cardiac excitation, Aliev, R.R. and Panfilov, A.V., 1996, - Chaos, Solitons and Fractals - , 7, 293-301. PubMed ID: 8796189 - - - -The raw CellML description of the simplified cardiac myocyte models can be downloaded in various formats as described in . For an example of a more complete documentation for an electrophysiological model, see The Hodgkin-Huxley Squid Axon Model, 1952. - - - -
- - - - - - - - - - - - - - - - - - - - - - - t - - v - - - - 1 - - - - - - - v - - - v - alpha - - - - 1 - v - - - w - - I - - - - - - - - - t - - w - - - - 1 - epsilon - - - v - - - gamma - w - - - - - - - - - - - - - - - - - - - - - J - Nagumo - - - - - - - - - - - - - - S - Yoshizawa - - - 1962-10-01 00:00 - - - - - - - - Peter - Villiger - J - - - - An active pulse transmission line simulating nerve axon - 50 - 2061 - - - 2070 - - - J - Nagumo - - - Penny - Noble - J - - - - - - - - - - - - - - - - - - Penny - Noble - - - - 1000 - 10000 - - - - - - - Department of Physiology, Anatomy & Genetics, University of Oxford - - - - - - - Biophysical Journal - - - S - Arimoto - - - - - - - - Impulses and Physiological States in Theoretical Models of Nerve Membrane - 1 - 445 - - - 466 - - - 2005-06-14T00:00:00+00:00 - - - - - - - - keyword - - - simplified model - neuron - electrophysiology - cardiac - Myocyte - - - - - - - - - added metadata - - - - - Units checked, curated. - - - - - - - - - - - 2007-11-29T12:16:16+13:00 - - - - - - Oxford University - The Bioengineering Institute - - - Biophysical Journal - - - - - - Richard - Fitzhugh - A - - - - - - - - - - - penny.noble@physiol.ox.ac.uk - - - 1961-01-01 - - - - - - - 2006-03-31 - - - \ No newline at end of file diff --git a/Bioelectrics/Monodomain/Fortran/LRd.xml b/Bioelectrics/Monodomain/Fortran/LRd.xml deleted file mode 100644 index 1fd24b84..00000000 --- a/Bioelectrics/Monodomain/Fortran/LRd.xml +++ /dev/null @@ -1,4320 +0,0 @@ - - - - - - - - - - - - - Lloyd - Catherine - May - - - c.lloyd@auckland.ac.nz - - - - The University of Auckland - The Bioengineering Institute - - - - - - 2002-03-28 - - - - - - Fixed maths. - - - - Lloyd - Catherine - May - - - - 2003-07-30 - - - - - Fixed maths: alpha_J_calculation in fast_sodium_current_j_gate, - beta_K1_calculation in time_independent_potassium_current_K1_gate, and i_NaK_calculation in sodium_potassium_pump. - - - - Lloyd - Catherine - May - - - - 2003-06-05 - - - - - - The University of Auckland, The Bioengineering Institute - - - - - - - - The Luo-Rudy II Model of Mammalian Ventricular Cardiac Action - Potentials, 1994 - - - - - - This is the CellML description of Luo and Rudy's mathematical model of - the mammalian cardiac ventricular action potential. It is a - significant development on their original 1991 model. While this - version of the model qualitatively compares well to the LR II paper - for the action potential, the intracellular calcium dynamics have not - been included correctly - namely there is no calcium-induced - calcium-release (CICR) process in this version of the model. The - original version of the model simulates CICR via a mechanism whereby - CICR is induced if and only if the calcium accumulated in the cell in - the 2 ms following (dV/dt)max exceeds a given threshold. This sort of - process is a bit tricky to include in the CellML (or at least in a way - that will work with the CellML abilitites of CMISS) so has been left - out for now. - - - - Catherine Lloyd - - - - - Mammalia - - Ventricular Myocyte - - - - 7514509 - - - - bdf - newton - dense - - - - - - - 0.01 - - - 1.0 - - - 0 - - - 700 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The main component for the model, contains all ionic currents and - defines the transmembrane potential. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - We need to use dV/dt in the calulation of calcium-induced - calcium-release, so we make it accessible here. - - - - - - - dV_dt - - - I_st - - i_Na - i_Ca_L - i_K - i_K1 - i_Kp - i_NaCa - i_p_Ca - i_Na_b - i_Ca_b - i_NaK - i_ns_Ca - - - Cm - - - - - - - - - Assign the rate of change of potential for the differential - equation. - - - - - - - - time - V - - dV_dt - - - - - - - - - - - The fast sodium current is primarily responsible for the upstroke of - the action potential. - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the fast sodium current. - - - - - - - i_Na - - g_Na - - m - 3.0 - - h - j - - V - E_Na - - - - - - - - - - Calculation of reversal potential for the fast sodium channel. - - - - - - - E_Na - - - - R - T - - F - - - - Nao - Nai - - - - - - - - - - - - - The voltage-dependent activation gate for the fast sodium channel - - the m gate. - - - - - - - - - - - - - - - - - - The opening rate for the m gate. - - - - - - - alpha_m - - - 0.32 - - V - 47.13 - - - - 1.0 - - - -0.1 - - V - 47.13 - - - - - - - - - - - - - The closing rate for the m gate. - - - - - - - beta_m - - 0.08 - - - - V - - 11.0 - - - - - - - - - - - The kinetics of the m gate. - - - - - - - - time - m - - - - alpha_m - - 1.0 - m - - - - beta_m - m - - - - - - - - - - - - The voltage-dependent inactivation gate for the fast sodium channel - - the h gate. - - - - - - - - - - - - - - - - - - The opening rate for the h gate. - - - - - - - alpha_h - - - - 0.135 - - - - 80.0 - V - - -6.8 - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate for the h gate. - - - - - - - beta_h - - - - - 3.56 - - - 0.079 - V - - - - - 310000.0 - - - 0.35 - V - - - - - - V - -40.0 - - - - - 1.0 - - 0.13 - - 1.0 - - - - V - 10.66 - - -11.1 - - - - - - - - - - - - - - - The kinetics of the h gate. - - - - - - - - time - h - - - - alpha_h - - 1.0 - h - - - - beta_h - h - - - - - - - - - - - - The voltage-dependent slow inactivation gate for the fast sodium - channel - the j gate. - - - - - - - - - - - - - - - - - - The opening rate for the j gate. - - - - - - - alpha_j - - - - - - -127140.0 - - - 0.2444 - V - - - - - 0.00003474 - - - -0.04391 - V - - - - - - - V - 37.78 - - - 1.0 - - - 0.311 - - V - 79.23 - - - - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate for the j gate. - - - - - - - beta_j - - - - - 0.1212 - - - -0.01052 - V - - - - - 1.0 - - - -0.1378 - - V - 40.14 - - - - - - - V - -40.0 - - - - - - 0.3 - - - -0.0000002535 - V - - - - - 1.0 - - - -0.1 - - V - 32.0 - - - - - - - - - - - - - - - The kinetics of for the j gate. - - - - - - - - time - j - - - - alpha_j - - 1.0 - j - - - - beta_j - j - - - - - - - - - - - - The L-type calcium channel. Primarily a calcium specific channel, - but with small potassium and sodium components, activated at plateau - potentials. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The calcium component of the total L-type channel current. - - - - - - - i_CaCa - - d - f - f_Ca - I_CaCa - - - - - - - - - The sodium component of the total L-type channel current. - - - - - - - i_CaNa - - d - f - f_Ca - I_CaNa - - - - - - - - - The potassium component of the total L-type channel current. - - - - - - - i_CaK - - d - f - f_Ca - I_CaK - - - - - - - - - The maximum calcium component of the total L-type channel current. - - - - - - - I_CaCa - - P_Ca - - 2.0 - 2.0 - - - - V - - F - 2.0 - - - - R - T - - - - - - gamma_Cai - Cai - - - - 2.0 - V - F - - - R - T - - - - - - gamma_Cao - Cao - - - - - - - 2.0 - V - F - - - R - T - - - - 1.0 - - - - - - - - - - - The maximum sodium component of the total L-type channel current. - - - - - - - I_CaNa - - P_Na - - 1.0 - 2.0 - - - - V - - F - 2.0 - - - - R - T - - - - - - gamma_Nai - Nai - - - - 1.0 - V - F - - - R - T - - - - - - gamma_Nao - Nao - - - - - - - 1.0 - V - F - - - R - T - - - - 1.0 - - - - - - - - - - - The maximum potassium component of the total L-type channel current. - - - - - - - I_CaK - - P_K - - 1.0 - 2.0 - - - - V - - F - 2.0 - - - - R - T - - - - - - gamma_Ki - Ki - - - - 1.0 - V - F - - - R - T - - - - - - gamma_Ko - Ko - - - - - - - 1.0 - V - F - - - R - T - - - - 1.0 - - - - - - - - - - - The total current of the L-type channel current. - - - - - - - i_Ca_L - - i_CaCa - i_CaK - i_CaNa - - - - - - - - - - - The voltage-dependent activation gate for the L-type calcium - channel - the d gate. - - - - - - - - - - - - - - - - - - - - The opening rate of the d gate. - - - - - - - alpha_d - - d_infinity - tau_d - - - - - - - d_infinity - - 1.0 - - 1.0 - - - - - V - 10.0 - - 6.24 - - - - - - - - - - - tau_d - - d_infinity - - - 1.0 - - - - - V - 10.0 - - 6.24 - - - - - - 0.035 - - V - 10.0 - - - - - - - - - - - - The closing rate of the d gate. - - - - - - - beta_d - - - 1.0 - d_infinity - - tau_d - - - - - - - - - The kinetics of the d gate. - - - - - - - - time - d - - - - alpha_d - - 1.0 - d - - - - beta_d - d - - - - - - - - - - - - The voltage-dependent inactivation gate for the L-type calcium - channel - the f gate. - - - - - - - - - - - - - - - - - - - - The opening rate of the f gate. - - - - - - - alpha_f - - f_infinity - tau_f - - - - - - - f_infinity - - - 1.0 - - 1.0 - - - - V - 35.06 - - 8.6 - - - - - - 0.6 - - 1.0 - - - - 50.0 - V - - 20.0 - - - - - - - - - - - tau_f - - 1.0 - - - 0.0197 - - - - - 0.0337 - - V - 10.0 - - - 2.0 - - - - - 0.02 - - - - - - - - - - The closing rate of the f gate. - - - - - - - beta_f - - - 1.0 - f_infinity - - tau_f - - - - - - - - - The kinetics of the f gate. - - - - - - - - time - f - - - - alpha_f - - 1.0 - f - - - - beta_f - f - - - - - - - - - - - - The calcium-dependent inactivation gate for the L-type calcium - channel - the fCa gate. - - - - - - - - - - - - - - - - - - The kinetics of the fCa gate. - - - - - - - f_Ca - - 1.0 - - 1.0 - - - Cai - Km_Ca - - 2.0 - - - - - - - - - - - - - The time-dependent potassium reploarisation current. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The conductance for the channel. - - - - - - - g_K - - g_K_max - - - Ko - 5.4 - - - - - - - - - - - The reversal potential of the channel. - - - - - - - E_K - - - - R - T - - F - - - - - Ko - - PR_NaK - Nao - - - - Ki - - PR_NaK - Nai - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_K - - g_K - - X - 2.0 - - Xi - - V - E_K - - - - - - - - - - - - The time-dependent activation gate for the time-dependent potassium - current - the X gate. - - - - - - - - - - - - - - - - - - The opening rate for the X gate. - - - - - - - alpha_X - - - 0.0000719 - - V - 30.0 - - - - 1.0 - - - -0.148 - - V - 30.0 - - - - - - - - - - - - - The closing rate for the X gate. - - - - - - - beta_X - - - 0.000131 - - V - 30.0 - - - - -1.0 - - - 0.0687 - - V - 30.0 - - - - - - - - - - - - - The kinetics of the X gate. - - - - - - - - time - X - - - - alpha_X - - 1.0 - X - - - - beta_X - X - - - - - - - - - - - - The time-independent inactivation gate for the time-dependent - potassium current - the Xi gate. - - - - - - - - - - - - - - - The kinetics of the Xi gate. - - - - - - - Xi - - 1.0 - - 1.0 - - - - V - 56.26 - - 32.1 - - - - - - - - - - - - - - The time-independent potassium repolarisation current. - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the channel conductance. - - - - - - - g_K1 - - g_K1_max - - - Ko - 5.4 - - - - - - - - - - - Calculation of the channel reversal potential. - - - - - - - E_K1 - - - - R - T - - F - - - - Ko - Ki - - - - - - - - - - - Calculation of the channel current. - - - - - - - i_K1 - - g_K1 - K1_infinity - - V - E_K1 - - - - - - - - - - - - The gating variable for the time-independent potassium current - the - K1 gate. - - - - - - - - - - - - - - - - - - The opening rate for the K1 gate. - - - - - - - alpha_K1 - - 1.02 - - 1.0 - - - 0.2385 - - - V - E_K1 - - 59.215 - - - - - - - - - - - - - The closing rate for the K1 gate. - - - - - - - beta_K1 - - - - 0.49124 - - - 0.08032 - - - V - 5.476 - - E_K1 - - - - - - - 0.06175 - - V - - E_K1 - 594.31 - - - - - - - 1.0 - - - -0.5143 - - - V - E_K1 - - 4.753 - - - - - - - - - - - - - The steady-state kinetics of the K1 gate. - - - - - - - K1_infinity - - alpha_K1 - - alpha_K1 - beta_K1 - - - - - - - - - - - - The potassium current active at plateau potentials. - - - - - - - - - - - - - - - - - - - - The reversal potential for the channel. - - - - - - - E_Kp - E_K1 - - - - - - - - The gating kinetics for the channel. - - - - - - - Kp - - 1.0 - - 1.0 - - - - 7.488 - V - - 5.98 - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Kp - - g_Kp - Kp - - V - E_Kp - - - - - - - - - - - - A calcium pump for removal of calcium from the cytosol to the - extracellular space. - - - - - - - - - - - - - - - - - - The calcium pump current. - - - - - - - i_p_Ca - - I_pCa - - Cai - - K_mpCa - Cai - - - - - - - - - - - - - The background sodium current. - - - - - - - - - - - - - - - - - - - The reversal potential for the channel. - - - - - - - E_NaN - E_Na - - - - - - - - Calculation of the current. - - - - - - - i_Na_b - - g_Nab - - V - E_NaN - - - - - - - - - - - - The background calcium current. - - - - - - - - - - - - - - - - - - - - - - - The reversal potential for the channel. - - - - - - - E_CaN - - - - R - T - - - 2.0 - F - - - - - Cao - Cai - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ca_b - - g_Cab - - V - E_CaN - - - - - - - - - - - - The sodium/potassium exchanger current which extrudes three sodium - ions from the cell in exchange for two potassium ions entering the - cell. - - - - - - - - - - - - - - - - - - - - - - - - - f_NaK - - 1.0 - - - 1.0 - - 0.1245 - - - -0.1 - - - V - F - - - R - T - - - - - - - - 0.0365 - sigma - - - - - V - F - - - R - T - - - - - - - - - - - - - sigma - - - 1.0 - 7.0 - - - - - Nao - 67.3 - - - 1.0 - - - - - - - - - - Calculation of the exchanger current. - - - - - - - i_NaK - - I_NaK - f_NaK - - 1.0 - - 1.0 - - - K_mNai - Nai - - 1.5 - - - - - Ko - - Ko - K_mKo - - - - - - - - - - - - - A non-specific calcium activated channel - assumed impermeable to - calcium ions but permeable to sodium and potassium ions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The channel reversal potential. - - - - - - - EnsCa - - - - R - T - - F - - - - - Ko - Nao - - - Ki - Nai - - - - - - - - - - Vns - - V - EnsCa - - - - - - - - - The sodium component of the channel's current. - - - - - - - i_ns_Na - - I_ns_Na - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The potassium component of the channel's current. - - - - - - - i_ns_K - - I_ns_K - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The total current through the channel. - - - - - - - i_ns_Ca - - i_ns_Na - i_ns_K - - - - - - - - - The maximum sodium component of the channel's current. - - - - - - - I_ns_Na - - P_ns_Ca - - 1.0 - 2.0 - - - - Vns - - F - 2.0 - - - - R - T - - - - - - gamma_Nai - Nai - - - - 1.0 - Vns - F - - - R - T - - - - - - gamma_Nao - Nao - - - - - - - 1.0 - Vns - F - - - R - T - - - - 1.0 - - - - - - - - - - - The maximum potassium component of the channel's current. - - - - - - - I_ns_K - - P_ns_Ca - - 1.0 - 2.0 - - - - Vns - - F - 2.0 - - - - R - T - - - - - - gamma_Ki - Ki - - - - 1.0 - Vns - F - - - R - T - - - - - - gamma_Ko - Ko - - - - - - - 1.0 - Vns - F - - - R - T - - - - 1.0 - - - - - - - - - - - - - The sodium-calcium exchanger current, exchanges three sodium ions - for one calcium ion. - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the exchanger current. - - - - - - - i_NaCa - - K_NaCa - - 1.0 - - - K_mNa - 3.0 - - - Nao - 3.0 - - - - - 1.0 - - K_mCa - Cao - - - - 1.0 - - 1.0 - - K_sat - - - - eta - 1.0 - - V - - F - - R - T - - - - - - - - - - - - eta - V - - F - - R - T - - - - - - Nai - 3.0 - - Cao - - - - - - eta - 1.0 - - V - - F - - R - T - - - - - - Nao - 3.0 - - Cai - - - - - - - - - - - - - The various calcium fluxes into and from the sarcoplasmic reticulum. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The release flux from the junctional sarcoplasmic reticulum into the - cytosol. - - - - - - - i_rel - - G_rel - - Ca_JSR - Cai - - - - - - - - - - Calculation of the release channel conductance. This is incorrect as - there is no CICR induced via the accumulation of calcium in the - cytosol in the period following max(dV/dt) - - - - - - - G_rel - - G_rel_peak - - - delta_Ca_i2 - delta_Ca_ith - - - - K_mrel - delta_Ca_i2 - - delta_Ca_ith - - - - 1.0 - - - - t_CICR - tau_on - - - - - - - - t_CICR - tau_off - - - - - - - - - - G_rel_peak - - - 0.0 - - delta_Ca_i2 - delta_Ca_ith - - - - G_rel_max - - - - - - - - - - The uptake flux into the sarcoplasmic reticulum from the cytosol. - - - - - - - i_up - - I_up - - Cai - - Cai - K_mup - - - - - - - - - - - Calcium leak flux from the network sarcoplasmic reticulum into the - cytosol. - - - - - - - i_leak - - K_leak - Ca_NSR - - - - - - - K_leak - - I_up - Ca_NSR_max - - - - - - - - - Translocation flux from the network to the junctional sarcoplasmic - reticulum. - - - - - - - i_tr - - - Ca_NSR - Ca_JSR - - tau_tr - - - - - - - - - - - Component grouping together the differential equations for the - various ionic concentrations that the model tracks. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The change in intracellular sodium concentration. - - - - - - - - time - Nai - - - - - i_Na - i_CaNa - i_Na_b - i_ns_Na - - i_NaCa - 3.0 - - - i_NaK - 3.0 - - - - - Am - - V_myo - F - - - - - - - - - - - The change in intracellular calcium concentration. - - - - - - - - time - Cai - - - - - - - i_CaCa - i_p_Ca - i_Ca_b - - i_NaCa - - - - Am - - 2.0 - V_myo - F - - - - - i_rel - - V_JSR - V_myo - - - - - i_leak - i_up - - - V_NSR - V_myo - - - - - - - - - - - The change in intracellular potassium concentration. - - - - - - - - time - Ki - - - - - i_CaK - i_K - i_K1 - i_Kp - i_ns_K - - - i_NaK - 2.0 - - - - - - Am - - V_myo - F - - - - - - - - - - - The change in calcium concentration in the junctional sarcoplasmic - reticulum. - - - - - - - - time - Ca_JSR - - - - i_rel - - i_tr - - V_NSR - V_JSR - - - - - - - - - - - - The change in calcium concentration in the network sarcoplasmic - reticulum. - - - - - - - - time - Ca_NSR - - - - - i_leak - i_tr - - i_up - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Bioelectrics/Monodomain/Fortran/Makefile b/Bioelectrics/Monodomain/Fortran/Makefile deleted file mode 100644 index ffb2b294..00000000 --- a/Bioelectrics/Monodomain/Fortran/Makefile +++ /dev/null @@ -1,71 +0,0 @@ -# -#-*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../.. - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Bioelectrics/Monodomain/ - -EXAMPLE_NAME = Fortran - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Bioelectrics/Monodomain/Fortran/n98.xml b/Bioelectrics/Monodomain/Fortran/input/n98.xml similarity index 100% rename from Bioelectrics/Monodomain/Fortran/n98.xml rename to Bioelectrics/Monodomain/Fortran/input/n98.xml diff --git a/Bioelectrics/Monodomain/Fortran/jrw-1998.xml b/Bioelectrics/Monodomain/Fortran/jrw-1998.xml deleted file mode 100644 index 6a407ee4..00000000 --- a/Bioelectrics/Monodomain/Fortran/jrw-1998.xml +++ /dev/null @@ -1,5332 +0,0 @@ - - - - - - - - - - - - - Lloyd - Catherine - May - - - c.lloyd@auckland.ac.nz - - - - The University of Auckland - The Bioengineering Research Group - - - - - - 2001-09-24 - - - - - - Corrected equations. - - - - Lloyd - Catherine - May - - - - 2003-07-30 - - - - - Corrected equations: alpha_j_calculation and beta_j_calculation in - fast_sodium_current_j_gate, alpha_X_calculation and beta_X_calculation in time_dependent_potassium_current_X_gate, and f_NaK_calculation and - i_NaK_calculation in Ca_release_current_from_JSR. - - - - Lloyd - Catherine - May - - - - 2003-06-04 - - - - - Added some initial values from Penny Noble's documentation. - - - - Lloyd - Catherine - May - - - - 2002-05-06 - - - - - Corrected several equations, variable units and their initial values. - - - - Lloyd - Catherine - May - - - - 2002-02-28 - - - - - Corrected several equations. - - - - Lloyd - Catherine - May - - - - 2002-02-25 - - - - - Altered some of the connections. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Changed tau_y_calculation after checking mathml using the validator. - - - - Lloyd - Catherine - May - - - - 2001-12-07 - - - - - Removed document type definition as this is declared as optional - according to the W3C recommendation. - - - - Lloyd - Catherine - May - - - - 2001-10-19 - - - - - - - The University of Auckland, Bioengineering Research Group - - - - - - - - The Jafri-Rice-Winslow Model for Calcium Regulation in the Ventricular - Myocyte, 1997 - - - - - - This is the CellML description of Jafri, Rice and Winslow's - mathematical model for calcium regulation in the ventricular myocyte. - It is based on an accurate model of the membrane currents and adds a - more sophisticated model of calcium handling. The JRW model is based - on the LR-II model for ventricular action potentials, with several - modifications. - - - - Catherine Lloyd - - - - - Mammalia - - Ventricular Myocyte - - - - 9512016 - - - - - - - Jafri - M - Saleet - - - - - - - Rice - John - Jeremy - - - - - - - Winslow - Raimond - L - - - - - - - Cardiac Ca2+ Dynamics: The Roles of Ryanodine Receptor Adaptation - and Sarcoplasmic Reticulum Load - - - 1998-03 - - - Biophysical Journal - - 74 - 1149 - 1168 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The main component of the model which defines the action potential. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The kinetics of the transmembrane potential, defined as the sum of - all the sarcolemmal currents and an applied stimulus current. - - - - - - - - time - V - - - - I_stim - - i_Na - i_Ca_L_Ca - i_Ca_L_K - i_K - i_NaCa - i_K1 - i_Kp - i_p_Ca - i_Na_b - i_Ca_b - i_NaK - i_ns_Ca - - - Cm - - - - - - - - This is a dummy equation that we simply use to make grabbing the - value in CMISS much easier. - - - - - - - - IStimC - I_stim - - - - - - - - - - The fast sodium current component contains the differential - equations governing the influx of sodium ions through the cell - surface membrane into the cell. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the fast sodium current using the three - Hodkin-Huxley type voltage-dependent gating variables m, h, and j. - - - - - - - i_Na - - g_Na - - m - 3.0 - - h - j - - V - E_Na - - - - - - - - - - The sodium reversal potential. - - - - - - - E_Na - - - - R - T - - F - - - - Nao - Nai - - - - - - - - - - - - - - The voltage-dependent activation gate for the fast sodium current - - the m gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the m gate. - - - - - - - alpha_m - - - 0.32 - - V - 47.13 - - - - 1.0 - - - -0.1 - - V - 47.13 - - - - - - - - - - - - - The closing rate of the m gate. - - - - - - - beta_m - - 0.08 - - - - V - - 11.0 - - - - - - - - - - - The kinetics of the m gate. - - - - - - - - time - m - - - - alpha_m - - 1.0 - m - - - - beta_m - m - - - - - - - - - - - - - The voltage-dependent inactivation gate for the fast sodium current - - the h gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the h gate. - - - - - - - alpha_h - - - - 0.135 - - - - 80.0 - V - - -6.8 - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate of the h gate. - - - - - - - beta_h - - - - - 3.56 - - - 0.079 - V - - - - - 310000.0 - - - 0.35 - V - - - - - - V - -40.0 - - - - - 1.0 - - 0.13 - - 1.0 - - - - V - 10.66 - - -11.1 - - - - - - - - - - - - - - - The kinetics of the h gate. - - - - - - - - time - h - - - - alpha_h - - 1.0 - h - - - - beta_h - h - - - - - - - - - - - - - The voltage-dependent slow inactivation gate for the fast sodium - current - the j gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the j gate. - - - - - - - alpha_j - - - - - - -127140.0 - - - 0.2444 - V - - - - - 0.00003474 - - - -0.04391 - V - - - - - - - V - 37.78 - - - 1.0 - - - 0.311 - - V - 79.23 - - - - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate of the j gate. - - - - - - - beta_j - - - - 0.1212 - - - - -0.01052 - V - - - - 1.0 - - - -0.1378 - - V - 40.14 - - - - - - - - V - -40.0 - - - - - 0.3 - - - - -0.0000002535 - V - - - - 1.0 - - - -0.1 - - V - 32.0 - - - - - - - - - - - - - - - - The kinetics of the j gate. - - - - - - - - time - j - - - - alpha_j - - 1.0 - j - - - - beta_j - j - - - - - - - - - - - - - The JWR model creates a new mathematical model to describe the - L-type calcium channel that is based on the experimentally observed - mode-switching behaviour of the channel. Inactivation occurs as - calcium ion binding induces the channel to switch (from mode normal) - to a mode in which transitions to open states are extremely slow - (mode Ca). The channel has one voltage inactivation gate, y. As well - as Ca, the channel is assumed permeable to K ions also. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the calcium current component of the total channel - current, given as the maximal current multiplied by the - voltage-dependent inactivation gate and the open probability of the - channel based on the mode-switching model. - - - - - - - i_Ca_L_Ca - - i_Ca_L_Ca_max - y - - O - O_Ca - - - - - - - - - - Calculation of the potassium current component of the total channel - current. - - - - - - - i_Ca_L_K - - p_k - y - - O - O_Ca - - - - V - - F - 2.0 - - - - R - T - - - - - - Ki - - - - V - F - - - R - T - - - - - Ko - - - - - - V - F - - - R - T - - - - 1.0 - - - - - - - - - - - The potassium permeability of the channel, which depends on the - calcium current component. - - - - - - - p_k - - P_K - - 1.0 - - i_Ca_L_Ca_max - i_Ca_L_Ca_half - - - - - - - - - - - The maximal calcium current through the channel. - - - - - - - i_Ca_L_Ca_max - - P_Ca - 4.0 - - - V - - F - 2.0 - - - - R - T - - - - - - 0.001 - - - 2.0 - V - - F - - R - T - - - - - - - 0.341 - Cao - - - - - - 2.0 - V - - F - - R - T - - - - - 1.0 - - - - - - - - - - - Rate constants for state changes in mode normal. - - - - - - - alpha - - 0.4 - - - - V - 12.0 - - 10.0 - - - - - - - - beta - - 0.05 - - - - V - 12.0 - - -13.0 - - - - - - - - - - - Rate constants for state changes in mode Ca (corresponding to - alpha-prime and beta-prime in the JRW paper). - - - - - - - alpha_a - - alpha - a - - - - - - beta_b - - beta - b - - - - - - - - - Rate constant for switching between mode normal and mode Ca. - - - - - - - gamma - - 0.1875 - Ca_SS - - - - - - - - - The kinetics of the state transitions in mode normal. - In the normal mode, the calcium channel is able to make the - transition to the open, conducting state (O) from the closed state - (C) at a normal rate. - - - - - - - - time - C0 - - - - - beta - C1 - - - omega - C_Ca0 - - - - - - 4.0 - alpha - - gamma - - C0 - - - - - - - - time - C1 - - - - - 4.0 - alpha - C0 - - - 2.0 - beta - C2 - - - - omega - b - - C_Ca1 - - - - - beta - - 3.0 - alpha - - - gamma - a - - - C1 - - - - - - - - time - C2 - - - - - 3.0 - alpha - C1 - - - 3.0 - beta - C3 - - - - omega - - b - 2.0 - - - C_Ca2 - - - - - - beta - 2.0 - - - 2.0 - alpha - - - gamma - - a - 2.0 - - - - C2 - - - - - - - - time - C3 - - - - - 2.0 - alpha - C2 - - - 4.0 - beta - C4 - - - - omega - - b - 3.0 - - - C_Ca3 - - - - - - beta - 3.0 - - alpha - - gamma - - a - 3.0 - - - - C3 - - - - - - - - time - C4 - - - - - alpha - C3 - - - g - O - - - - omega - - b - 4.0 - - - C_Ca4 - - - - - - beta - 4.0 - - f - - gamma - - a - 4.0 - - - - C4 - - - - - - - - time - O - - - - f - C4 - - - g - O - - - - - - - - - - The kinetics of the state transitions in mode Ca. - Calcium binding to the Ca channel induces a conformational change - from normal mode to mode Ca. This effectively inhibits the - conduction of calcium ions because in mode Ca, the calcium channel - makes the transition to the open, conducting state (O) extremely - slowly. - - - - - - - - time - C_Ca0 - - - - - beta_b - C_Ca1 - - - gamma - C_Ca0 - - - - - - 4.0 - alpha_a - - omega - - C_Ca0 - - - - - - - - time - C_Ca1 - - - - - 4.0 - alpha_a - C_Ca0 - - - 2.0 - beta_b - C_Ca2 - - - gamma - a - C1 - - - - - beta_b - - 3.0 - alpha_a - - - omega - b - - - C_Ca1 - - - - - - - - time - C_Ca2 - - - - - 3.0 - alpha_a - C_Ca1 - - - 3.0 - beta_b - C_Ca3 - - - gamma - - a - 2.0 - - C2 - - - - - - beta_b - 2.0 - - - 2.0 - alpha_a - - - omega - - b - 2.0 - - - - C_Ca2 - - - - - - - - time - C_Ca3 - - - - - 2.0 - alpha_a - C_Ca2 - - - 4.0 - beta_b - C_Ca4 - - - gamma - - a - 3.0 - - C3 - - - - - - beta_b - 3.0 - - alpha_a - - omega - - b - 3.0 - - - - C_Ca3 - - - - - - - - time - C_Ca4 - - - - - alpha_a - C_Ca3 - - - g_ - O_Ca - - - gamma - - a - 4.0 - - C4 - - - - - - beta_b - 4.0 - - f_ - - omega - - b - 4.0 - - - - C_Ca4 - - - - - - - - time - O_Ca - - - - f_ - C_Ca4 - - - g_ - O_Ca - - - - - - - - - - - - - The voltage-dependent inactivation gate for the L-type calcium - channel - the y gate. - - - - - - - - - - - - - - - - - - - - - The kinetics of the y gate. - - - - - - - - time - y - - - - y_infinity - y - - tau_y - - - - - - y_infinity - - - 1.0 - - 1.0 - - - - V - 55.0 - - 7.5 - - - - - - 0.1 - - 1.0 - - - - - V - - 21.0 - - 6.0 - - - - - - - - - - tau_y - - 20.0 - - 600.0 - - 1.0 - - - - V - 30.0 - - 9.5 - - - - - - - - - - - - - - - - The time-dependent potassium current has an X^2 dependence on it's - activation gate, and an Xi inactivation gate. This channel is also - assumed permeable to sodium ions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the maximal channel conductance, dependent on - extracellular potassium concentration. - - - - - - - g_K - - g_K_max - - - Ko - 5.4 - - - - - - - - - - - The reversal potential of the channel. - - - - - - - E_K - - - - R - T - - F - - - - - Ko - - P_NaK - Nao - - - - Ki - - P_NaK - Nai - - - - - - - - - - - - - Calculation of the time-dependent potassium current. - - - - - - - i_K - - g_K - Xi - - X - 2.0 - - - V - E_K - - - - - - - - - - - - - The voltage- and time-dependent activation gate for the - time-dependent potassium current - the X gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the X gate. - - - - - - - alpha_X - - 0.0000719 - - - V - 30.0 - - - 1.0 - - - -0.148 - - V - 30.0 - - - - - - - - - - - - - - The closing rate of the X gate. - - - - - - - beta_X - - 0.000131 - - - V - 30.0 - - - -1.0 - - - 0.0687 - - V - 30.0 - - - - - - - - - - - - - - The kinetics of the X gate. - - - - - - - - time - X - - - - alpha_X - - 1.0 - X - - - - beta_X - X - - - - - - - - - - - - - The time-independent inactivation gate for the time-dependent - potassium channel. - - - - - - - - - - - - - - - - - Xi is the inward rectification parameter and is given by the - following equation. - - - - - - - Xi - - 1.0 - - 1.0 - - - - V - 56.26 - - 32.1 - - - - - - - - - - - - - - - - The time-independent potassium current. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the maximal channel conductance, dependent on - extracellular potassium concentration. - - - - - - - g_K1 - - g_K1_max - - - Ko - 5.4 - - - - - - - - - - - The following equation calculates the reversal potential of the - time-independent potassium current. - - - - - - - E_K1 - - - - R - T - - F - - - - Ko - Ki - - - - - - - - - - - Calculate the current. - - - - - - - i_K1 - - g_K1 - K1_infinity - - V - E_K1 - - - - - - - - - - - - - - The time constants for the K1 gate are small enough that the gating - variable can be approximated with it's steady-state value. - - - - - - - - - - - - - - - - - - - - - The opening rate of the K1 gate. - - - - - - - alpha_K1 - - 1.02 - - 1.0 - - - 0.2385 - - - V - E_K1 - - 59.215 - - - - - - - - - - - - - The closing rate of the K1 gate. - - - - - - - beta_K1 - - - - 0.49124 - - - 0.08032 - - - V - 5.476 - - E_K1 - - - - - - - 0.06175 - - V - - E_K1 - 594.31 - - - - - - - 1.0 - - - -0.5143 - - - V - E_K1 - - 4.753 - - - - - - - - - - - - - The steady-state approximation for the K1 gating kinetics. - - - - - - - K1_infinity - - alpha_K1 - - alpha_K1 - beta_K1 - - - - - - - - - - - - - - The plateau potassium current component contains the equations which - describe the contribution of a time independent [K]o-insensitive - channel at plateau potentials. - - - - - - - - - - - - - - - - - - - - - - - The channel's reversal potential. - - - - - - - E_Kp - E_K1 - - - - - - - - The activation variable. - - - - - - - Kp - - 1.0 - - 1.0 - - - - 7.488 - V - - 5.98 - - - - - - - - - - - - Calculation of the plateau potassium current. - - - - - - - i_Kp - - g_Kp - Kp - - V - E_Kp - - - - - - - - - - - - - - The Na/Ca exchanger component describes how a protein molecule in - the cell surface membrane transports Na ions into the cytosol and - exports Ca ions into the extracellular volume, in a ratio of 3:1 - respectively. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the Na/Ca exchanger current. - - - - - - - i_NaCa - - k_NaCa - - 1.0 - - - K_mNa - 3.0 - - - Nao - 3.0 - - - - - 1.0 - - K_mCa - Cao - - - - 1.0 - - 1.0 - - k_sat - - - - eta - 1.0 - - V - - F - - R - T - - - - - - - - - - - - eta - V - - F - - R - T - - - - - - Nai - 3.0 - - Cao - - - - - - eta - 1.0 - - V - - F - - R - T - - - - - - Nao - 3.0 - - Cai - - - - - - - - - - - - - - - The sarcolemmal calcium pump is an additional mechanism for removing - Ca ions from the myoplasm to help maintain a low intracellular - calcium concentration when at rest. - - - - - - - - - - - - - - - - - - - - - The calcium pump current. - - - - - - - i_p_Ca - - I_pCa - - Cai - - K_mpCa - Cai - - - - - - - - - - - - - - The sodium background current is a time-independent diffusion of - Na ions down their electrochemical gradient, through the cell - surface membrane into the cytosol. - - - - - - - - - - - - - - - - - - - - - - The reversal potential for the background sodium channel. - - - - - - - E_NaN - E_Na - - - - - - - - Calculation of the background sodium current. - - - - - - - i_Na_b - - g_Nab - - V - E_NaN - - - - - - - - - - - - - The calcium background current describes a time-independent - diffusion of Ca ions down their electrochemical gradient through the - cell surface membrane into the cytosol. However, calcium is not - allowed to accumulate to high intracellular concentrations. This - influx is balanced by the Ca ion extrusion through the Na-Ca - exchanger and the sarcolemmal Ca pump. - - - - - - - - - - - - - - - - - - - - - - - - - - The reversal potential for the background calcium current. - - - - - - - E_CaN - - - - R - T - - - 2.0 - F - - - - - Cao - Cai - - - - - - - - - - - Calculation of the background calcium current. - - - - - - - i_Ca_b - - g_Cab - - V - E_CaN - - - - - - - - - - - - - The sodium potassium pump is an active protein in the cell membrane - which couples the free energy released by the hydrolysis of ATP to - the movement of Na and K ions against their electrochemical - gradients through the cell membrane. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the Na/K pump current. - - - - - - - f_NaK - - 1.0 - - - 1.0 - - 0.1245 - - - - -0.1 - V - F - - - R - T - - - - - - - 0.0365 - sigma - - - - - V - - F - - - R - T - - - - - - - - - - - sigma - - - 1.0 - 7.0 - - - - - Nao - 67.3 - - - 1.0 - - - - - - - i_NaK - - I_NaK - f_NaK - - 1.0 - - 1.0 - - - K_mNai - Nai - - 1.5 - - - - - Ko - - Ko - K_mKo - - - - - - - - - \ - - - - - The nonspecific calcium activated current describes a channel which - is activated by calcium ions, but is permeable to only sodium and - potassium ions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The reversal potential of the channel. - - - - - - - EnsCa - - - - R - T - - F - - - - - Ko - Nao - - - Ki - Nai - - - - - - - - - - - - The potential offset for the channel. - - - - - - - VnsCa - - V - EnsCa - - - - - - - - - The sodium component of the channel's current. - - - - - - - i_ns_Na - - I_ns_Na - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The potassium component of the channel's current. - - - - - - - i_ns_K - - I_ns_K - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The total nonspecific calcium activated current. - - - - - - - i_ns_Ca - - i_ns_Na - i_ns_K - - - - - - - - - The maximal sodium component current. - - - - - - - I_ns_Na - - P_ns_Ca - - 1.0 - 2.0 - - - - VnsCa - - F - 2.0 - - - - R - T - - - - - - 0.75 - Nai - - - - VnsCa - F - - - R - T - - - - - - 0.75 - Nao - - - - - - - VnsCa - F - - - R - T - - - - 1.0 - - - - - - - - - - - The maximal potassium component current. - - - - - - - I_ns_K - - P_ns_Ca - - 1.0 - 2.0 - - - - VnsCa - - F - 2.0 - - - - R - T - - - - - - 0.75 - Ki - - - - VnsCa - F - - - R - T - - - - - - 0.75 - Ko - - - - - - - VnsCa - F - - - R - T - - - - 1.0 - - - - - - - - - - - - - - - In the JRW model, subcellular calcium regulatory mechanisms are - described in detail. There are six calcium fluxes to consider; - J_rel, J_leak, J_up, J_tr, J_xfer and J_trpn. In addition, three - membrane current fluxes are also necessary for the formulation of - calcium regulation; i_p_Ca, i_Ca_L_Ca and i_NaCa. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculate some volume fractions as proportions of the total - myoplasmic volume. - - - - - - - V_SS - - 5.828e-5 - V_myo - - - - - - V_NSR - - 0.081 - V_myo - - - - - - V_JSR - - 0.00464 - V_myo - - - - - - - - - The calcium release flux from the JSR into the restricted subspace - is governed by the fraction of RyR channels in an open state. - - - - - - - J_rel - - v1 - RyR_open - - Ca_JSR - Ca_SS - - - - - - - - - - The "open" RyR's are those P_O1 and P_O2 states. - - - - - - - RyR_open - - P_O1 - P_O2 - - - - - - - - - The kinetic equations governing the transitions between the four - states used to model the RyR's. - - - - - - - - time - P_C1 - - - - - k_a_plus - - - Ca_SS - nCa - - P_C1 - - - k_a_minus - P_O1 - - - - - - - - time - P_O1 - - - - - k_a_plus - - Ca_SS - nCa - - P_C1 - - - - k_a_minus - P_O1 - - - k_b_plus - - Ca_SS - mCa - - P_O1 - - - k_c_plus - P_O1 - - - - - k_b_minus - P_O2 - - - k_c_minus - P_C2 - - - - - - - - time - P_O2 - - - - k_b_plus - - Ca_SS - mCa - - P_O1 - - - k_b_minus - P_O2 - - - - - - - - time - P_C2 - - - - k_c_plus - P_O1 - - - k_c_minus - P_C2 - - - - - - - - - - Calculate the leakage flux from the NSR into the myoplasm. - - - - - - - J_leak - - v2 - - Ca_NSR - Cai - - - - - - - - - - Calculate the uptake flux into the NSR from the myoplasm. - - - - - - - J_up - - v3 - - - Cai - 2.0 - - - - K_mup - 2.0 - - - Cai - 2.0 - - - - - - - - - - - - Calculate the translocation flux between the uptake (NSR) and - release (JSR) stores. - - - - - - - J_tr - - - Ca_NSR - Ca_JSR - - tau_tr - - - - - - - - - Calculate the calcium flux from the diffusion of calcium out of the - restricted subspace into the myoplasm. - - - - - - - J_xfer - - - Ca_SS - Cai - - tau_xfer - - - - - - - - - The kinetics of calcium binding to the myoplasm buffer troponin - - both high and low affinity binding sites. - - - - - - - J_htrpn - - - k_htrpn_plus - Cai - - HTRPN_tot - HTRPNCa - - - - k_htrpn_minus - HTRPNCa - - - - - - - J_ltrpn - - - k_ltrpn_plus - Cai - - LTRPN_tot - LTRPNCa - - - - k_ltrpn_minus - LTRPNCa - - - - - - - J_trpn - - J_htrpn - J_ltrpn - - - - - - - - - Keep track of the concentration of calcium ions bound to high and - low affinity troponin binding sites. - - - - - - - - time - HTRPNCa - - J_htrpn - - - - - - time - LTRPNCa - - J_ltrpn - - - - - - - - Calcium is buffered by calmodulin (CMDN) in the subspace and - myoplasm, and by calsequestrin (CSQN) in the JSR. These are fast - buffers and their effect is modelled using the rapid buffering - approximation. - - - - - - - Bi - - 1.0 - - 1.0 - - - CMDN_tot - K_mCMDN - - - - K_mCMDN - Cai - - 2.0 - - - - - - - - - B_SS - - 1.0 - - 1.0 - - - CMDN_tot - K_mCMDN - - - - K_mCMDN - Ca_SS - - 2.0 - - - - - - - - - B_JSR - - 1.0 - - 1.0 - - - CSQN_tot - K_mCSQN - - - - K_mCSQN - Ca_JSR - - 2.0 - - - - - - - - - - - - The kinetics of the calcium ion concentration changes in the various - compartments of the model. - - - - - - - - time - Cai - - - Bi - - - J_leak - J_xfer - - - J_up - J_trpn - - - - i_Ca_b - - 2.0 - i_NaCa - - - i_p_Ca - - - Am - - 2.0 - V_myo - F - - - - - - - - - - - - time - Ca_SS - - - B_SS - - - - J_rel - - V_JSR - V_SS - - - - J_xfer - - V_myo - V_SS - - - - - i_Ca_L_Ca - - Am - - 2.0 - V_SS - F - - - - - - - - - - - time - Ca_JSR - - - B_JSR - - J_tr - J_rel - - - - - - - - time - Ca_NSR - - - - - J_up - J_leak - - - V_myo - V_NSR - - - - J_tr - - V_JSR - V_NSR - - - - - - - - - - - - - - The descriptions of the rate of change of [Na]i and [K]i are the - same as the LR-II model. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The rate of change of intracellular sodium ion concentration. - - - - - - - - time - Nai - - - - - i_Na - i_Na_b - i_ns_Na - - i_NaCa - 3.0 - - - i_NaK - 3.0 - - - - - Am - - V_myo - F - - - - - - - - - - - The rate of change of intracellular potassium ion concentration. - - - - - - - - time - Ki - - - - - i_Ca_L_K - i_K - i_K1 - i_Kp - i_ns_K - - - i_NaK - 2.0 - - - - - - Am - - V_myo - F - - - - - - - - - - - The rate of change of extracellular potassium ion concentration. - - - - - - - - time - Ko - - - - i_Ca_L_K - i_K - i_K1 - i_Kp - i_ns_K - - - i_NaK - 2.0 - - - - - Am - - V_myo - F - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Bioelectrics/Monodomain/Fortran/src/FortranExample.f90 b/Bioelectrics/Monodomain/Fortran/src/FortranExample.f90 index a89b230c..7c454a61 100644 --- a/Bioelectrics/Monodomain/Fortran/src/FortranExample.f90 +++ b/Bioelectrics/Monodomain/Fortran/src/FortranExample.f90 @@ -165,12 +165,14 @@ PROGRAM MONODOMAINEXAMPLE WRITE(*, '("CellML File: ", A)') CellmlFile inquire(file=CellmlFile, exist=fileExist) if (.not. fileExist) then - write(*, '(">>ERROR: File does not exist")') + write(*, '(">>ERROR: File does not exist")') stop endif ELSE !If there are not enough arguments die horribly + WRITE(*,*) " " WRITE(*,'(">>USAGE: ",A)') "MonodomainExample " + WRITE(*,*) " " STOP ENDIF diff --git a/Bioelectrics/Monodomain/OpenCMISS.cmake b/Bioelectrics/Monodomain/OpenCMISS.cmake new file mode 100644 index 00000000..d1798862 --- /dev/null +++ b/Bioelectrics/Monodomain/OpenCMISS.cmake @@ -0,0 +1,95 @@ +########################### +# *DO NOT CHANGE THIS FILE* +########################### +# +# Prepares the use of OpenCMISS by scanning at various path locations for OpenCMISS (SDK) installations. +# +# Search order: +# - OPENCMISS_INSTALL_DIR variable +# - OPENCMISS_INSTALL_DIR environment variable +# - OPENCMISS_SDK_DIR variable +# - OPENCMISS_SDK_DIR environment variable +# - [Windows only] The Registry is searched additionally for installed SDKs. +# +# If found +# - Includes the toolchain config script of the found opencmiss installation to enable toolchain selection logic (non-windows) + +# Convenience: The OPENCMISS_INSTALL_DIR may also be defined in the environment and various other places +if (DEFINED OPENCMISS_INSTALL_DIR) + get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE) + if (EXISTS "${OPENCMISS_INSTALL_DIR}") + message(STATUS "Using specified installation directory '${OPENCMISS_INSTALL_DIR}'") + else() + message(WARNING "The specified OPENCMISS_INSTALL_DIR '${OPENCMISS_INSTALL_DIR}' does not exist. Skipping.") + unset(OPENCMISS_INSTALL_DIR) + endif() +endif() +if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_INSTALL_DIR}" STREQUAL "") + file(TO_CMAKE_PATH "$ENV{OPENCMISS_INSTALL_DIR}" OPENCMISS_INSTALL_DIR) + get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE) + if (EXISTS "${OPENCMISS_INSTALL_DIR}") + message(STATUS "Using environment installation directory '${OPENCMISS_INSTALL_DIR}'") + else() + message(WARNING "The environment variable OPENCMISS_INSTALL_DIR='${OPENCMISS_INSTALL_DIR}' contains an invalid path. Skipping.") + unset(OPENCMISS_INSTALL_DIR) + endif() +endif() +if (NOT OPENCMISS_INSTALL_DIR AND DEFINED OPENCMISS_SDK_DIR) + get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE) + if (EXISTS "${OPENCMISS_SDK_DIR}") + message(STATUS "Using SDK installation directory: ${OPENCMISS_SDK_DIR}") + set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}") + else() + message(WARNING "The specified OPENCMISS_SDK_DIR '${OPENCMISS_SDK_DIR}' does not exist. Skipping.") + endif() +endif() +if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_SDK_DIR}" STREQUAL "") + file(TO_CMAKE_PATH "$ENV{OPENCMISS_SDK_DIR}" OPENCMISS_SDK_DIR) + get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE) + if (EXISTS "${OPENCMISS_SDK_DIR}") + message(STATUS "Using environment SDK installation directory: ${OPENCMISS_SDK_DIR}") + set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}") + else() + message(WARNING "The environment variable OPENCMISS_SDK_DIR='${OPENCMISS_SDK_DIR}' contains an invalid path. Skipping.") + unset(OPENCMISS_SDK_DIR) + endif() +endif() +# On windows: check the registry for installed OpenCMISS SDKs +if(NOT OPENCMISS_INSTALL_DIR AND WIN32) + foreach(ROOT HKEY_CURRENT_USER HKEY_LOCAL_MACHINE) + foreach(PACKAGE OpenCMISSUserSDK OpenCMISSDeveloperSDK) + set(_REG_KEY "[${ROOT}\\Software\\Auckland Bioengineering Institute\\${PACKAGE}]") + get_filename_component(OPENCMISS_INSTALL_DIR "${_REG_KEY}" ABSOLUTE) + #message(STATUS "Trying registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}") + if (EXISTS "${OPENCMISS_INSTALL_DIR}") + message(STATUS "Found ${PACKAGE} in Windows registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}") + break() + else() + unset(OPENCMISS_INSTALL_DIR) + endif() + endforeach() + if (EXISTS "${OPENCMISS_INSTALL_DIR}") + break() + endif() + endforeach() +endif() + +if(OPENCMISS_INSTALL_DIR) + message(STATUS "OPENCMISS_INSTALL_DIR=${OPENCMISS_INSTALL_DIR}") + # Use the OpenCMISS scripts to also allow choosing a separate toolchain + # This file is located at the opencmiss installation rather than the local example + # as it avoids file replication and makes maintenance much easier + if (TOOLCHAIN) + set(_OCTC ${OPENCMISS_INSTALL_DIR}/cmake/OCToolchainCompilers.cmake) + if (EXISTS "${_OCTC}") + include(${_OCTC}) + else() + message(WARNING "TOOLCHAIN specified but OpenCMISS config script could not be found at ${_OCTC}. Trying CMake defaults.") + endif() + unset(_OCTC) + endif() + set(OpenCMISS_DIR "${OPENCMISS_INSTALL_DIR}" CACHE PATH "Path to the found OpenCMISS (SDK) installation") +else() + message(WARNING "No OpenCMISS (SDK) installation directory detected. Using default system environment.") +endif() + diff --git a/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py b/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py index e18d22fd..6f1aca2e 100644 --- a/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py +++ b/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py @@ -2,11 +2,12 @@ #DOC-START imports import sys, os, math -# Make sure $OPENCMISS_ROOT/cm/bindings/python is first in our PYTHONPATH. -sys.path.insert(1, os.path.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +# Make required inclusions into PYTHONPATH. +sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/python' ) +sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/x86_64_linux/gnu-C5.4-gnu-F5.4/mpich_release/release/python/RELEASE' ) # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron #DOC-END imports # Set problem parameters From bf3180a8de09221bbaca10a3ac94e5a5933b3958 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Fri, 14 Oct 2016 16:00:06 +1300 Subject: [PATCH 07/28] added CMAKE support to CellML and Bioelectrics examples --- Bioelectrics/Bidomain/CMakeLists.txt | 50 +++++++++++++ Bioelectrics/Bidomain/Makefile | 71 ------------------- .../Bidomain/{ => input}/jrw-1998.xml | 0 Bioelectrics/Bidomain/{ => input}/n98.xml | 0 Bioelectrics/CMakeLists.txt | 37 ++++++++++ Bioelectrics/Monodomain/CMakeLists.txt | 2 +- .../Monodomain/Fortran/CMakeLists.txt | 50 +++++++++++++ .../MonodomainBuenoOrovio/CMakeLists.txt | 32 +++++++++ Bioelectrics/MonodomainBuenoOrovio/Makefile | 70 ------------------ Bioelectrics/MonodomainTP06/CMakeLists.txt | 32 +++++++++ Bioelectrics/MonodomainTP06/Makefile | 70 ------------------ .../Monodomain_Shiqiang/CMakeLists.txt | 32 +++++++++ Bioelectrics/Monodomain_Shiqiang/Makefile | 71 ------------------- .../Monodomain_Shiqiang/{ => input}/FHN.xml | 0 .../Monodomain_Shiqiang/{ => input}/LRd.xml | 0 .../{ => input}/jrw-1998.xml | 0 .../lindblad_murphey_clark_giles_1996.xml | 0 .../{ => input}/maltsev_rate_modulation.xml | 0 .../Monodomain_Shiqiang/{ => input}/n98.xml | 0 .../OpenCMISS.cmake => OpenCMISS.cmake | 0 cellml/CMakeLists.txt | 34 +++++++++ cellml/Fortran/CMakeLists.txt | 50 +++++++++++++ .../model-integration/Fortran/CMakeLists.txt | 50 +++++++++++++ 23 files changed, 368 insertions(+), 283 deletions(-) create mode 100644 Bioelectrics/Bidomain/CMakeLists.txt delete mode 100644 Bioelectrics/Bidomain/Makefile rename Bioelectrics/Bidomain/{ => input}/jrw-1998.xml (100%) rename Bioelectrics/Bidomain/{ => input}/n98.xml (100%) create mode 100644 Bioelectrics/CMakeLists.txt create mode 100644 Bioelectrics/Monodomain/Fortran/CMakeLists.txt create mode 100644 Bioelectrics/MonodomainBuenoOrovio/CMakeLists.txt delete mode 100644 Bioelectrics/MonodomainBuenoOrovio/Makefile create mode 100644 Bioelectrics/MonodomainTP06/CMakeLists.txt delete mode 100644 Bioelectrics/MonodomainTP06/Makefile create mode 100644 Bioelectrics/Monodomain_Shiqiang/CMakeLists.txt delete mode 100644 Bioelectrics/Monodomain_Shiqiang/Makefile rename Bioelectrics/Monodomain_Shiqiang/{ => input}/FHN.xml (100%) rename Bioelectrics/Monodomain_Shiqiang/{ => input}/LRd.xml (100%) rename Bioelectrics/Monodomain_Shiqiang/{ => input}/jrw-1998.xml (100%) rename Bioelectrics/Monodomain_Shiqiang/{ => input}/lindblad_murphey_clark_giles_1996.xml (100%) rename Bioelectrics/Monodomain_Shiqiang/{ => input}/maltsev_rate_modulation.xml (100%) rename Bioelectrics/Monodomain_Shiqiang/{ => input}/n98.xml (100%) rename Bioelectrics/Monodomain/OpenCMISS.cmake => OpenCMISS.cmake (100%) create mode 100644 cellml/CMakeLists.txt create mode 100644 cellml/Fortran/CMakeLists.txt create mode 100644 cellml/model-integration/Fortran/CMakeLists.txt diff --git a/Bioelectrics/Bidomain/CMakeLists.txt b/Bioelectrics/Bidomain/CMakeLists.txt new file mode 100644 index 00000000..ecff1fc2 --- /dev/null +++ b/Bioelectrics/Bidomain/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(bidomain.x src/BidomainExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(bidomain.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(bidomain.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME BiDomain COMMAND bidomain.x) +add_opencmiss_environment(BiDomain) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Bioelectrics/Bidomain/Makefile b/Bioelectrics/Bidomain/Makefile deleted file mode 100644 index c008a5a2..00000000 --- a/Bioelectrics/Bidomain/Makefile +++ /dev/null @@ -1,71 +0,0 @@ -# -#-*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Bioelectrics/ - -EXAMPLE_NAME = Bidomain - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Bioelectrics/Bidomain/jrw-1998.xml b/Bioelectrics/Bidomain/input/jrw-1998.xml similarity index 100% rename from Bioelectrics/Bidomain/jrw-1998.xml rename to Bioelectrics/Bidomain/input/jrw-1998.xml diff --git a/Bioelectrics/Bidomain/n98.xml b/Bioelectrics/Bidomain/input/n98.xml similarity index 100% rename from Bioelectrics/Bidomain/n98.xml rename to Bioelectrics/Bidomain/input/n98.xml diff --git a/Bioelectrics/CMakeLists.txt b/Bioelectrics/CMakeLists.txt new file mode 100644 index 00000000..35e27f44 --- /dev/null +++ b/Bioelectrics/CMakeLists.txt @@ -0,0 +1,37 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(Bidomain) + add_subdirectory(Monodomain/Fortran) + add_subdirectory(Monodomain_Shiqiang) + add_subdirectory(MonodomainTP06) + add_subdirectory(MonodomainBuenoOrovio) +endif() diff --git a/Bioelectrics/Monodomain/CMakeLists.txt b/Bioelectrics/Monodomain/CMakeLists.txt index 4c514945..65d54ffe 100644 --- a/Bioelectrics/Monodomain/CMakeLists.txt +++ b/Bioelectrics/Monodomain/CMakeLists.txt @@ -6,7 +6,7 @@ # For more information see http://www.opencmiss.org/documentation # Include the OpenCMISS initalisation & macro definition file. -include(./OpenCMISS.cmake) +include(../../OpenCMISS.cmake) # Project setup # ------------- diff --git a/Bioelectrics/Monodomain/Fortran/CMakeLists.txt b/Bioelectrics/Monodomain/Fortran/CMakeLists.txt new file mode 100644 index 00000000..2244a375 --- /dev/null +++ b/Bioelectrics/Monodomain/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(monodomain.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(monodomain.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(monodomain.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MonoDomain COMMAND monodomain.x) +add_opencmiss_environment(MonoDomain) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Bioelectrics/MonodomainBuenoOrovio/CMakeLists.txt b/Bioelectrics/MonodomainBuenoOrovio/CMakeLists.txt new file mode 100644 index 00000000..7699fbf6 --- /dev/null +++ b/Bioelectrics/MonodomainBuenoOrovio/CMakeLists.txt @@ -0,0 +1,32 @@ +# Add example executable +add_executable(monodomainbueno.x src/MonodomainBuenoOrovioExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(monodomainbueno.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(monodomainbueno.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MonoDomainBueno COMMAND monodomainbueno.x) +add_opencmiss_environment(MonoDomainBueno) + diff --git a/Bioelectrics/MonodomainBuenoOrovio/Makefile b/Bioelectrics/MonodomainBuenoOrovio/Makefile deleted file mode 100644 index 1b28b47b..00000000 --- a/Bioelectrics/MonodomainBuenoOrovio/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=Bioelectrics/ - -EXAMPLE_NAME = MonodomainBuenoOrovio - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Bioelectrics/MonodomainTP06/CMakeLists.txt b/Bioelectrics/MonodomainTP06/CMakeLists.txt new file mode 100644 index 00000000..d33ef747 --- /dev/null +++ b/Bioelectrics/MonodomainTP06/CMakeLists.txt @@ -0,0 +1,32 @@ +# Add example executable +add_executable(monodomaintp06.x src/MonodomainTP06Example.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(monodomaintp06.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(monodomaintp06.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MonoDomainTP06 COMMAND monodomaintp06.x) +add_opencmiss_environment(MonoDomainTP06) + diff --git a/Bioelectrics/MonodomainTP06/Makefile b/Bioelectrics/MonodomainTP06/Makefile deleted file mode 100644 index 663c09c4..00000000 --- a/Bioelectrics/MonodomainTP06/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=Bioelectrics/ - -EXAMPLE_NAME = MonodomainTP06 - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Bioelectrics/Monodomain_Shiqiang/CMakeLists.txt b/Bioelectrics/Monodomain_Shiqiang/CMakeLists.txt new file mode 100644 index 00000000..e96ba834 --- /dev/null +++ b/Bioelectrics/Monodomain_Shiqiang/CMakeLists.txt @@ -0,0 +1,32 @@ +# Add example executable +add_executable(monodomain_shiqiang.x src/Monodomain_ShiqiangExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(monodomain_shiqiang.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(monodomain_shiqiang.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MonoDomain_Shiqiang COMMAND monodomain_shiqiang.x) +add_opencmiss_environment(MonoDomain_Shiqiang) + diff --git a/Bioelectrics/Monodomain_Shiqiang/Makefile b/Bioelectrics/Monodomain_Shiqiang/Makefile deleted file mode 100644 index abf2dd2b..00000000 --- a/Bioelectrics/Monodomain_Shiqiang/Makefile +++ /dev/null @@ -1,71 +0,0 @@ -# -#-*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Bioelectrics/ - -EXAMPLE_NAME = Monodomain_Shiqiang - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Bioelectrics/Monodomain_Shiqiang/FHN.xml b/Bioelectrics/Monodomain_Shiqiang/input/FHN.xml similarity index 100% rename from Bioelectrics/Monodomain_Shiqiang/FHN.xml rename to Bioelectrics/Monodomain_Shiqiang/input/FHN.xml diff --git a/Bioelectrics/Monodomain_Shiqiang/LRd.xml b/Bioelectrics/Monodomain_Shiqiang/input/LRd.xml similarity index 100% rename from Bioelectrics/Monodomain_Shiqiang/LRd.xml rename to Bioelectrics/Monodomain_Shiqiang/input/LRd.xml diff --git a/Bioelectrics/Monodomain_Shiqiang/jrw-1998.xml b/Bioelectrics/Monodomain_Shiqiang/input/jrw-1998.xml similarity index 100% rename from Bioelectrics/Monodomain_Shiqiang/jrw-1998.xml rename to Bioelectrics/Monodomain_Shiqiang/input/jrw-1998.xml diff --git a/Bioelectrics/Monodomain_Shiqiang/lindblad_murphey_clark_giles_1996.xml b/Bioelectrics/Monodomain_Shiqiang/input/lindblad_murphey_clark_giles_1996.xml similarity index 100% rename from Bioelectrics/Monodomain_Shiqiang/lindblad_murphey_clark_giles_1996.xml rename to Bioelectrics/Monodomain_Shiqiang/input/lindblad_murphey_clark_giles_1996.xml diff --git a/Bioelectrics/Monodomain_Shiqiang/maltsev_rate_modulation.xml b/Bioelectrics/Monodomain_Shiqiang/input/maltsev_rate_modulation.xml similarity index 100% rename from Bioelectrics/Monodomain_Shiqiang/maltsev_rate_modulation.xml rename to Bioelectrics/Monodomain_Shiqiang/input/maltsev_rate_modulation.xml diff --git a/Bioelectrics/Monodomain_Shiqiang/n98.xml b/Bioelectrics/Monodomain_Shiqiang/input/n98.xml similarity index 100% rename from Bioelectrics/Monodomain_Shiqiang/n98.xml rename to Bioelectrics/Monodomain_Shiqiang/input/n98.xml diff --git a/Bioelectrics/Monodomain/OpenCMISS.cmake b/OpenCMISS.cmake similarity index 100% rename from Bioelectrics/Monodomain/OpenCMISS.cmake rename to OpenCMISS.cmake diff --git a/cellml/CMakeLists.txt b/cellml/CMakeLists.txt new file mode 100644 index 00000000..b1bf5fca --- /dev/null +++ b/cellml/CMakeLists.txt @@ -0,0 +1,34 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(Fortran) + add_subdirectory(model-integration/Fortran) +endif() diff --git a/cellml/Fortran/CMakeLists.txt b/cellml/Fortran/CMakeLists.txt new file mode 100644 index 00000000..7d52a2ca --- /dev/null +++ b/cellml/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cellml_example.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cellml_example.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cellml_example.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME CellMLExample COMMAND cellml_example.x) +add_opencmiss_environment(CellMLExample) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/cellml/model-integration/Fortran/CMakeLists.txt b/cellml/model-integration/Fortran/CMakeLists.txt new file mode 100644 index 00000000..265292e6 --- /dev/null +++ b/cellml/model-integration/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(model_integrate.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(model_integrate.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(model_integrate.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME ModelIntegrate COMMAND model_integrate.x) +add_opencmiss_environment(ModelIntegrate) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# From e3c231d3eb8d45f41a349d12adf690711e722780 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Fri, 14 Oct 2016 16:06:55 +1300 Subject: [PATCH 08/28] modified CellML Python examples to get them running again --- cellml/Python/README.rst | 6 ------ cellml/model-integration/Python/cellml-integration.py | 7 ++++--- cellml/model-integration/Python/sine-integration.py | 6 +++--- 3 files changed, 7 insertions(+), 12 deletions(-) delete mode 100644 cellml/Python/README.rst diff --git a/cellml/Python/README.rst b/cellml/Python/README.rst deleted file mode 100644 index 8fc63d8c..00000000 --- a/cellml/Python/README.rst +++ /dev/null @@ -1,6 +0,0 @@ -.. _examples-cellml-python: - -Python introduction to CellML in OpenCMISS ------------------------------------------- - -This example provides an entry level demonstration of creating fields in OpenCMISS to be defined using CellML models. This demonstration uses Python, see :ref:`examples-cellml-fortran` for the correpsponding Fortran example. \ No newline at end of file diff --git a/cellml/model-integration/Python/cellml-integration.py b/cellml/model-integration/Python/cellml-integration.py index 541a46fc..8307aea1 100644 --- a/cellml/model-integration/Python/cellml-integration.py +++ b/cellml/model-integration/Python/cellml-integration.py @@ -3,11 +3,12 @@ #DOC-START imports import sys, os, math #from scipy.special.basic import euler -# Make sure $OPENCMISS_ROOT/cm/bindings/python is first in our PYTHONPATH. -sys.path.insert(1, os.path.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +# Make required inclusions into PYTHONPATH. +sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/python' ) +sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/x86_64_linux/gnu-C5.4-gnu-F5.4/mpich_release/release/python/RELEASE' ) # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron #DOC-END imports usageString = "Usage: " + sys.argv[0] + " [euler | bdf] [ode time step]" diff --git a/cellml/model-integration/Python/sine-integration.py b/cellml/model-integration/Python/sine-integration.py index 25b5d598..cf039dac 100644 --- a/cellml/model-integration/Python/sine-integration.py +++ b/cellml/model-integration/Python/sine-integration.py @@ -2,11 +2,11 @@ #DOC-START imports import sys, os, math -# Make sure $OPENCMISS_ROOT/cm/bindings/python is first in our PYTHONPATH. -sys.path.insert(1, os.path.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/python' ) +sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/x86_64_linux/gnu-C5.4-gnu-F5.4/mpich_release/release/python/RELEASE' ) # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron #DOC-END imports # Set problem parameters From f849779706580a50eeb17d58904b9e50732eaf2e Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 09:33:00 +1300 Subject: [PATCH 09/28] added CMake support to Classical/AdvectionDiffusion examples --- .../AdvectionDiffusion/CMakeLists.txt | 34 +++++++++ .../StaticAdvectionDiffusion/CMakeLists.txt | 50 +++++++++++++ .../StaticAdvectionDiffusion/Makefile | 70 ------------------- .../CMakeLists.txt | 50 +++++++++++++ .../StaticAdvectionDiffusionSUPG/Makefile | 70 ------------------- 5 files changed, 134 insertions(+), 140 deletions(-) create mode 100644 ClassicalField/AdvectionDiffusion/CMakeLists.txt create mode 100644 ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusion/CMakeLists.txt delete mode 100755 ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusion/Makefile create mode 100644 ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusionSUPG/CMakeLists.txt delete mode 100755 ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusionSUPG/Makefile diff --git a/ClassicalField/AdvectionDiffusion/CMakeLists.txt b/ClassicalField/AdvectionDiffusion/CMakeLists.txt new file mode 100644 index 00000000..67821da4 --- /dev/null +++ b/ClassicalField/AdvectionDiffusion/CMakeLists.txt @@ -0,0 +1,34 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(StaticAdvectionDiffusion) + add_subdirectory(StaticAdvectionDiffusionSUPG) +endif() diff --git a/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusion/CMakeLists.txt b/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusion/CMakeLists.txt new file mode 100644 index 00000000..33d08a92 --- /dev/null +++ b/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusion/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(static.x src/StaticAdvectionDiffusionExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(static.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(static.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME StaticAdvectionDiffusion COMMAND static.x) +add_opencmiss_environment(StaticAdvectionDiffusion) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusion/Makefile b/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusion/Makefile deleted file mode 100755 index fa442e15..00000000 --- a/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusion/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../.. - GLOBAL_ROOT := $(CURDIR)/../../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/AdvectionDiffusion/ - -EXAMPLE_NAME = StaticAdvectionDiffusion - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusionSUPG/CMakeLists.txt b/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusionSUPG/CMakeLists.txt new file mode 100644 index 00000000..e136cf2a --- /dev/null +++ b/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusionSUPG/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(static_supg.x src/StaticAdvectionDiffusionSUPGExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(static_supg.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(static_supg.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME StaticAdvectionDiffusionSUPG COMMAND static_supg.x) +add_opencmiss_environment(StaticAdvectionDiffusionSUPG) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusionSUPG/Makefile b/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusionSUPG/Makefile deleted file mode 100755 index 1ec8a2ab..00000000 --- a/ClassicalField/AdvectionDiffusion/StaticAdvectionDiffusionSUPG/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../.. - GLOBAL_ROOT := $(CURDIR)/../../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/AdvectionDiffusion/ - -EXAMPLE_NAME = StaticAdvectionDiffusionSUPG - -include $(GLOBAL_ROOT)/ExampleMakefile - From 5b7db24be95b190add67eb1897dbea7479e28caf Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 09:58:57 +1300 Subject: [PATCH 10/28] added CMAKE support for ClassicalField/Diffusion examples --- .../Analytic1DDiffusion/CMakeLists.txt | 50 +++++++++++++ .../Diffusion/Analytic1DDiffusion/Makefile | 70 ------------------- ClassicalField/Diffusion/CMakeLists.txt | 41 +++++++++++ .../CubicConvergenceTest/CMakeLists.txt | 50 +++++++++++++ .../Diffusion/CubicConvergenceTest/Makefile | 70 ------------------- .../Diffusion/Diffusion/CMakeLists.txt | 50 +++++++++++++ ClassicalField/Diffusion/Diffusion/Makefile | 70 ------------------- .../DiffusionConstantSource/CMakeLists.txt | 50 +++++++++++++ .../DiffusionConstantSource/Makefile | 70 ------------------- .../DiffusionExponentialSource/CMakeLists.txt | 50 +++++++++++++ .../DiffusionExponentialSource/Makefile | 70 ------------------- .../DiffusionLinearSource/CMakeLists.txt | 50 +++++++++++++ .../Diffusion/DiffusionLinearSource/Makefile | 70 ------------------- .../DiffusionQuadraticSource/CMakeLists.txt | 50 +++++++++++++ .../DiffusionQuadraticSource/Makefile | 70 ------------------- .../LinearConvergenceTest/CMakeLists.txt | 50 +++++++++++++ .../Diffusion/LinearConvergenceTest/Makefile | 70 ------------------- .../QuadraticConvergenceTest/CMakeLists.txt | 50 +++++++++++++ .../QuadraticConvergenceTest/Makefile | 70 ------------------- 19 files changed, 491 insertions(+), 630 deletions(-) create mode 100644 ClassicalField/Diffusion/Analytic1DDiffusion/CMakeLists.txt delete mode 100755 ClassicalField/Diffusion/Analytic1DDiffusion/Makefile create mode 100644 ClassicalField/Diffusion/CMakeLists.txt create mode 100644 ClassicalField/Diffusion/CubicConvergenceTest/CMakeLists.txt delete mode 100755 ClassicalField/Diffusion/CubicConvergenceTest/Makefile create mode 100644 ClassicalField/Diffusion/Diffusion/CMakeLists.txt delete mode 100755 ClassicalField/Diffusion/Diffusion/Makefile create mode 100644 ClassicalField/Diffusion/DiffusionConstantSource/CMakeLists.txt delete mode 100755 ClassicalField/Diffusion/DiffusionConstantSource/Makefile create mode 100644 ClassicalField/Diffusion/DiffusionExponentialSource/CMakeLists.txt delete mode 100755 ClassicalField/Diffusion/DiffusionExponentialSource/Makefile create mode 100644 ClassicalField/Diffusion/DiffusionLinearSource/CMakeLists.txt delete mode 100755 ClassicalField/Diffusion/DiffusionLinearSource/Makefile create mode 100644 ClassicalField/Diffusion/DiffusionQuadraticSource/CMakeLists.txt delete mode 100755 ClassicalField/Diffusion/DiffusionQuadraticSource/Makefile create mode 100644 ClassicalField/Diffusion/LinearConvergenceTest/CMakeLists.txt delete mode 100755 ClassicalField/Diffusion/LinearConvergenceTest/Makefile create mode 100644 ClassicalField/Diffusion/QuadraticConvergenceTest/CMakeLists.txt delete mode 100755 ClassicalField/Diffusion/QuadraticConvergenceTest/Makefile diff --git a/ClassicalField/Diffusion/Analytic1DDiffusion/CMakeLists.txt b/ClassicalField/Diffusion/Analytic1DDiffusion/CMakeLists.txt new file mode 100644 index 00000000..719a6830 --- /dev/null +++ b/ClassicalField/Diffusion/Analytic1DDiffusion/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(AnalyticDiff.x src/Analytic1DDiffusionExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(AnalyticDiff.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(AnalyticDiff.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME AnalyticDiff COMMAND AnalyticDiff.x) +add_opencmiss_environment(AnalyticDiff) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Diffusion/Analytic1DDiffusion/Makefile b/ClassicalField/Diffusion/Analytic1DDiffusion/Makefile deleted file mode 100755 index 77c3eacc..00000000 --- a/ClassicalField/Diffusion/Analytic1DDiffusion/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Diffusion/ - -EXAMPLE_NAME = Analytic1DDiffusion - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Diffusion/CMakeLists.txt b/ClassicalField/Diffusion/CMakeLists.txt new file mode 100644 index 00000000..a084a9f4 --- /dev/null +++ b/ClassicalField/Diffusion/CMakeLists.txt @@ -0,0 +1,41 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(Analytic1DDiffusion) + add_subdirectory(CubicConvergenceTest) + add_subdirectory(Diffusion) + add_subdirectory(DiffusionConstantSource) + add_subdirectory(DiffusionExponentialSource) + add_subdirectory(DiffusionLinearSource) + add_subdirectory(DiffusionQuadraticSource) + add_subdirectory(LinearConvergenceTest) + add_subdirectory(QuadraticConvergenceTest) +endif() diff --git a/ClassicalField/Diffusion/CubicConvergenceTest/CMakeLists.txt b/ClassicalField/Diffusion/CubicConvergenceTest/CMakeLists.txt new file mode 100644 index 00000000..8385402a --- /dev/null +++ b/ClassicalField/Diffusion/CubicConvergenceTest/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cubic_converge.x src/CubicConvergenceTestExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cubic_converge.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cubic_converge.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME CubicConvergence COMMAND cubic_converge.x) +add_opencmiss_environment(CubicConvergence) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Diffusion/CubicConvergenceTest/Makefile b/ClassicalField/Diffusion/CubicConvergenceTest/Makefile deleted file mode 100755 index 7da7ecd7..00000000 --- a/ClassicalField/Diffusion/CubicConvergenceTest/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../.. - GLOBAL_ROOT := $(CURDIR)/../../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Diffusion/ - -EXAMPLE_NAME = CubicConvergenceTest - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Diffusion/Diffusion/CMakeLists.txt b/ClassicalField/Diffusion/Diffusion/CMakeLists.txt new file mode 100644 index 00000000..51bea8ef --- /dev/null +++ b/ClassicalField/Diffusion/Diffusion/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(diff.x src/DiffusionExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(diff.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(diff.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Diffusion COMMAND diff.x) +add_opencmiss_environment(Diffusion) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Diffusion/Diffusion/Makefile b/ClassicalField/Diffusion/Diffusion/Makefile deleted file mode 100755 index c232bb0f..00000000 --- a/ClassicalField/Diffusion/Diffusion/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Diffusion/ - -EXAMPLE_NAME = Diffusion - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Diffusion/DiffusionConstantSource/CMakeLists.txt b/ClassicalField/Diffusion/DiffusionConstantSource/CMakeLists.txt new file mode 100644 index 00000000..18eb875c --- /dev/null +++ b/ClassicalField/Diffusion/DiffusionConstantSource/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(diff_constant.x src/DiffusionConstantSourceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(diff_constant.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(diff_constant.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME DiffusionConstant COMMAND diff_constant.x) +add_opencmiss_environment(DiffusionConstant) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Diffusion/DiffusionConstantSource/Makefile b/ClassicalField/Diffusion/DiffusionConstantSource/Makefile deleted file mode 100755 index a9bf263c..00000000 --- a/ClassicalField/Diffusion/DiffusionConstantSource/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Diffusion/ - -EXAMPLE_NAME = DiffusionConstantSource - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Diffusion/DiffusionExponentialSource/CMakeLists.txt b/ClassicalField/Diffusion/DiffusionExponentialSource/CMakeLists.txt new file mode 100644 index 00000000..9f327e86 --- /dev/null +++ b/ClassicalField/Diffusion/DiffusionExponentialSource/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(diff_exp.x src/DiffusionExponentialSourceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(diff_exp.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(diff_exp.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME DiffusionExponential COMMAND diff_exp.x) +add_opencmiss_environment(DiffusionExponential) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Diffusion/DiffusionExponentialSource/Makefile b/ClassicalField/Diffusion/DiffusionExponentialSource/Makefile deleted file mode 100755 index 6f5655ba..00000000 --- a/ClassicalField/Diffusion/DiffusionExponentialSource/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Diffusion/ - -EXAMPLE_NAME = DiffusionExponentialSource - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Diffusion/DiffusionLinearSource/CMakeLists.txt b/ClassicalField/Diffusion/DiffusionLinearSource/CMakeLists.txt new file mode 100644 index 00000000..d67259aa --- /dev/null +++ b/ClassicalField/Diffusion/DiffusionLinearSource/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(diff_linear.x src/DiffusionLinearSourceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(diff_linear.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(diff_linear.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME DiffusionLinear COMMAND diff_linear.x) +add_opencmiss_environment(DiffusionLinear) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Diffusion/DiffusionLinearSource/Makefile b/ClassicalField/Diffusion/DiffusionLinearSource/Makefile deleted file mode 100755 index 0bda9c35..00000000 --- a/ClassicalField/Diffusion/DiffusionLinearSource/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Diffusion/ - -EXAMPLE_NAME = DiffusionLinearSource - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Diffusion/DiffusionQuadraticSource/CMakeLists.txt b/ClassicalField/Diffusion/DiffusionQuadraticSource/CMakeLists.txt new file mode 100644 index 00000000..badf77d4 --- /dev/null +++ b/ClassicalField/Diffusion/DiffusionQuadraticSource/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(diff_quadratic.x src/DiffusionQuadraticSourceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(diff_quadratic.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(diff_quadratic.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME DiffusionQuadratic COMMAND diff_quadratic.x) +add_opencmiss_environment(DiffusionQuadratic) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Diffusion/DiffusionQuadraticSource/Makefile b/ClassicalField/Diffusion/DiffusionQuadraticSource/Makefile deleted file mode 100755 index aadf390a..00000000 --- a/ClassicalField/Diffusion/DiffusionQuadraticSource/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Diffusion/ - -EXAMPLE_NAME = DiffusionQuadraticSource - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Diffusion/LinearConvergenceTest/CMakeLists.txt b/ClassicalField/Diffusion/LinearConvergenceTest/CMakeLists.txt new file mode 100644 index 00000000..6d73a595 --- /dev/null +++ b/ClassicalField/Diffusion/LinearConvergenceTest/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(linear_converge.x src/LinearConvergenceTestExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(linear_converge.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(linear_converge.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME LinearConvergence COMMAND linear_converge.x) +add_opencmiss_environment(LinearConvergence) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Diffusion/LinearConvergenceTest/Makefile b/ClassicalField/Diffusion/LinearConvergenceTest/Makefile deleted file mode 100755 index 9d8fef97..00000000 --- a/ClassicalField/Diffusion/LinearConvergenceTest/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../.. - GLOBAL_ROOT := $(CURDIR)/../../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Diffusion/ - -EXAMPLE_NAME = LinearConvergenceTest - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Diffusion/QuadraticConvergenceTest/CMakeLists.txt b/ClassicalField/Diffusion/QuadraticConvergenceTest/CMakeLists.txt new file mode 100644 index 00000000..9a0c013d --- /dev/null +++ b/ClassicalField/Diffusion/QuadraticConvergenceTest/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(quadratic_converge.x src/QuadraticConvergenceTestExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(quadratic_converge.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(quadratic_converge.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME QuadraticConvergence COMMAND quadratic_converge.x) +add_opencmiss_environment(QuadraticConvergence) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Diffusion/QuadraticConvergenceTest/Makefile b/ClassicalField/Diffusion/QuadraticConvergenceTest/Makefile deleted file mode 100755 index e8c8a4c9..00000000 --- a/ClassicalField/Diffusion/QuadraticConvergenceTest/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../.. - GLOBAL_ROOT := $(CURDIR)/../../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Diffusion/ - -EXAMPLE_NAME = QuadraticConvergenceTest - -include $(GLOBAL_ROOT)/ExampleMakefile - From 7261ddb3597330759a60e6bc647463a8923ab389 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 10:30:12 +1300 Subject: [PATCH 11/28] Added CMake support to ClassicalField/Helmholtz example --- ClassicalField/Helmholtz/CMakeLists.txt | 33 ++++++++++++ .../Helmholtz/Helmholtz/CMakeLists.txt | 50 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 ClassicalField/Helmholtz/CMakeLists.txt create mode 100644 ClassicalField/Helmholtz/Helmholtz/CMakeLists.txt diff --git a/ClassicalField/Helmholtz/CMakeLists.txt b/ClassicalField/Helmholtz/CMakeLists.txt new file mode 100644 index 00000000..41e7cb91 --- /dev/null +++ b/ClassicalField/Helmholtz/CMakeLists.txt @@ -0,0 +1,33 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(Helmholtz) +endif() diff --git a/ClassicalField/Helmholtz/Helmholtz/CMakeLists.txt b/ClassicalField/Helmholtz/Helmholtz/CMakeLists.txt new file mode 100644 index 00000000..8323f1ae --- /dev/null +++ b/ClassicalField/Helmholtz/Helmholtz/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(helmholtz.x src/HelmholtzExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(helmholtz.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(helmholtz.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Helmholtz COMMAND helmholtz.x) +add_opencmiss_environment(Helmholtz) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# From dd4724099c9b41aa301ffeef64dfb0ee2b23d519 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 12:12:47 +1300 Subject: [PATCH 12/28] added CMake support for ClassicalField/Laplace examples --- .../Laplace/{Laplace => }/CMakeLists.txt | 21 ++-- .../Laplace/Cylinder/CylinderExample.py | 13 +-- .../Laplace/Embedded1DLaplace/CMakeLists.txt | 50 ++++++++++ .../Laplace/Embedded1DLaplace/Makefile | 70 -------------- .../Laplace/Embedded2DLaplace/CMakeLists.txt | 50 ++++++++++ .../Laplace/Embedded2DLaplace/Makefile | 70 -------------- .../GeneralisedLaplace/Fortran/CMakeLists.txt | 44 +++++++++ .../GeneralisedLaplace/Fortran/Makefile | 70 -------------- .../Laplace/Laplace/C/CMakeLists.txt | 1 - ClassicalField/Laplace/Laplace/C/Makefile | 70 -------------- .../Laplace/Laplace/Fortran/Makefile | 70 -------------- .../Laplace/Laplace/OpenCMISS.cmake | 95 ------------------- .../Laplace/Laplace/Python/LaplaceExample.py | 9 +- .../Laplace/LaplaceEllipsoid/CMakeLists.txt | 50 ++++++++++ .../Laplace/LaplaceEllipsoid/Makefile | 70 -------------- .../Laplace/LaplaceEllipsoid_FieldML/Makefile | 72 -------------- .../Laplace/NumberLaplace/CMakeLists.txt | 50 ++++++++++ ClassicalField/Laplace/NumberLaplace/Makefile | 70 -------------- .../Laplace/ParallelLaplace/CMakeLists.txt | 50 ++++++++++ .../Laplace/ParallelLaplace/Makefile | 70 -------------- .../SimplexLaplace/Linear/CMakeLists.txt | 50 ++++++++++ .../Laplace/SimplexLaplace/Linear/Makefile | 70 -------------- 22 files changed, 368 insertions(+), 817 deletions(-) rename ClassicalField/Laplace/{Laplace => }/CMakeLists.txt (77%) create mode 100644 ClassicalField/Laplace/Embedded1DLaplace/CMakeLists.txt delete mode 100644 ClassicalField/Laplace/Embedded1DLaplace/Makefile create mode 100644 ClassicalField/Laplace/Embedded2DLaplace/CMakeLists.txt delete mode 100644 ClassicalField/Laplace/Embedded2DLaplace/Makefile create mode 100644 ClassicalField/Laplace/GeneralisedLaplace/Fortran/CMakeLists.txt delete mode 100644 ClassicalField/Laplace/GeneralisedLaplace/Fortran/Makefile delete mode 100755 ClassicalField/Laplace/Laplace/C/Makefile delete mode 100644 ClassicalField/Laplace/Laplace/Fortran/Makefile delete mode 100644 ClassicalField/Laplace/Laplace/OpenCMISS.cmake create mode 100644 ClassicalField/Laplace/LaplaceEllipsoid/CMakeLists.txt delete mode 100644 ClassicalField/Laplace/LaplaceEllipsoid/Makefile delete mode 100644 ClassicalField/Laplace/LaplaceEllipsoid_FieldML/Makefile create mode 100644 ClassicalField/Laplace/NumberLaplace/CMakeLists.txt delete mode 100644 ClassicalField/Laplace/NumberLaplace/Makefile create mode 100644 ClassicalField/Laplace/ParallelLaplace/CMakeLists.txt delete mode 100644 ClassicalField/Laplace/ParallelLaplace/Makefile create mode 100644 ClassicalField/Laplace/SimplexLaplace/Linear/CMakeLists.txt delete mode 100644 ClassicalField/Laplace/SimplexLaplace/Linear/Makefile diff --git a/ClassicalField/Laplace/Laplace/CMakeLists.txt b/ClassicalField/Laplace/CMakeLists.txt similarity index 77% rename from ClassicalField/Laplace/Laplace/CMakeLists.txt rename to ClassicalField/Laplace/CMakeLists.txt index a57d23ef..5ea48276 100644 --- a/ClassicalField/Laplace/Laplace/CMakeLists.txt +++ b/ClassicalField/Laplace/CMakeLists.txt @@ -6,20 +6,14 @@ # For more information see http://www.opencmiss.org/documentation # Include the OpenCMISS initalisation & macro definition file. -include(./OpenCMISS.cmake) +include(../../OpenCMISS.cmake) # Project setup # ------------- cmake_minimum_required(VERSION 3.3 FATAL_ERROR) project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) -#enable_language(C OPTIONAL) enable_testing() -message(STATUS "C Compiler: ${CMAKE_C_COMPILER}") -message(STATUS "FORTRAN Compiler: ${CMAKE_Fortran_COMPILER}") -message(STATUS "MPI: ${MPI}") - - # Find OpenCMISS # -------------- # @@ -35,8 +29,13 @@ find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) # CMake application code # ---------------------- if (CMAKE_Fortran_COMPILER) - add_subdirectory(Fortran) -endif() -if (CMAKE_C_COMPILER) - add_subdirectory(C) + add_subdirectory(Embedded1DLaplace) + add_subdirectory(Embedded2DLaplace) + add_subdirectory(Laplace/C) + add_subdirectory(Laplace/Fortran) + add_subdirectory(GeneralisedLaplace/Fortran) + add_subdirectory(LaplaceEllipsoid) + add_subdirectory(NumberLaplace) + add_subdirectory(ParallelLaplace) + add_subdirectory(SimplexLaplace/Linear) endif() diff --git a/ClassicalField/Laplace/Cylinder/CylinderExample.py b/ClassicalField/Laplace/Cylinder/CylinderExample.py index 2eb8b912..286710c3 100755 --- a/ClassicalField/Laplace/Cylinder/CylinderExample.py +++ b/ClassicalField/Laplace/Cylinder/CylinderExample.py @@ -50,18 +50,19 @@ from optparse import OptionParser # Add OpenCMISS python bindings directory to path so we can import it -sys.path.append(os.sep.join(( - os.environ['OPENCMISS_ROOT'], 'cm', 'bindings', 'python'))) -from opencmiss import iron +sys.path.append(os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich_release/release', + 'python/RELEASE'))) +from opencmiss.iron import iron # Read in number of elements parser = OptionParser() -parser.add_option("-r", "--r-elements", dest="r", type="int", default=2, +parser.add_option("-r", "--r-elements", dest="r", type="int", default=4, help="Number of radial elements") -parser.add_option("-c", "--c-elements", dest="c", type="int", default=16, +parser.add_option("-c", "--c-elements", dest="c", type="int", default=32, help="Number of circumferential elements") -parser.add_option("-z", "--z-elements", dest="z", type="int", default=2, +parser.add_option("-z", "--z-elements", dest="z", type="int", default=4, help="Number of z elements") (opts, args) = parser.parse_args() if opts.r <= 0: diff --git a/ClassicalField/Laplace/Embedded1DLaplace/CMakeLists.txt b/ClassicalField/Laplace/Embedded1DLaplace/CMakeLists.txt new file mode 100644 index 00000000..1b073add --- /dev/null +++ b/ClassicalField/Laplace/Embedded1DLaplace/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(embed_1D.x src/Embedded1DLaplaceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(embed_1D.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(embed_1D.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Laplace COMMAND embed_1D.x) +add_opencmiss_environment(Laplace) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Laplace/Embedded1DLaplace/Makefile b/ClassicalField/Laplace/Embedded1DLaplace/Makefile deleted file mode 100644 index 43113dd4..00000000 --- a/ClassicalField/Laplace/Embedded1DLaplace/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Laplace/ - -EXAMPLE_NAME = Embedded1DLaplace - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Laplace/Embedded2DLaplace/CMakeLists.txt b/ClassicalField/Laplace/Embedded2DLaplace/CMakeLists.txt new file mode 100644 index 00000000..24ca53c5 --- /dev/null +++ b/ClassicalField/Laplace/Embedded2DLaplace/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(embed_2D.x src/Embedded2DLaplaceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(embed_2D.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(embed_2D.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Laplace COMMAND embed_2D.x) +add_opencmiss_environment(Laplace) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Laplace/Embedded2DLaplace/Makefile b/ClassicalField/Laplace/Embedded2DLaplace/Makefile deleted file mode 100644 index 77036e53..00000000 --- a/ClassicalField/Laplace/Embedded2DLaplace/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Laplace/ - -EXAMPLE_NAME = Embedded2DLaplace - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Laplace/GeneralisedLaplace/Fortran/CMakeLists.txt b/ClassicalField/Laplace/GeneralisedLaplace/Fortran/CMakeLists.txt new file mode 100644 index 00000000..0b20e9de --- /dev/null +++ b/ClassicalField/Laplace/GeneralisedLaplace/Fortran/CMakeLists.txt @@ -0,0 +1,44 @@ +# Add example executable +add_executable(example1.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(example1.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(example1.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Laplace_Fortran COMMAND example1.x) +add_opencmiss_environment(Laplace_Fortran) + +add_executable(example2.x src/FortranExample_2D_testproblem.f90) +target_compile_options(example2.x PRIVATE ${PROC_OPT}) +target_link_libraries(example2.x PRIVATE opencmiss) + +add_executable(example3.x src/FortranExample_3D_testproblem.f90) +target_compile_options(example3.x PRIVATE ${PROC_OPT}) +target_link_libraries(example3.x PRIVATE opencmiss) + +add_executable(example4.x src/FortranExample_3D_tests.f90) +target_compile_options(example4.x PRIVATE ${PROC_OPT}) +target_link_libraries(example4.x PRIVATE opencmiss) + diff --git a/ClassicalField/Laplace/GeneralisedLaplace/Fortran/Makefile b/ClassicalField/Laplace/GeneralisedLaplace/Fortran/Makefile deleted file mode 100644 index 97b1bb8a..00000000 --- a/ClassicalField/Laplace/GeneralisedLaplace/Fortran/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Laplace/GeneralisedLaplace/ - -EXAMPLE_NAME = Fortran - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Laplace/Laplace/C/CMakeLists.txt b/ClassicalField/Laplace/Laplace/C/CMakeLists.txt index e6e04ed5..9f59b6b9 100644 --- a/ClassicalField/Laplace/Laplace/C/CMakeLists.txt +++ b/ClassicalField/Laplace/Laplace/C/CMakeLists.txt @@ -15,7 +15,6 @@ add_executable(laplace_c src/CExample.c) # find_package(PETSC REQUIRED) # target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) # -# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. target_link_libraries(laplace_c PRIVATE opencmiss) # Add a simple test that runs the executable diff --git a/ClassicalField/Laplace/Laplace/C/Makefile b/ClassicalField/Laplace/Laplace/C/Makefile deleted file mode 100755 index 38de1889..00000000 --- a/ClassicalField/Laplace/Laplace/C/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Laplace/Laplace/ - -EXAMPLE_NAME = C - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Laplace/Laplace/Fortran/Makefile b/ClassicalField/Laplace/Laplace/Fortran/Makefile deleted file mode 100644 index 2af4ce06..00000000 --- a/ClassicalField/Laplace/Laplace/Fortran/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Laplace/Laplace/ - -EXAMPLE_NAME = Fortran - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Laplace/Laplace/OpenCMISS.cmake b/ClassicalField/Laplace/Laplace/OpenCMISS.cmake deleted file mode 100644 index d1798862..00000000 --- a/ClassicalField/Laplace/Laplace/OpenCMISS.cmake +++ /dev/null @@ -1,95 +0,0 @@ -########################### -# *DO NOT CHANGE THIS FILE* -########################### -# -# Prepares the use of OpenCMISS by scanning at various path locations for OpenCMISS (SDK) installations. -# -# Search order: -# - OPENCMISS_INSTALL_DIR variable -# - OPENCMISS_INSTALL_DIR environment variable -# - OPENCMISS_SDK_DIR variable -# - OPENCMISS_SDK_DIR environment variable -# - [Windows only] The Registry is searched additionally for installed SDKs. -# -# If found -# - Includes the toolchain config script of the found opencmiss installation to enable toolchain selection logic (non-windows) - -# Convenience: The OPENCMISS_INSTALL_DIR may also be defined in the environment and various other places -if (DEFINED OPENCMISS_INSTALL_DIR) - get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE) - if (EXISTS "${OPENCMISS_INSTALL_DIR}") - message(STATUS "Using specified installation directory '${OPENCMISS_INSTALL_DIR}'") - else() - message(WARNING "The specified OPENCMISS_INSTALL_DIR '${OPENCMISS_INSTALL_DIR}' does not exist. Skipping.") - unset(OPENCMISS_INSTALL_DIR) - endif() -endif() -if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_INSTALL_DIR}" STREQUAL "") - file(TO_CMAKE_PATH "$ENV{OPENCMISS_INSTALL_DIR}" OPENCMISS_INSTALL_DIR) - get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE) - if (EXISTS "${OPENCMISS_INSTALL_DIR}") - message(STATUS "Using environment installation directory '${OPENCMISS_INSTALL_DIR}'") - else() - message(WARNING "The environment variable OPENCMISS_INSTALL_DIR='${OPENCMISS_INSTALL_DIR}' contains an invalid path. Skipping.") - unset(OPENCMISS_INSTALL_DIR) - endif() -endif() -if (NOT OPENCMISS_INSTALL_DIR AND DEFINED OPENCMISS_SDK_DIR) - get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE) - if (EXISTS "${OPENCMISS_SDK_DIR}") - message(STATUS "Using SDK installation directory: ${OPENCMISS_SDK_DIR}") - set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}") - else() - message(WARNING "The specified OPENCMISS_SDK_DIR '${OPENCMISS_SDK_DIR}' does not exist. Skipping.") - endif() -endif() -if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_SDK_DIR}" STREQUAL "") - file(TO_CMAKE_PATH "$ENV{OPENCMISS_SDK_DIR}" OPENCMISS_SDK_DIR) - get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE) - if (EXISTS "${OPENCMISS_SDK_DIR}") - message(STATUS "Using environment SDK installation directory: ${OPENCMISS_SDK_DIR}") - set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}") - else() - message(WARNING "The environment variable OPENCMISS_SDK_DIR='${OPENCMISS_SDK_DIR}' contains an invalid path. Skipping.") - unset(OPENCMISS_SDK_DIR) - endif() -endif() -# On windows: check the registry for installed OpenCMISS SDKs -if(NOT OPENCMISS_INSTALL_DIR AND WIN32) - foreach(ROOT HKEY_CURRENT_USER HKEY_LOCAL_MACHINE) - foreach(PACKAGE OpenCMISSUserSDK OpenCMISSDeveloperSDK) - set(_REG_KEY "[${ROOT}\\Software\\Auckland Bioengineering Institute\\${PACKAGE}]") - get_filename_component(OPENCMISS_INSTALL_DIR "${_REG_KEY}" ABSOLUTE) - #message(STATUS "Trying registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}") - if (EXISTS "${OPENCMISS_INSTALL_DIR}") - message(STATUS "Found ${PACKAGE} in Windows registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}") - break() - else() - unset(OPENCMISS_INSTALL_DIR) - endif() - endforeach() - if (EXISTS "${OPENCMISS_INSTALL_DIR}") - break() - endif() - endforeach() -endif() - -if(OPENCMISS_INSTALL_DIR) - message(STATUS "OPENCMISS_INSTALL_DIR=${OPENCMISS_INSTALL_DIR}") - # Use the OpenCMISS scripts to also allow choosing a separate toolchain - # This file is located at the opencmiss installation rather than the local example - # as it avoids file replication and makes maintenance much easier - if (TOOLCHAIN) - set(_OCTC ${OPENCMISS_INSTALL_DIR}/cmake/OCToolchainCompilers.cmake) - if (EXISTS "${_OCTC}") - include(${_OCTC}) - else() - message(WARNING "TOOLCHAIN specified but OpenCMISS config script could not be found at ${_OCTC}. Trying CMake defaults.") - endif() - unset(_OCTC) - endif() - set(OpenCMISS_DIR "${OPENCMISS_INSTALL_DIR}" CACHE PATH "Path to the found OpenCMISS (SDK) installation") -else() - message(WARNING "No OpenCMISS (SDK) installation directory detected. Using default system environment.") -endif() - diff --git a/ClassicalField/Laplace/Laplace/Python/LaplaceExample.py b/ClassicalField/Laplace/Laplace/Python/LaplaceExample.py index 8295e587..290cabaf 100755 --- a/ClassicalField/Laplace/Laplace/Python/LaplaceExample.py +++ b/ClassicalField/Laplace/Laplace/Python/LaplaceExample.py @@ -51,10 +51,15 @@ # Add Python bindings directory to PATH import sys, os -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append(os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'python'))) +sys.path.append(os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/intel-C16.0-intel-F16.0/intel_release/release', + 'python', + 'RELEASE'))) # Intialise OpenCMISS-Iron -from opencmiss import iron +from opencmiss.iron import iron parameters.parse() diff --git a/ClassicalField/Laplace/LaplaceEllipsoid/CMakeLists.txt b/ClassicalField/Laplace/LaplaceEllipsoid/CMakeLists.txt new file mode 100644 index 00000000..7ec8b284 --- /dev/null +++ b/ClassicalField/Laplace/LaplaceEllipsoid/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(laplace_ellipsoid.x src/LaplaceEllipsoidExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(laplace_ellipsoid.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(laplace_ellipsoid.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Laplace_Fortran COMMAND laplace_ellipsoid.x) +add_opencmiss_environment(Laplace_Fortran) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Laplace/LaplaceEllipsoid/Makefile b/ClassicalField/Laplace/LaplaceEllipsoid/Makefile deleted file mode 100644 index 41677a8f..00000000 --- a/ClassicalField/Laplace/LaplaceEllipsoid/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Laplace/ - -EXAMPLE_NAME = LaplaceEllipsoid - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Laplace/LaplaceEllipsoid_FieldML/Makefile b/ClassicalField/Laplace/LaplaceEllipsoid_FieldML/Makefile deleted file mode 100644 index 9df860f8..00000000 --- a/ClassicalField/Laplace/LaplaceEllipsoid_FieldML/Makefile +++ /dev/null @@ -1,72 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Laplace/ - -EXAMPLE_NAME = LaplaceEllipsoid_FieldML - -USEFIELDML = true - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Laplace/NumberLaplace/CMakeLists.txt b/ClassicalField/Laplace/NumberLaplace/CMakeLists.txt new file mode 100644 index 00000000..ab3beaed --- /dev/null +++ b/ClassicalField/Laplace/NumberLaplace/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(laplace_number.x src/NumberLaplaceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(laplace_number.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(laplace_number.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Laplace_Fortran COMMAND laplace_number.x) +add_opencmiss_environment(Laplace_Fortran) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Laplace/NumberLaplace/Makefile b/ClassicalField/Laplace/NumberLaplace/Makefile deleted file mode 100644 index ea77305b..00000000 --- a/ClassicalField/Laplace/NumberLaplace/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Laplace/ - -EXAMPLE_NAME = NumberLaplace - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Laplace/ParallelLaplace/CMakeLists.txt b/ClassicalField/Laplace/ParallelLaplace/CMakeLists.txt new file mode 100644 index 00000000..4120cd3a --- /dev/null +++ b/ClassicalField/Laplace/ParallelLaplace/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(laplace_parallel.x src/ParallelLaplaceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(laplace_parallel.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(laplace_parallel.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Laplace_Fortran COMMAND laplace_parallel.x) +add_opencmiss_environment(Laplace_Fortran) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Laplace/ParallelLaplace/Makefile b/ClassicalField/Laplace/ParallelLaplace/Makefile deleted file mode 100644 index df6ed8c4..00000000 --- a/ClassicalField/Laplace/ParallelLaplace/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Laplace/ - -EXAMPLE_NAME = ParallelLaplace - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Laplace/SimplexLaplace/Linear/CMakeLists.txt b/ClassicalField/Laplace/SimplexLaplace/Linear/CMakeLists.txt new file mode 100644 index 00000000..1c5ff5b6 --- /dev/null +++ b/ClassicalField/Laplace/SimplexLaplace/Linear/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(linear.x src/LinearExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(linear.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(linear.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Laplace_Fortran COMMAND linear.x) +add_opencmiss_environment(Laplace_Fortran) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Laplace/SimplexLaplace/Linear/Makefile b/ClassicalField/Laplace/SimplexLaplace/Linear/Makefile deleted file mode 100644 index 0400ba21..00000000 --- a/ClassicalField/Laplace/SimplexLaplace/Linear/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = ClassicalField/Laplace/SimplexLaplace/ - -EXAMPLE_NAME = Linear - -include $(GLOBAL_ROOT)/ExampleMakefile - From 3d9f17f85c4c2850d80aa58b49f47b38aaa9ced3 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 14:00:00 +1300 Subject: [PATCH 13/28] added CMake support for ClassicalField/Poisson examples --- Bioelectrics/input/FHN.xml | 355 + Bioelectrics/input/LRd.xml | 4320 ++++++++++++ Bioelectrics/input/jrw-1998.xml | 5333 +++++++++++++++ .../lindblad_murphey_clark_giles_1996.xml | 3779 +++++++++++ .../input/maltsev_rate_modulation.xml | 4487 +++++++++++++ Bioelectrics/input/n98.xml | 5799 +++++++++++++++++ .../AnalyticNonlinearPoisson/CMakeLists.txt | 50 + .../Poisson/AnalyticNonlinearPoisson/Makefile | 70 - ClassicalField/Poisson/CMakeLists.txt | 35 + .../Fortran/CMakeLists.txt | 50 + .../ExtracellularBidomain/Fortran/Makefile | 70 - .../Poisson/NonlinearPoisson/CMakeLists.txt | 50 + .../Poisson/NonlinearPoisson/Makefile | 70 - 13 files changed, 24258 insertions(+), 210 deletions(-) create mode 100644 Bioelectrics/input/FHN.xml create mode 100644 Bioelectrics/input/LRd.xml create mode 100644 Bioelectrics/input/jrw-1998.xml create mode 100644 Bioelectrics/input/lindblad_murphey_clark_giles_1996.xml create mode 100644 Bioelectrics/input/maltsev_rate_modulation.xml create mode 100644 Bioelectrics/input/n98.xml create mode 100644 ClassicalField/Poisson/AnalyticNonlinearPoisson/CMakeLists.txt delete mode 100644 ClassicalField/Poisson/AnalyticNonlinearPoisson/Makefile create mode 100644 ClassicalField/Poisson/CMakeLists.txt create mode 100644 ClassicalField/Poisson/ExtracellularBidomain/Fortran/CMakeLists.txt delete mode 100644 ClassicalField/Poisson/ExtracellularBidomain/Fortran/Makefile create mode 100644 ClassicalField/Poisson/NonlinearPoisson/CMakeLists.txt delete mode 100644 ClassicalField/Poisson/NonlinearPoisson/Makefile diff --git a/Bioelectrics/input/FHN.xml b/Bioelectrics/input/FHN.xml new file mode 100644 index 00000000..c01c9d20 --- /dev/null +++ b/Bioelectrics/input/FHN.xml @@ -0,0 +1,355 @@ + + + + +
+ + The FitzHugh-Nagumo Simplified Cardiac Myocyte Model + + Catherine + Lloyd + + Bioengineering Institute, University of Auckland + + + +
+ Model Status + + This version of the model has been curated by Penny Noble using + COR and is also known to read in to JSim and PCEnv. There is also a PCEnv session file associated with this model. + +
+ +Model Structure + + +Often it is not necessary to model the ionic currents of a cell with the accuracy and complexity inherent in the biophysically based models. With a view to investigating phenomena on a larger spatial and temporal scale, several ionic current models have been developed that do not seek to model subcellular processes but only to provide an action potential at a minimal computational cost. + + + +The FitzHugh-Nagumo model (1961) is based on the cubic excitation model (see The Polynomial Model, 1975), but it also includes a recovery variable so both depolarisation and repolarisation can be modelled. In 1994, Rogers and McCulloch modified the original model to generate a more realistic action potential. The velocity of the upstroke was increased and the large hyperpolarisation at the end of the recovery phase was removed. The model parameters were also updated. In 1996, this form of the already modified FitzHugh_Nagumo model was further updated by Aliev and Panfilov. They altered the equation which modelled the change of the recovery variable to provide a more realistic restitution period and to allow for reentrant phenomena. + + + +The complete original paper references are cited below: + + + +Impulses and physiological states in theoretical models of nerve membrane, FitzHugh, R.A., 1961, + Biophys. J. + , 1, 445-466. + + + +An active pulse transmission line simulating nerve axon, Nagumo, J., Animoto, S., Yoshizawa, S., 1962, Proc. Inst. Radio Engineers, 50, 2061-2070. + + + +A collocation-Galerkin finite element model of cardiac action potential propagation, Rogers, J.M., McCulloch, A.D., 1994a, + IEEE Trans. Biomed. Eng. + , 41, 743-757. + + + +A simple two-variable model of cardiac excitation, Aliev, R.R. and Panfilov, A.V., 1996, + Chaos, Solitons and Fractals + , 7, 293-301. PubMed ID: 8796189 + + + +The raw CellML description of the simplified cardiac myocyte models can be downloaded in various formats as described in . For an example of a more complete documentation for an electrophysiological model, see The Hodgkin-Huxley Squid Axon Model, 1952. + + + +
+ + + + + + + + + + + + + + + + + + + + + + + t + + v + + + + 1 + + + + + + + v + + + v + alpha + + + + 1 + v + + + w + + I + + + + + + + + + t + + w + + + + 1 + epsilon + + + v + + + gamma + w + + + + + + + + + + + + + + + + + + + + + J + Nagumo + + + + + + + + + + + + + + S + Yoshizawa + + + 1962-10-01 00:00 + + + + + + + + Peter + Villiger + J + + + + An active pulse transmission line simulating nerve axon + 50 + 2061 + + + 2070 + + + J + Nagumo + + + Penny + Noble + J + + + + + + + + + + + + + + + + + + Penny + Noble + + + + 1000 + 10000 + + + + + + + Department of Physiology, Anatomy & Genetics, University of Oxford + + + + + + + Biophysical Journal + + + S + Arimoto + + + + + + + + Impulses and Physiological States in Theoretical Models of Nerve Membrane + 1 + 445 + + + 466 + + + 2005-06-14T00:00:00+00:00 + + + + + + + + keyword + + + simplified model + neuron + electrophysiology + cardiac + Myocyte + + + + + + + + + added metadata + + + + + Units checked, curated. + + + + + + + + + + + 2007-11-29T12:16:16+13:00 + + + + + + Oxford University + The Bioengineering Institute + + + Biophysical Journal + + + + + + Richard + Fitzhugh + A + + + + + + + + + + + penny.noble@physiol.ox.ac.uk + + + 1961-01-01 + + + + + + + 2006-03-31 + + + \ No newline at end of file diff --git a/Bioelectrics/input/LRd.xml b/Bioelectrics/input/LRd.xml new file mode 100644 index 00000000..1fd24b84 --- /dev/null +++ b/Bioelectrics/input/LRd.xml @@ -0,0 +1,4320 @@ + + + + + + + + + + + + + Lloyd + Catherine + May + + + c.lloyd@auckland.ac.nz + + + + The University of Auckland + The Bioengineering Institute + + + + + + 2002-03-28 + + + + + + Fixed maths. + + + + Lloyd + Catherine + May + + + + 2003-07-30 + + + + + Fixed maths: alpha_J_calculation in fast_sodium_current_j_gate, + beta_K1_calculation in time_independent_potassium_current_K1_gate, and i_NaK_calculation in sodium_potassium_pump. + + + + Lloyd + Catherine + May + + + + 2003-06-05 + + + + + + The University of Auckland, The Bioengineering Institute + + + + + + + + The Luo-Rudy II Model of Mammalian Ventricular Cardiac Action + Potentials, 1994 + + + + + + This is the CellML description of Luo and Rudy's mathematical model of + the mammalian cardiac ventricular action potential. It is a + significant development on their original 1991 model. While this + version of the model qualitatively compares well to the LR II paper + for the action potential, the intracellular calcium dynamics have not + been included correctly - namely there is no calcium-induced + calcium-release (CICR) process in this version of the model. The + original version of the model simulates CICR via a mechanism whereby + CICR is induced if and only if the calcium accumulated in the cell in + the 2 ms following (dV/dt)max exceeds a given threshold. This sort of + process is a bit tricky to include in the CellML (or at least in a way + that will work with the CellML abilitites of CMISS) so has been left + out for now. + + + + Catherine Lloyd + + + + + Mammalia + + Ventricular Myocyte + + + + 7514509 + + + + bdf + newton + dense + + + + + + + 0.01 + + + 1.0 + + + 0 + + + 700 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The main component for the model, contains all ionic currents and + defines the transmembrane potential. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + We need to use dV/dt in the calulation of calcium-induced + calcium-release, so we make it accessible here. + + + + + + + dV_dt + + + I_st + + i_Na + i_Ca_L + i_K + i_K1 + i_Kp + i_NaCa + i_p_Ca + i_Na_b + i_Ca_b + i_NaK + i_ns_Ca + + + Cm + + + + + + + + + Assign the rate of change of potential for the differential + equation. + + + + + + + + time + V + + dV_dt + + + + + + + + + + + The fast sodium current is primarily responsible for the upstroke of + the action potential. + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the fast sodium current. + + + + + + + i_Na + + g_Na + + m + 3.0 + + h + j + + V + E_Na + + + + + + + + + + Calculation of reversal potential for the fast sodium channel. + + + + + + + E_Na + + + + R + T + + F + + + + Nao + Nai + + + + + + + + + + + + + The voltage-dependent activation gate for the fast sodium channel - + the m gate. + + + + + + + + + + + + + + + + + + The opening rate for the m gate. + + + + + + + alpha_m + + + 0.32 + + V + 47.13 + + + + 1.0 + + + -0.1 + + V + 47.13 + + + + + + + + + + + + + The closing rate for the m gate. + + + + + + + beta_m + + 0.08 + + + + V + + 11.0 + + + + + + + + + + + The kinetics of the m gate. + + + + + + + + time + m + + + + alpha_m + + 1.0 + m + + + + beta_m + m + + + + + + + + + + + + The voltage-dependent inactivation gate for the fast sodium channel - + the h gate. + + + + + + + + + + + + + + + + + + The opening rate for the h gate. + + + + + + + alpha_h + + + + 0.135 + + + + 80.0 + V + + -6.8 + + + + + V + -40.0 + + + + 0.0 + + + + + + + + + + The closing rate for the h gate. + + + + + + + beta_h + + + + + 3.56 + + + 0.079 + V + + + + + 310000.0 + + + 0.35 + V + + + + + + V + -40.0 + + + + + 1.0 + + 0.13 + + 1.0 + + + + V + 10.66 + + -11.1 + + + + + + + + + + + + + + + The kinetics of the h gate. + + + + + + + + time + h + + + + alpha_h + + 1.0 + h + + + + beta_h + h + + + + + + + + + + + + The voltage-dependent slow inactivation gate for the fast sodium + channel - the j gate. + + + + + + + + + + + + + + + + + + The opening rate for the j gate. + + + + + + + alpha_j + + + + + + -127140.0 + + + 0.2444 + V + + + + + 0.00003474 + + + -0.04391 + V + + + + + + + V + 37.78 + + + 1.0 + + + 0.311 + + V + 79.23 + + + + + + + + V + -40.0 + + + + 0.0 + + + + + + + + + + The closing rate for the j gate. + + + + + + + beta_j + + + + + 0.1212 + + + -0.01052 + V + + + + + 1.0 + + + -0.1378 + + V + 40.14 + + + + + + + V + -40.0 + + + + + + 0.3 + + + -0.0000002535 + V + + + + + 1.0 + + + -0.1 + + V + 32.0 + + + + + + + + + + + + + + + The kinetics of for the j gate. + + + + + + + + time + j + + + + alpha_j + + 1.0 + j + + + + beta_j + j + + + + + + + + + + + + The L-type calcium channel. Primarily a calcium specific channel, + but with small potassium and sodium components, activated at plateau + potentials. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The calcium component of the total L-type channel current. + + + + + + + i_CaCa + + d + f + f_Ca + I_CaCa + + + + + + + + + The sodium component of the total L-type channel current. + + + + + + + i_CaNa + + d + f + f_Ca + I_CaNa + + + + + + + + + The potassium component of the total L-type channel current. + + + + + + + i_CaK + + d + f + f_Ca + I_CaK + + + + + + + + + The maximum calcium component of the total L-type channel current. + + + + + + + I_CaCa + + P_Ca + + 2.0 + 2.0 + + + + V + + F + 2.0 + + + + R + T + + + + + + gamma_Cai + Cai + + + + 2.0 + V + F + + + R + T + + + + + + gamma_Cao + Cao + + + + + + + 2.0 + V + F + + + R + T + + + + 1.0 + + + + + + + + + + + The maximum sodium component of the total L-type channel current. + + + + + + + I_CaNa + + P_Na + + 1.0 + 2.0 + + + + V + + F + 2.0 + + + + R + T + + + + + + gamma_Nai + Nai + + + + 1.0 + V + F + + + R + T + + + + + + gamma_Nao + Nao + + + + + + + 1.0 + V + F + + + R + T + + + + 1.0 + + + + + + + + + + + The maximum potassium component of the total L-type channel current. + + + + + + + I_CaK + + P_K + + 1.0 + 2.0 + + + + V + + F + 2.0 + + + + R + T + + + + + + gamma_Ki + Ki + + + + 1.0 + V + F + + + R + T + + + + + + gamma_Ko + Ko + + + + + + + 1.0 + V + F + + + R + T + + + + 1.0 + + + + + + + + + + + The total current of the L-type channel current. + + + + + + + i_Ca_L + + i_CaCa + i_CaK + i_CaNa + + + + + + + + + + + The voltage-dependent activation gate for the L-type calcium + channel - the d gate. + + + + + + + + + + + + + + + + + + + + The opening rate of the d gate. + + + + + + + alpha_d + + d_infinity + tau_d + + + + + + + d_infinity + + 1.0 + + 1.0 + + + + + V + 10.0 + + 6.24 + + + + + + + + + + + tau_d + + d_infinity + + + 1.0 + + + + + V + 10.0 + + 6.24 + + + + + + 0.035 + + V + 10.0 + + + + + + + + + + + + The closing rate of the d gate. + + + + + + + beta_d + + + 1.0 + d_infinity + + tau_d + + + + + + + + + The kinetics of the d gate. + + + + + + + + time + d + + + + alpha_d + + 1.0 + d + + + + beta_d + d + + + + + + + + + + + + The voltage-dependent inactivation gate for the L-type calcium + channel - the f gate. + + + + + + + + + + + + + + + + + + + + The opening rate of the f gate. + + + + + + + alpha_f + + f_infinity + tau_f + + + + + + + f_infinity + + + 1.0 + + 1.0 + + + + V + 35.06 + + 8.6 + + + + + + 0.6 + + 1.0 + + + + 50.0 + V + + 20.0 + + + + + + + + + + + tau_f + + 1.0 + + + 0.0197 + + + + + 0.0337 + + V + 10.0 + + + 2.0 + + + + + 0.02 + + + + + + + + + + The closing rate of the f gate. + + + + + + + beta_f + + + 1.0 + f_infinity + + tau_f + + + + + + + + + The kinetics of the f gate. + + + + + + + + time + f + + + + alpha_f + + 1.0 + f + + + + beta_f + f + + + + + + + + + + + + The calcium-dependent inactivation gate for the L-type calcium + channel - the fCa gate. + + + + + + + + + + + + + + + + + + The kinetics of the fCa gate. + + + + + + + f_Ca + + 1.0 + + 1.0 + + + Cai + Km_Ca + + 2.0 + + + + + + + + + + + + + The time-dependent potassium reploarisation current. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The conductance for the channel. + + + + + + + g_K + + g_K_max + + + Ko + 5.4 + + + + + + + + + + + The reversal potential of the channel. + + + + + + + E_K + + + + R + T + + F + + + + + Ko + + PR_NaK + Nao + + + + Ki + + PR_NaK + Nai + + + + + + + + + + + + + Calculation of the current. + + + + + + + i_K + + g_K + + X + 2.0 + + Xi + + V + E_K + + + + + + + + + + + + The time-dependent activation gate for the time-dependent potassium + current - the X gate. + + + + + + + + + + + + + + + + + + The opening rate for the X gate. + + + + + + + alpha_X + + + 0.0000719 + + V + 30.0 + + + + 1.0 + + + -0.148 + + V + 30.0 + + + + + + + + + + + + + The closing rate for the X gate. + + + + + + + beta_X + + + 0.000131 + + V + 30.0 + + + + -1.0 + + + 0.0687 + + V + 30.0 + + + + + + + + + + + + + The kinetics of the X gate. + + + + + + + + time + X + + + + alpha_X + + 1.0 + X + + + + beta_X + X + + + + + + + + + + + + The time-independent inactivation gate for the time-dependent + potassium current - the Xi gate. + + + + + + + + + + + + + + + The kinetics of the Xi gate. + + + + + + + Xi + + 1.0 + + 1.0 + + + + V + 56.26 + + 32.1 + + + + + + + + + + + + + + The time-independent potassium repolarisation current. + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the channel conductance. + + + + + + + g_K1 + + g_K1_max + + + Ko + 5.4 + + + + + + + + + + + Calculation of the channel reversal potential. + + + + + + + E_K1 + + + + R + T + + F + + + + Ko + Ki + + + + + + + + + + + Calculation of the channel current. + + + + + + + i_K1 + + g_K1 + K1_infinity + + V + E_K1 + + + + + + + + + + + + The gating variable for the time-independent potassium current - the + K1 gate. + + + + + + + + + + + + + + + + + + The opening rate for the K1 gate. + + + + + + + alpha_K1 + + 1.02 + + 1.0 + + + 0.2385 + + + V + E_K1 + + 59.215 + + + + + + + + + + + + + The closing rate for the K1 gate. + + + + + + + beta_K1 + + + + 0.49124 + + + 0.08032 + + + V + 5.476 + + E_K1 + + + + + + + 0.06175 + + V + + E_K1 + 594.31 + + + + + + + 1.0 + + + -0.5143 + + + V + E_K1 + + 4.753 + + + + + + + + + + + + + The steady-state kinetics of the K1 gate. + + + + + + + K1_infinity + + alpha_K1 + + alpha_K1 + beta_K1 + + + + + + + + + + + + The potassium current active at plateau potentials. + + + + + + + + + + + + + + + + + + + + The reversal potential for the channel. + + + + + + + E_Kp + E_K1 + + + + + + + + The gating kinetics for the channel. + + + + + + + Kp + + 1.0 + + 1.0 + + + + 7.488 + V + + 5.98 + + + + + + + + + + + + Calculation of the current. + + + + + + + i_Kp + + g_Kp + Kp + + V + E_Kp + + + + + + + + + + + + A calcium pump for removal of calcium from the cytosol to the + extracellular space. + + + + + + + + + + + + + + + + + + The calcium pump current. + + + + + + + i_p_Ca + + I_pCa + + Cai + + K_mpCa + Cai + + + + + + + + + + + + + The background sodium current. + + + + + + + + + + + + + + + + + + + The reversal potential for the channel. + + + + + + + E_NaN + E_Na + + + + + + + + Calculation of the current. + + + + + + + i_Na_b + + g_Nab + + V + E_NaN + + + + + + + + + + + + The background calcium current. + + + + + + + + + + + + + + + + + + + + + + + The reversal potential for the channel. + + + + + + + E_CaN + + + + R + T + + + 2.0 + F + + + + + Cao + Cai + + + + + + + + + + + Calculation of the current. + + + + + + + i_Ca_b + + g_Cab + + V + E_CaN + + + + + + + + + + + + The sodium/potassium exchanger current which extrudes three sodium + ions from the cell in exchange for two potassium ions entering the + cell. + + + + + + + + + + + + + + + + + + + + + + + + + f_NaK + + 1.0 + + + 1.0 + + 0.1245 + + + -0.1 + + + V + F + + + R + T + + + + + + + + 0.0365 + sigma + + + + + V + F + + + R + T + + + + + + + + + + + + + sigma + + + 1.0 + 7.0 + + + + + Nao + 67.3 + + + 1.0 + + + + + + + + + + Calculation of the exchanger current. + + + + + + + i_NaK + + I_NaK + f_NaK + + 1.0 + + 1.0 + + + K_mNai + Nai + + 1.5 + + + + + Ko + + Ko + K_mKo + + + + + + + + + + + + + A non-specific calcium activated channel - assumed impermeable to + calcium ions but permeable to sodium and potassium ions. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The channel reversal potential. + + + + + + + EnsCa + + + + R + T + + F + + + + + Ko + Nao + + + Ki + Nai + + + + + + + + + + Vns + + V + EnsCa + + + + + + + + + The sodium component of the channel's current. + + + + + + + i_ns_Na + + I_ns_Na + + 1.0 + + 1.0 + + + K_m_ns_Ca + Cai + + 3.0 + + + + + + + + + + + + The potassium component of the channel's current. + + + + + + + i_ns_K + + I_ns_K + + 1.0 + + 1.0 + + + K_m_ns_Ca + Cai + + 3.0 + + + + + + + + + + + + The total current through the channel. + + + + + + + i_ns_Ca + + i_ns_Na + i_ns_K + + + + + + + + + The maximum sodium component of the channel's current. + + + + + + + I_ns_Na + + P_ns_Ca + + 1.0 + 2.0 + + + + Vns + + F + 2.0 + + + + R + T + + + + + + gamma_Nai + Nai + + + + 1.0 + Vns + F + + + R + T + + + + + + gamma_Nao + Nao + + + + + + + 1.0 + Vns + F + + + R + T + + + + 1.0 + + + + + + + + + + + The maximum potassium component of the channel's current. + + + + + + + I_ns_K + + P_ns_Ca + + 1.0 + 2.0 + + + + Vns + + F + 2.0 + + + + R + T + + + + + + gamma_Ki + Ki + + + + 1.0 + Vns + F + + + R + T + + + + + + gamma_Ko + Ko + + + + + + + 1.0 + Vns + F + + + R + T + + + + 1.0 + + + + + + + + + + + + + The sodium-calcium exchanger current, exchanges three sodium ions + for one calcium ion. + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the exchanger current. + + + + + + + i_NaCa + + K_NaCa + + 1.0 + + + K_mNa + 3.0 + + + Nao + 3.0 + + + + + 1.0 + + K_mCa + Cao + + + + 1.0 + + 1.0 + + K_sat + + + + eta + 1.0 + + V + + F + + R + T + + + + + + + + + + + + eta + V + + F + + R + T + + + + + + Nai + 3.0 + + Cao + + + + + + eta + 1.0 + + V + + F + + R + T + + + + + + Nao + 3.0 + + Cai + + + + + + + + + + + + + The various calcium fluxes into and from the sarcoplasmic reticulum. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The release flux from the junctional sarcoplasmic reticulum into the + cytosol. + + + + + + + i_rel + + G_rel + + Ca_JSR + Cai + + + + + + + + + + Calculation of the release channel conductance. This is incorrect as + there is no CICR induced via the accumulation of calcium in the + cytosol in the period following max(dV/dt) + + + + + + + G_rel + + G_rel_peak + + + delta_Ca_i2 + delta_Ca_ith + + + + K_mrel + delta_Ca_i2 + + delta_Ca_ith + + + + 1.0 + + + + t_CICR + tau_on + + + + + + + + t_CICR + tau_off + + + + + + + + + + G_rel_peak + + + 0.0 + + delta_Ca_i2 + delta_Ca_ith + + + + G_rel_max + + + + + + + + + + The uptake flux into the sarcoplasmic reticulum from the cytosol. + + + + + + + i_up + + I_up + + Cai + + Cai + K_mup + + + + + + + + + + + Calcium leak flux from the network sarcoplasmic reticulum into the + cytosol. + + + + + + + i_leak + + K_leak + Ca_NSR + + + + + + + K_leak + + I_up + Ca_NSR_max + + + + + + + + + Translocation flux from the network to the junctional sarcoplasmic + reticulum. + + + + + + + i_tr + + + Ca_NSR + Ca_JSR + + tau_tr + + + + + + + + + + + Component grouping together the differential equations for the + various ionic concentrations that the model tracks. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The change in intracellular sodium concentration. + + + + + + + + time + Nai + + + + + i_Na + i_CaNa + i_Na_b + i_ns_Na + + i_NaCa + 3.0 + + + i_NaK + 3.0 + + + + + Am + + V_myo + F + + + + + + + + + + + The change in intracellular calcium concentration. + + + + + + + + time + Cai + + + + + + + i_CaCa + i_p_Ca + i_Ca_b + + i_NaCa + + + + Am + + 2.0 + V_myo + F + + + + + i_rel + + V_JSR + V_myo + + + + + i_leak + i_up + + + V_NSR + V_myo + + + + + + + + + + + The change in intracellular potassium concentration. + + + + + + + + time + Ki + + + + + i_CaK + i_K + i_K1 + i_Kp + i_ns_K + + + i_NaK + 2.0 + + + + + + Am + + V_myo + F + + + + + + + + + + + The change in calcium concentration in the junctional sarcoplasmic + reticulum. + + + + + + + + time + Ca_JSR + + + + i_rel + + i_tr + + V_NSR + V_JSR + + + + + + + + + + + + The change in calcium concentration in the network sarcoplasmic + reticulum. + + + + + + + + time + Ca_NSR + + + + + i_leak + i_tr + + i_up + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Bioelectrics/input/jrw-1998.xml b/Bioelectrics/input/jrw-1998.xml new file mode 100644 index 00000000..2227e96f --- /dev/null +++ b/Bioelectrics/input/jrw-1998.xml @@ -0,0 +1,5333 @@ + + + + + + + + + + + + + Lloyd + Catherine + May + + + c.lloyd@auckland.ac.nz + + + + The University of Auckland + The Bioengineering Research Group + + + + + + 2001-09-24 + + + + + + Corrected equations. + + + + Lloyd + Catherine + May + + + + 2003-07-30 + + + + + Corrected equations: alpha_j_calculation and beta_j_calculation in + fast_sodium_current_j_gate, alpha_X_calculation and beta_X_calculation in time_dependent_potassium_current_X_gate, and f_NaK_calculation and + i_NaK_calculation in Ca_release_current_from_JSR. + + + + Lloyd + Catherine + May + + + + 2003-06-04 + + + + + Added some initial values from Penny Noble's documentation. + + + + Lloyd + Catherine + May + + + + 2002-05-06 + + + + + Corrected several equations, variable units and their initial values. + + + + Lloyd + Catherine + May + + + + 2002-02-28 + + + + + Corrected several equations. + + + + Lloyd + Catherine + May + + + + 2002-02-25 + + + + + Altered some of the connections. + + + + Lloyd + Catherine + May + + + + 2002-01-04 + + + + + Changed tau_y_calculation after checking mathml using the validator. + + + + Lloyd + Catherine + May + + + + 2001-12-07 + + + + + Removed document type definition as this is declared as optional + according to the W3C recommendation. + + + + Lloyd + Catherine + May + + + + 2001-10-19 + + + + + + + The University of Auckland, Bioengineering Research Group + + + + + + + + The Jafri-Rice-Winslow Model for Calcium Regulation in the Ventricular + Myocyte, 1997 + + + + + + This is the CellML description of Jafri, Rice and Winslow's + mathematical model for calcium regulation in the ventricular myocyte. + It is based on an accurate model of the membrane currents and adds a + more sophisticated model of calcium handling. The JRW model is based + on the LR-II model for ventricular action potentials, with several + modifications. + + + + Catherine Lloyd + + + + + Mammalia + + Ventricular Myocyte + + + + 9512016 + + + + + + + Jafri + M + Saleet + + + + + + + Rice + John + Jeremy + + + + + + + Winslow + Raimond + L + + + + + + + Cardiac Ca2+ Dynamics: The Roles of Ryanodine Receptor Adaptation + and Sarcoplasmic Reticulum Load + + + 1998-03 + + + Biophysical Journal + + 74 + 1149 + 1168 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The main component of the model which defines the action potential. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The kinetics of the transmembrane potential, defined as the sum of + all the sarcolemmal currents and an applied stimulus current. + + + + + + + + time + V + + + + I_stim + + i_Na + i_Ca_L_Ca + i_Ca_L_K + i_K + i_NaCa + i_K1 + i_Kp + i_p_Ca + i_Na_b + i_Ca_b + i_NaK + i_ns_Ca + + + Cm + + + + + + + + This is a dummy equation that we simply use to make grabbing the + value in CMISS much easier. + + + + + + + + IStimC + I_stim + + + + + + + + + + The fast sodium current component contains the differential + equations governing the influx of sodium ions through the cell + surface membrane into the cell. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the fast sodium current using the three + Hodkin-Huxley type voltage-dependent gating variables m, h, and j. + + + + + + + i_Na + + g_Na + + m + 3.0 + + h + j + + V + E_Na + + + + + + + + + + The sodium reversal potential. + + + + + + + E_Na + + + + R + T + + F + + + + Nao + Nai + + + + + + + + + + + + + + The voltage-dependent activation gate for the fast sodium current - + the m gate. + + + + + + + + + + + + + + + + + + + + + The opening rate of the m gate. + + + + + + + alpha_m + + + 0.32 + + V + 47.13 + + + + 1.0 + + + -0.1 + + V + 47.13 + + + + + + + + + + + + + The closing rate of the m gate. + + + + + + + beta_m + + 0.08 + + + + V + + 11.0 + + + + + + + + + + + The kinetics of the m gate. + + + + + + + + time + m + + + + alpha_m + + 1.0 + m + + + + beta_m + m + + + + + + + + + + + + + The voltage-dependent inactivation gate for the fast sodium current + - the h gate. + + + + + + + + + + + + + + + + + + + + + The opening rate of the h gate. + + + + + + + alpha_h + + + + 0.135 + + + + 80.0 + V + + -6.8 + + + + + V + -40.0 + + + + 0.0 + + + + + + + + + + The closing rate of the h gate. + + + + + + + beta_h + + + + + 3.56 + + + 0.079 + V + + + + + 310000.0 + + + 0.35 + V + + + + + + V + -40.0 + + + + + 1.0 + + 0.13 + + 1.0 + + + + V + 10.66 + + -11.1 + + + + + + + + + + + + + + + The kinetics of the h gate. + + + + + + + + time + h + + + + alpha_h + + 1.0 + h + + + + beta_h + h + + + + + + + + + + + + + The voltage-dependent slow inactivation gate for the fast sodium + current - the j gate. + + + + + + + + + + + + + + + + + + + + + The opening rate of the j gate. + + + + + + + alpha_j + + + + + + -127140.0 + + + 0.2444 + V + + + + + 0.00003474 + + + -0.04391 + V + + + + + + + V + 37.78 + + + 1.0 + + + 0.311 + + V + 79.23 + + + + + + + + V + -40.0 + + + + 0.0 + + + + + + + + + + The closing rate of the j gate. + + + + + + + beta_j + + + + 0.1212 + + + + -0.01052 + V + + + + 1.0 + + + -0.1378 + + V + 40.14 + + + + + + + + V + -40.0 + + + + + 0.3 + + + + -0.0000002535 + V + + + + 1.0 + + + -0.1 + + V + 32.0 + + + + + + + + + + + + + + + + The kinetics of the j gate. + + + + + + + + time + j + + + + alpha_j + + 1.0 + j + + + + beta_j + j + + + + + + + + + + + + + The JWR model creates a new mathematical model to describe the + L-type calcium channel that is based on the experimentally observed + mode-switching behaviour of the channel. Inactivation occurs as + calcium ion binding induces the channel to switch (from mode normal) + to a mode in which transitions to open states are extremely slow + (mode Ca). The channel has one voltage inactivation gate, y. As well + as Ca, the channel is assumed permeable to K ions also. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the calcium current component of the total channel + current, given as the maximal current multiplied by the + voltage-dependent inactivation gate and the open probability of the + channel based on the mode-switching model. + + + + + + + i_Ca_L_Ca + + i_Ca_L_Ca_max + y + + O + O_Ca + + + + + + + + + + Calculation of the potassium current component of the total channel + current. + + + + + + + i_Ca_L_K + + p_k + y + + O + O_Ca + + + + V + + F + 2.0 + + + + R + T + + + + + + Ki + + + + V + F + + + R + T + + + + + Ko + + + + + + V + F + + + R + T + + + + 1.0 + + + + + + + + + + + The potassium permeability of the channel, which depends on the + calcium current component. + + + + + + + p_k + + P_K + + 1.0 + + i_Ca_L_Ca_max + i_Ca_L_Ca_half + + + + + + + + + + + The maximal calcium current through the channel. + + + + + + + i_Ca_L_Ca_max + + P_Ca + 4.0 + + + V + + F + 2.0 + + + + R + T + + + + + + 0.001 + + + 2.0 + V + + F + + R + T + + + + + + + 0.341 + Cao + + + + + + 2.0 + V + + F + + R + T + + + + + 1.0 + + + + + + + + + + + Rate constants for state changes in mode normal. + + + + + + + alpha + + 0.4 + + + + V + 12.0 + + 10.0 + + + + + + + + beta + + 0.05 + + + + V + 12.0 + + -13.0 + + + + + + + + + + + Rate constants for state changes in mode Ca (corresponding to + alpha-prime and beta-prime in the JRW paper). + + + + + + + alpha_a + + alpha + a + + + + + + beta_b + + beta + b + + + + + + + + + Rate constant for switching between mode normal and mode Ca. + + + + + + + gamma + + 0.1875 + Ca_SS + + + + + + + + + The kinetics of the state transitions in mode normal. + In the normal mode, the calcium channel is able to make the + transition to the open, conducting state (O) from the closed state + (C) at a normal rate. + + + + + + + + time + C0 + + + + + beta + C1 + + + omega + C_Ca0 + + + + + + 4.0 + alpha + + gamma + + C0 + + + + + + + + time + C1 + + + + + 4.0 + alpha + C0 + + + 2.0 + beta + C2 + + + + omega + b + + C_Ca1 + + + + + beta + + 3.0 + alpha + + + gamma + a + + + C1 + + + + + + + + time + C2 + + + + + 3.0 + alpha + C1 + + + 3.0 + beta + C3 + + + + omega + + b + 2.0 + + + C_Ca2 + + + + + + beta + 2.0 + + + 2.0 + alpha + + + gamma + + a + 2.0 + + + + C2 + + + + + + + + time + C3 + + + + + 2.0 + alpha + C2 + + + 4.0 + beta + C4 + + + + omega + + b + 3.0 + + + C_Ca3 + + + + + + beta + 3.0 + + alpha + + gamma + + a + 3.0 + + + + C3 + + + + + + + + time + C4 + + + + + alpha + C3 + + + g + O + + + + omega + + b + 4.0 + + + C_Ca4 + + + + + + beta + 4.0 + + f + + gamma + + a + 4.0 + + + + C4 + + + + + + + + time + O + + + + f + C4 + + + g + O + + + + + + + + + + The kinetics of the state transitions in mode Ca. + Calcium binding to the Ca channel induces a conformational change + from normal mode to mode Ca. This effectively inhibits the + conduction of calcium ions because in mode Ca, the calcium channel + makes the transition to the open, conducting state (O) extremely + slowly. + + + + + + + + time + C_Ca0 + + + + + beta_b + C_Ca1 + + + gamma + C_Ca0 + + + + + + 4.0 + alpha_a + + omega + + C_Ca0 + + + + + + + + time + C_Ca1 + + + + + 4.0 + alpha_a + C_Ca0 + + + 2.0 + beta_b + C_Ca2 + + + gamma + a + C1 + + + + + beta_b + + 3.0 + alpha_a + + + omega + b + + + C_Ca1 + + + + + + + + time + C_Ca2 + + + + + 3.0 + alpha_a + C_Ca1 + + + 3.0 + beta_b + C_Ca3 + + + gamma + + a + 2.0 + + C2 + + + + + + beta_b + 2.0 + + + 2.0 + alpha_a + + + omega + + b + 2.0 + + + + C_Ca2 + + + + + + + + time + C_Ca3 + + + + + 2.0 + alpha_a + C_Ca2 + + + 4.0 + beta_b + C_Ca4 + + + gamma + + a + 3.0 + + C3 + + + + + + beta_b + 3.0 + + alpha_a + + omega + + b + 3.0 + + + + C_Ca3 + + + + + + + + time + C_Ca4 + + + + + alpha_a + C_Ca3 + + + g_ + O_Ca + + + gamma + + a + 4.0 + + C4 + + + + + + beta_b + 4.0 + + f_ + + omega + + b + 4.0 + + + + C_Ca4 + + + + + + + + time + O_Ca + + + + f_ + C_Ca4 + + + g_ + O_Ca + + + + + + + + + + + + + The voltage-dependent inactivation gate for the L-type calcium + channel - the y gate. + + + + + + + + + + + + + + + + + + + + + The kinetics of the y gate. + + + + + + + + time + y + + + + y_infinity + y + + tau_y + + + + + + y_infinity + + + 1.0 + + 1.0 + + + + V + 55.0 + + 7.5 + + + + + + 0.1 + + 1.0 + + + + + V + + 21.0 + + 6.0 + + + + + + + + + + tau_y + + 20.0 + + 600.0 + + 1.0 + + + + V + 30.0 + + 9.5 + + + + + + + + + + + + + + + + The time-dependent potassium current has an X^2 dependence on it's + activation gate, and an Xi inactivation gate. This channel is also + assumed permeable to sodium ions. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the maximal channel conductance, dependent on + extracellular potassium concentration. + + + + + + + g_K + + g_K_max + + + Ko + 5.4 + + + + + + + + + + + The reversal potential of the channel. + + + + + + + E_K + + + + R + T + + F + + + + + Ko + + P_NaK + Nao + + + + Ki + + P_NaK + Nai + + + + + + + + + + + + + Calculation of the time-dependent potassium current. + + + + + + + i_K + + g_K + Xi + + X + 2.0 + + + V + E_K + + + + + + + + + + + + + The voltage- and time-dependent activation gate for the + time-dependent potassium current - the X gate. + + + + + + + + + + + + + + + + + + + + + The opening rate of the X gate. + + + + + + + alpha_X + + 0.0000719 + + + V + 30.0 + + + 1.0 + + + -0.148 + + V + 30.0 + + + + + + + + + + + + + + The closing rate of the X gate. + + + + + + + beta_X + + 0.000131 + + + V + 30.0 + + + -1.0 + + + 0.0687 + + V + 30.0 + + + + + + + + + + + + + + The kinetics of the X gate. + + + + + + + + time + X + + + + alpha_X + + 1.0 + X + + + + beta_X + X + + + + + + + + + + + + + The time-independent inactivation gate for the time-dependent + potassium channel. + + + + + + + + + + + + + + + + + Xi is the inward rectification parameter and is given by the + following equation. + + + + + + + Xi + + 1.0 + + 1.0 + + + + V + 56.26 + + 32.1 + + + + + + + + + + + + + + + + The time-independent potassium current. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the maximal channel conductance, dependent on + extracellular potassium concentration. + + + + + + + g_K1 + + g_K1_max + + + Ko + 5.4 + + + + + + + + + + + The following equation calculates the reversal potential of the + time-independent potassium current. + + + + + + + E_K1 + + + + R + T + + F + + + + Ko + Ki + + + + + + + + + + + Calculate the current. + + + + + + + i_K1 + + g_K1 + K1_infinity + + V + E_K1 + + + + + + + + + + + + + + The time constants for the K1 gate are small enough that the gating + variable can be approximated with it's steady-state value. + + + + + + + + + + + + + + + + + + + + + The opening rate of the K1 gate. + + + + + + + alpha_K1 + + 1.02 + + 1.0 + + + 0.2385 + + + V + E_K1 + + 59.215 + + + + + + + + + + + + + The closing rate of the K1 gate. + + + + + + + beta_K1 + + + + 0.49124 + + + 0.08032 + + + V + 5.476 + + E_K1 + + + + + + + 0.06175 + + V + + E_K1 + 594.31 + + + + + + + 1.0 + + + -0.5143 + + + V + E_K1 + + 4.753 + + + + + + + + + + + + + The steady-state approximation for the K1 gating kinetics. + + + + + + + K1_infinity + + alpha_K1 + + alpha_K1 + beta_K1 + + + + + + + + + + + + + + The plateau potassium current component contains the equations which + describe the contribution of a time independent [K]o-insensitive + channel at plateau potentials. + + + + + + + + + + + + + + + + + + + + + + + The channel's reversal potential. + + + + + + + E_Kp + E_K1 + + + + + + + + The activation variable. + + + + + + + Kp + + 1.0 + + 1.0 + + + + 7.488 + V + + 5.98 + + + + + + + + + + + + Calculation of the plateau potassium current. + + + + + + + i_Kp + + g_Kp + Kp + + V + E_Kp + + + + + + + + + + + + + + The Na/Ca exchanger component describes how a protein molecule in + the cell surface membrane transports Na ions into the cytosol and + exports Ca ions into the extracellular volume, in a ratio of 3:1 + respectively. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the Na/Ca exchanger current. + + + + + + + i_NaCa + + k_NaCa + + 1.0 + + + K_mNa + 3.0 + + + Nao + 3.0 + + + + + 1.0 + + K_mCa + Cao + + + + 1.0 + + 1.0 + + k_sat + + + + eta + 1.0 + + V + + F + + R + T + + + + + + + + + + + + eta + V + + F + + R + T + + + + + + Nai + 3.0 + + Cao + + + + + + eta + 1.0 + + V + + F + + R + T + + + + + + Nao + 3.0 + + Cai + + + + + + + + + + + + + + + The sarcolemmal calcium pump is an additional mechanism for removing + Ca ions from the myoplasm to help maintain a low intracellular + calcium concentration when at rest. + + + + + + + + + + + + + + + + + + + + + The calcium pump current. + + + + + + + i_p_Ca + + I_pCa + + Cai + + K_mpCa + Cai + + + + + + + + + + + + + + The sodium background current is a time-independent diffusion of + Na ions down their electrochemical gradient, through the cell + surface membrane into the cytosol. + + + + + + + + + + + + + + + + + + + + + + The reversal potential for the background sodium channel. + + + + + + + E_NaN + E_Na + + + + + + + + Calculation of the background sodium current. + + + + + + + i_Na_b + + g_Nab + + V + E_NaN + + + + + + + + + + + + + The calcium background current describes a time-independent + diffusion of Ca ions down their electrochemical gradient through the + cell surface membrane into the cytosol. However, calcium is not + allowed to accumulate to high intracellular concentrations. This + influx is balanced by the Ca ion extrusion through the Na-Ca + exchanger and the sarcolemmal Ca pump. + + + + + + + + + + + + + + + + + + + + + + + + + + The reversal potential for the background calcium current. + + + + + + + E_CaN + + + + R + T + + + 2.0 + F + + + + + Cao + Cai + + + + + + + + + + + Calculation of the background calcium current. + + + + + + + i_Ca_b + + g_Cab + + V + E_CaN + + + + + + + + + + + + + The sodium potassium pump is an active protein in the cell membrane + which couples the free energy released by the hydrolysis of ATP to + the movement of Na and K ions against their electrochemical + gradients through the cell membrane. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the Na/K pump current. + + + + + + + f_NaK + + 1.0 + + + 1.0 + + 0.1245 + + + + -0.1 + V + F + + + R + T + + + + + + + 0.0365 + sigma + + + + + V + + F + + + R + T + + + + + + + + + + + sigma + + + 1.0 + 7.0 + + + + + Nao + 67.3 + + + 1.0 + + + + + + + i_NaK + + I_NaK + f_NaK + + 1.0 + + 1.0 + + + K_mNai + Nai + + 1.5 + + + + + Ko + + Ko + K_mKo + + + + + + + + + \ + + + + + The nonspecific calcium activated current describes a channel which + is activated by calcium ions, but is permeable to only sodium and + potassium ions. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The reversal potential of the channel. + + + + + + + EnsCa + + + + R + T + + F + + + + + Ko + Nao + + + Ki + Nai + + + + + + + + + + + + The potential offset for the channel. + + + + + + + VnsCa + + V + EnsCa + + + + + + + + + The sodium component of the channel's current. + + + + + + + i_ns_Na + + I_ns_Na + + 1.0 + + 1.0 + + + K_m_ns_Ca + Cai + + 3.0 + + + + + + + + + + + + The potassium component of the channel's current. + + + + + + + i_ns_K + + I_ns_K + + 1.0 + + 1.0 + + + K_m_ns_Ca + Cai + + 3.0 + + + + + + + + + + + + The total nonspecific calcium activated current. + + + + + + + i_ns_Ca + + i_ns_Na + i_ns_K + + + + + + + + + The maximal sodium component current. + + + + + + + I_ns_Na + + P_ns_Ca + + 1.0 + 2.0 + + + + VnsCa + + F + 2.0 + + + + R + T + + + + + + 0.75 + Nai + + + + VnsCa + F + + + R + T + + + + + + 0.75 + Nao + + + + + + + VnsCa + F + + + R + T + + + + 1.0 + + + + + + + + + + + The maximal potassium component current. + + + + + + + I_ns_K + + P_ns_Ca + + 1.0 + 2.0 + + + + VnsCa + + F + 2.0 + + + + R + T + + + + + + 0.75 + Ki + + + + VnsCa + F + + + R + T + + + + + + 0.75 + Ko + + + + + + + VnsCa + F + + + R + T + + + + 1.0 + + + + + + + + + + + + + + + In the JRW model, subcellular calcium regulatory mechanisms are + described in detail. There are six calcium fluxes to consider; + J_rel, J_leak, J_up, J_tr, J_xfer and J_trpn. In addition, three + membrane current fluxes are also necessary for the formulation of + calcium regulation; i_p_Ca, i_Ca_L_Ca and i_NaCa. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculate some volume fractions as proportions of the total + myoplasmic volume. + + + + + + + V_SS + + 5.828e-5 + V_myo + + + + + + V_NSR + + 0.081 + V_myo + + + + + + V_JSR + + 0.00464 + V_myo + + + + + + + + + The calcium release flux from the JSR into the restricted subspace + is governed by the fraction of RyR channels in an open state. + + + + + + + J_rel + + v1 + RyR_open + + Ca_JSR + Ca_SS + + + + + + + + + + The "open" RyR's are those P_O1 and P_O2 states. + + + + + + + RyR_open + + P_O1 + P_O2 + + + + + + + + + The kinetic equations governing the transitions between the four + states used to model the RyR's. + + + + + + + + time + P_C1 + + + + + k_a_plus + + + Ca_SS + nCa + + P_C1 + + + k_a_minus + P_O1 + + + + + + + + time + P_O1 + + + + + k_a_plus + + Ca_SS + nCa + + P_C1 + + + + k_a_minus + P_O1 + + + k_b_plus + + Ca_SS + mCa + + P_O1 + + + k_c_plus + P_O1 + + + + + k_b_minus + P_O2 + + + k_c_minus + P_C2 + + + + + + + + time + P_O2 + + + + k_b_plus + + Ca_SS + mCa + + P_O1 + + + k_b_minus + P_O2 + + + + + + + + time + P_C2 + + + + k_c_plus + P_O1 + + + k_c_minus + P_C2 + + + + + + + + + + Calculate the leakage flux from the NSR into the myoplasm. + + + + + + + J_leak + + v2 + + Ca_NSR + Cai + + + + + + + + + + Calculate the uptake flux into the NSR from the myoplasm. + + + + + + + J_up + + v3 + + + Cai + 2.0 + + + + K_mup + 2.0 + + + Cai + 2.0 + + + + + + + + + + + + Calculate the translocation flux between the uptake (NSR) and + release (JSR) stores. + + + + + + + J_tr + + + Ca_NSR + Ca_JSR + + tau_tr + + + + + + + + + Calculate the calcium flux from the diffusion of calcium out of the + restricted subspace into the myoplasm. + + + + + + + J_xfer + + + Ca_SS + Cai + + tau_xfer + + + + + + + + + The kinetics of calcium binding to the myoplasm buffer troponin - + both high and low affinity binding sites. + + + + + + + J_htrpn + + + k_htrpn_plus + Cai + + HTRPN_tot + HTRPNCa + + + + k_htrpn_minus + HTRPNCa + + + + + + + J_ltrpn + + + k_ltrpn_plus + Cai + + LTRPN_tot + LTRPNCa + + + + k_ltrpn_minus + LTRPNCa + + + + + + + J_trpn + + J_htrpn + J_ltrpn + + + + + + + + + Keep track of the concentration of calcium ions bound to high and + low affinity troponin binding sites. + + + + + + + + time + HTRPNCa + + J_htrpn + + + + + + time + LTRPNCa + + J_ltrpn + + + + + + + + Calcium is buffered by calmodulin (CMDN) in the subspace and + myoplasm, and by calsequestrin (CSQN) in the JSR. These are fast + buffers and their effect is modelled using the rapid buffering + approximation. + + + + + + + Bi + + 1.0 + + 1.0 + + + CMDN_tot + K_mCMDN + + + + K_mCMDN + Cai + + 2.0 + + + + + + + + + B_SS + + 1.0 + + 1.0 + + + CMDN_tot + K_mCMDN + + + + K_mCMDN + Ca_SS + + 2.0 + + + + + + + + + B_JSR + + 1.0 + + 1.0 + + + CSQN_tot + K_mCSQN + + + + K_mCSQN + Ca_JSR + + 2.0 + + + + + + + + + + + + The kinetics of the calcium ion concentration changes in the various + compartments of the model. + + + + + + + + time + Cai + + + Bi + + + J_leak + J_xfer + + + J_up + J_trpn + + + + i_Ca_b + + 2.0 + i_NaCa + + + i_p_Ca + + + Am + + 2.0 + V_myo + F + + + + + + + + + + + + time + Ca_SS + + + B_SS + + + + J_rel + + V_JSR + V_SS + + + + J_xfer + + V_myo + V_SS + + + + + i_Ca_L_Ca + + Am + + 2.0 + V_SS + F + + + + + + + + + + + time + Ca_JSR + + + B_JSR + + J_tr + J_rel + + + + + + + + time + Ca_NSR + + + + + J_up + J_leak + + + V_myo + V_NSR + + + + J_tr + + V_JSR + V_NSR + + + + + + + + + + + + + + The descriptions of the rate of change of [Na]i and [K]i are the + same as the LR-II model. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The rate of change of intracellular sodium ion concentration. + + + + + + + + time + Nai + + + + + i_Na + i_Na_b + i_ns_Na + + i_NaCa + 3.0 + + + i_NaK + 3.0 + + + + + Am + + V_myo + F + + + + + + + + + + + The rate of change of intracellular potassium ion concentration. + + + + + + + + time + Ki + + + + + i_Ca_L_K + i_K + i_K1 + i_Kp + i_ns_K + + + i_NaK + 2.0 + + + + + + Am + + V_myo + F + + + + + + + + + + + The rate of change of extracellular potassium ion concentration. + + + + + + + + time + Ko + + + + i_Ca_L_K + i_K + i_K1 + i_Kp + i_ns_K + + + i_NaK + 2.0 + + + + + Am + + V_myo + F + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Bioelectrics/input/lindblad_murphey_clark_giles_1996.xml b/Bioelectrics/input/lindblad_murphey_clark_giles_1996.xml new file mode 100644 index 00000000..36ea698b --- /dev/null +++ b/Bioelectrics/input/lindblad_murphey_clark_giles_1996.xml @@ -0,0 +1,3779 @@ + + + + + +
+ +
+ Model Status + + This model runs in OpenCell and COR and reproduce the published results. The units have been checked and they are consistent. + +
+ +Model Structure + + +ABSTRACT: We have developed a mathematical model of the rabbit atrial myocyte and have used it in an examination of the ionic basis of the atrial action potential. Available biophysical data have been incorporated into the model to quantify the specific ultrastructural morphology, intracellular ion buffering, and time- and voltage-dependent currents and transport mechanisms of the rabbit atrial cell. When possible, mathematical expressions describing ionic currents identified in rabbit atrium are based on whole cell voltage-clamp data from enzymatically isolated rabbit atrial myocytes. This membrane model is coupled to equations describing Na+, K+, and Ca2+ homeostasis, including the uptake and release of Ca2+ by the sarcoplasmic reticulum and Ca2+ buffering. The resulting formulation can accurately simulate the whole cell voltage-clamp data on which it is based and provides fits to a family of rabbit atrial cell action potentials obtained at 35 degrees C over a range of stimulus rates (0.2-3.0 Hz). The model is utilized to provide a qualitative prediction of the intracellular Ca2+ concentration transient during the action potential and to illustrate the interactions between membrane currents that underlie repolarization in the rabbit atrial myocyte. + + + + + + + schematic diagram of Linblad et al 1996 model + + + + +A schematic representation of the Linblad et al 1996 model. + + + +The original paper reference is cited below: + + + +A model of the action potential and underlying membrane currents in a rabbit atrial cell, D. S. Lindblad, C. R. Murphey, J. W. Clark and W. R. Giles, 1996, American Journal of Physiology, 271, H1666-H1696. PubMed ID: 8897964. + + + +
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Clark + W + + + + + + + Department of Physiology, Anatomy & Genetics, University of Oxford + + + + + + + This model has been curated and unit checked and is known to run in PCEnv and COR and is able to reproduce the results published in the paper on which it is based. + + + 8897964 + + + + + + + + 1996-10-01 00:00 + + + Oxford University + Department of Physiology, Anatomy & Genetics + + + + + + + + + + 10 + 100000 + 0.0001 + + + Peter + Villiger + J + + + + + + + This is a CellML description of Lindblad et al.'s 1996 paper "A Model of the Action Potential and Underlying Membrane Currents in a Rabbit Atrial Cell" + + + + + + + keyword + + + electrophysiology + atrial myocyte + rabbit + + + + + + + + Penny + Noble + J + + + James Lawson + + + + added metadata + + + + D + Lindblad + S + + + + + + + + unknown + unknown + unknown + + + 2008-01-22T00:00:00+13:00 + + + unknown + unknown + + + + + + + + + + + 2007-03-22 + + + + A Model of the Action Potential and Underlying Membrane Currents in a Rabbit Atrial Cell + 271(4pt2) + H1666 + + + H1696 + + + + + + + 2006-03-31 + + + + + + + + \ No newline at end of file diff --git a/Bioelectrics/input/maltsev_rate_modulation.xml b/Bioelectrics/input/maltsev_rate_modulation.xml new file mode 100644 index 00000000..8804ac14 --- /dev/null +++ b/Bioelectrics/input/maltsev_rate_modulation.xml @@ -0,0 +1,4487 @@ + + + +
+ + Synergism of coupled subsarcolemmal Ca2+ clocks and sarcolemmal voltage clocks confers robust and flexible pacemaker function in a novel pacemaker cell model + + Catherine + Lloyd + + Auckland Bioengineering Institute, The University of Auckland + + + +
+ Model Status + + This CellML model has been tested in OpenCell and COR and the units are balanced. The model runs to recreate the published results. This particular variant of the model uses the initial conditions from the paper (and is not intended to be a steady state model). + +
+ + Model Structure + +ABSTRACT: Recent experimental studies have demonstrated that sinoatrial node cells (SANC) generate spontaneous, rhythmic, local subsarcolemmal Ca(2+) releases (Ca(2+) clock), which occur during late diastolic depolarization (DD) and interact with the classic sarcolemmal voltage oscillator (membrane clock) by activating Na(+)-Ca(2+) exchanger current (I(NCX)). This and other interactions between clocks, however, are not captured by existing essentially membrane-delimited cardiac pacemaker cell numerical models. Using wide-scale parametric analysis of classic formulations of membrane clock and Ca(2+) cycling, we have constructed and initially explored a prototype rabbit SANC model featuring both clocks. Our coupled oscillator system exhibits greater robustness and flexibility than membrane clock operating alone. Rhythmic spontaneous Ca(2+) releases of sarcoplasmic reticulum (SR)-based Ca(2+) clock ignite rhythmic action potentials via late DD I(NCX) over much broader ranges of membrane clock parameters [e.g., L-type Ca(2+) current (I(CaL)) and/or hyperpolarization-activated ("funny") current (I(f)) conductances]. The system Ca(2+) clock includes SR and sarcolemmal Ca(2+) fluxes, which optimize cell Ca(2+) balance to increase amplitudes of both SR Ca(2+) release and late DD I(NCX) as SR Ca(2+) pumping rate increases, resulting in a broad pacemaker rate modulation (1.8-4.6 Hz). In contrast, the rate modulation range via membrane clock parameters is substantially smaller when Ca(2+) clock is unchanged or lacking. When Ca(2+) clock is disabled, the system parametric space for fail-safe SANC operation considerably shrinks: without rhythmic late DD I(NCX) ignition signals membrane clock substantially slows, becomes dysrhythmic, or halts. In conclusion, the Ca(2+) clock is a new critical dimension in SANC function. A synergism of the coupled function of Ca(2+) and membrane clocks confers fail-safe SANC operation at greatly varying rates. + + +The original paper reference is cited below: + + +Synergism of coupled subsarcolemmal Ca2+ clocks and sarcolemmal voltage clocks confers robust and flexible pacemaker function in a novel pacemaker cell model, Victor A. Maltsev and Edward G. Lakatta, 2009, American Journal of Physiology, 286, H594-H615. PubMed ID: 19136600 + + + + + + reaction diagram + + + + + Schematic diagram of the interacting Ca2+ clock and membrane clock in a model of rabbit sinoatrial node cells. + + +
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+ + kb_CM + fCMs + + + + + + + + + time + + fCQ + + delta_fCQ + + + + delta_fCQ + + + + + kf_CQ + Ca_jsr + + + 1 + fCQ + + + + + kb_CQ + fCQ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + Cai + + + + + + + + + + j_Ca_dif + V_sub + + + + j_up + V_nsr + + + V_i + + + + + + CM_tot + delta_fCMi + + + + TC_tot + delta_fTC + + + + TMC_tot + delta_fTMC + + + + + + + + + + time + + Ca_sub + + + + + + + + j_SRCarel + V_jsr + + V_sub + + + + + + + + + + i_CaL + i_CaT + i_b_Ca + + + + 2 + i_NaCa + + + + + 2 + F + V_sub + + + j_Ca_dif + + + CM_tot + delta_fCMs + + + + + + + + + + time + + Ca_nsr + + + + j_up + + + + + j_tr + V_jsr + + V_nsr + + + + + + + + + time + + Ca_jsr + + + + j_tr + + + j_SRCarel + + + CQ_tot + delta_fCQ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + V_cell + + + 0.001 + + + + R_cell + 2 + + L_cell + + + + + V_sub + + + 0.001 + 2 + + L_sub + + + R_cell + + + L_sub + 2 + + + L_cell + + + + + V_jsr + + + V_jsr_part + V_cell + + + + + V_i + + + + + V_i_part + V_cell + + V_sub + + + + + V_nsr + + + V_nsr_part + V_cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + i_K_Ach + + + 0 + + + Ach + 0 + + + + + + a + g_K_Ach + + + Vm + E_K + + + + + + + + + + + + + + + + + + + alpha + + + 0.001 + 17 + + + + + 0.0133 + + + Vm + 40 + + + + + + + + beta + + + 0 + + + Ach + 0 + + + + + + + + 0.001 + 12.32 + + + + 1 + + + 0.0042 + Ach + + + + + + + + + a_infinity + + + beta + + + alpha + beta + + + + + + tau_a + + + 1 + + + alpha + beta + + + + + + + + + time + + a + + + + + + a_infinity + a + + tau_a + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + s + + + + + s_max + + + Ach + n_f + + + + + + + K_f_half + n_f + + + + Ach + n_f + + + + + + + VIf_half + + + VIf_half_basal + s + + + + + + + + + + + + + + + + + + + + + + + + b_cal + + + + + b_cal_max + Ach + + + + K_cal_half + Ach + + + + + + g_CaL + + + g_CaL_basal + + + 1 + b_cal + + + + + + + + + + + + + + + + + + Maltsev + V + A + + + + + + keyword + + + + + + + + + + + + + + + + + + + Non-steady state model translated from the published paper + + + + + + cardiac + electrophysiology + + + + + + + + + + + + Synergism of coupled subsarcolemmal Ca2+ clocks and sarcolemmal voltage clocks confers robust and flexible pacemaker function in a novel pacemaker cell model. + + + + + + + + + + + H561 + 296(3) + H562 + + + + + + + + + + + + + + + + + + + + + + + + Am J Physiol Heart Circ Physiol. + + + The University of Auckland + Auckland Bioengineering Institute + + + + + + 19136600 + + + 10000 + 10000 + 10 + + + Lloyd + Catherine + May + + + + + + + + + + + + + + 2009-03 + + + Lakatta + E + G + + + c.lloyd@auckland.ac.nz + + + + + + + + + + + + + + diff --git a/Bioelectrics/input/n98.xml b/Bioelectrics/input/n98.xml new file mode 100644 index 00000000..2945739a --- /dev/null +++ b/Bioelectrics/input/n98.xml @@ -0,0 +1,5799 @@ + + + + + + + + + + + + + + + + Lloyd + Catherine + May + + + c.lloyd@auckland.ac.nz + + + + The University of Auckland + The Bioengineering Research Group + + + + + + 2001-12-18 + + + + + + Added more metadata. + + + + Lloyd + Catherine + May + + + + 2002-07-22 + + + + + Corrected units. + + + + Lloyd + Catherine + May + + + + 2002-03-01 + + + + + Corrected several equations. + + + + Lloyd + Catherine + May + + + + 2002-02-26 + + + + + Corrected the i_K1 and i_K_ACh calculations. + + + + Lloyd + Catherine + May + + + + 2002-01-04 + + + + + Updated metadata to conform to the 16/1/02 CellML Metadata 1.0 + Specification. + + + + Cuellar + Autumn + A. + + + + 2002-01-21 + + + + + Altered some of the connections. + + + + Lloyd + Catherine + May + + + + 2002-01-04 + + + + + Added some initial values from Penny Noble's documentation. Removed + the blocked h_gate component from the fast sodium current as it + belongs to a separate model which considers the effect of drugs. + + + + Lloyd + Catherine + May + + + + 2002-05-06 + + + + + Fixed up the CellML/MathML to enable the model to be solved in CMISS. The + model is no longer a direct translation of the Noble 1998 article, but + I believe it accurately represents the intent of the model. + + + + Nickerson + David + P + + + + 2003-04-05 + + + + + + Bioengineering Institute, The University of Auckland. + + + + + + + + The Noble 1998 Improved Guinea-Pig Ventricular Cell Model + + + + + + This is the CellML description of Noble's 1998 improved guinea-pig + ventricular cell model. It incorporates a diadic space, rapid and + slow potassium currents and length- and tension-dependent processes. + + + + Catherine Lloyd + + + + Guinea-Pig + + Ventricular Myocyte + + + + 9487284 + + + + + + + Noble + Denis + + + + + + + Varghese + Anthony + + + + + + + Kohl + Peter + + + + + + + Noble + Penny + + + + + + + Improved guinea-pig ventricular cell model incorporating a diadic + space, IKr and IKs, and length- and tension-dependent processes + + + 1998 + + + Canadian Journal of Cardiology + + 14 + 123 + 134 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This component is used to declare variables that are used by + all or most of the other components, in this case just `time'. + + + + + + + + + + + + + This component is the `root' node of our model. + It defines the action potential variable `V'. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A dummy equation used to get the total stimulus current into CMISS. + + + + + + + IStimC + IStim + + + + + + + + The ODE governing the membrane potential -- given by the summation of the + ionic currents and an applied stimulus. + + + + + + + + time + V + + + + IStim + + i_K1 + i_to + i_K + i_K_ATP + i_b_K + i_NaK + i_Na + i_b_Na + i_p_Na + i_NaCa + i_NaCa_ds + i_Ca_L_Ca + i_Ca_L_Ca_ds + i_Ca_L_K + i_Ca_L_K_ds + i_Ca_L_Na + i_Ca_L_Na_ds + i_b_Ca + i_Na_stretch + i_K_stretch + i_Ca_stretch + i_Ns_stretch + i_An_stretch + i_K_ACh + + + Cm + + + + + + + + + + + A component that conveniently keeps the reversal potential calculations + together. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the sodium reversal potential from the current intra- and + extracellular concentration of sodium ions. + + + + + + + E_Na + + + + R + T + + F + + + + Na_o + Na_i + + + + + + + + + + Calculation of the potassium reversal potential from the current intra- and + extracellular concentration of potassium ions. + + + + + + + E_K + + + + R + T + + F + + + + K_o + K_i + + + + + + + + + + Calculation of the potassium reversal potential for the slow component of + the delayed rectifier. + + + + + + + E_Ks + + + + R + T + + F + + + + + K_o + + P_kna + Na_o + + + + K_i + + P_kna + Na_i + + + + + + + + + + + + Calculation of the calcium reversal potential. + + + + + + + E_Ca + + 0.5 + + + R + T + + F + + + + Ca_o + Ca_i + + + + + + + + + + Calculation of the reversal potential for the fast sodium channel. + + + + + + + E_mh + + + + R + T + + F + + + + + Na_o + + P_nak + K_o + + + + Na_i + + P_nak + K_i + + + + + + + + + + + + + + + Description of the time independent inward potassium current. + + + + + + + + + + + + + + + + + + + + + + + Calculation of the time independent potassium current. + + + + + + + i_K1 + + g_K1 + + K_o + + K_o + K_mk1 + + + + + V + E_K + + + 1.0 + + + + 1.25 + + V + + E_K + 10.0 + + + + + + R + T + + F + + + + + + + + + + + + + + + + A component to group the potassium currents. + + + + + + + + + + + + + + + Simple summation of the individual potassium currents into a + single current. + + + + + + + i_K + + i_Kr + i_Ks + i_KNa + + + + + + + + + + + The rapid component of the delayed rectifier current. + + + + + + + + + + + + + + + + + + + + + + Calculation of the rapid component of the delayed rectifier current. + + + + + + + i_Kr + + + + g_Kr1 + Xr1 + + + g_Kr2 + Xr2 + + + + 1.0 + + 1.0 + + + + V + 9.0 + + 22.4 + + + + + + V + E_K + + + + + + + + + + + + The fast activation gate for the rapid component of the delayed + rectifier. + + + + + + + + + + + + + + The gating kinetics for the fast gate of the rapid component + of the delayed rectifier. + + + + + + + + time + Xr1 + + + + + 0.05 + + 1.0 + + + + + V + 5.0 + + + 9.0 + + + + + + 1.0 + Xr1 + + + + 0.00005 + + + + + V + 20.0 + + 15.0 + + + + Xr1 + + + + + + + + + + + + The slow gate of the rapid component of the delayed rectifier. + + + + + + + + + + + + + + Gating kinetics for the slow gate of the rapid component of + the delayed rectifier. + + + + + + + + time + Xr2 + + + + + 0.05 + + 1.0 + + + + + V + 5.0 + + + 9.0 + + + + + + 1.0 + Xr2 + + + + 0.0004 + + + + + + V + 30.0 + + 30.0 + + 3.0 + + + + Xr2 + + + + + + + + + + + + The slow component of the delayed rectifier current. + + + + + + + + + + + + + + + + + + + + Calculation of the slow component current of the delayed rectifier. + + + + + + + i_Ks + + + g_Ks + + Xs + 2.0 + + + + V + E_Ks + + + + + + + + + + + + The gate for the slow component of the delayed rectifier current. + + + + + + + + + + + + + + The gating kinetics for the slow component of the delayed + rectifier current. + + + + + + + + time + Xs + + + + + 0.014 + + 1.0 + + + + + V + 40.0 + + + 9.0 + + + + + + 1.0 + Xs + + + + Xs + 0.001 + + + + V + + 45.0 + + + + + + + + + + + + + + Background potassium current. + + + + + + + + + + + + + + + + + + Calculation of the background potassium current. + + + + + + + i_b_K + + g_bk + + V + E_K + + + + + + + + + + + + An ATP dependent potassium current. Included here for completeness, but + this current is only used when modelling ischaemia - and this version + of the model has not been tested for this. + + + + + + + + + + + + + + + + + + + Calculation of the ATP dependent potassium current. + + + + + + + i_K_ATP + + + g_K_ATP + + V + 80.0 + + + + 1.0 + + + ATP + K_ATP + + 2.0 + + + + + + + + + + + + + A sodium activated potassium current. Again, included for completeness + but generally not used and untested. + + + + + + + + + + + + + + + + + + + + Calculation of the sodium activated potassium current. + + + + + + + i_KNa + + g_K_Na + + Na_i + + Na_i + K_kna + + + + V + E_K + + + + + + + + + + + + The fast sodium current - the driving force of the upstroke of the + cardiac action potential. + + + + + + + + + + + + + + + + + + + + + Calculation of the fast sodium current. + + + + + + + i_Na + + g_Na + + m + 3.0 + + h + + V + E_mh + + + + + + + + + + + + The activation gate for the fast sodium current. + + + + + + + + + + + + + + + + + The gating kinetics for the activation gate of the fast sodium current. + + + + + + + + time + m + + + + alpha + + 1.0 + m + + + + beta + m + + + + + + + + + Calculation of the opening rate of the activation gate for the fast + sodium current. + + + + + + + alpha + + + 2.0 + + + + V + 41.0 + + + 0.1e-4 + + + + + + 0.2 + + V + 41.0 + + + + 1.0 + + + -0.1 + + V + 41.0 + + + + + + + + + + + + + + Calculation of the closing rate of the activation gate for the fast + sodium current. + + + + + + + beta + + 8.0 + + + -0.055556 + + V + 66.0 + + + + + + + + + + + + + + The inactivation gate for the fast sodium current. + + + + + + + + + + + + + + The gating kinetics for the inactivation gate of the fast sodium + current. + + + + + + + + time + h + + + + + 0.02 + + + -0.125 + + V + 75.0 + + + + + + 1.0 + h + + + + h + + 2.0 + + 1.0 + + 320.0 + + + -0.1 + + V + 75.0 + + + + + + + + + + + + + + + + + + The persistent sodium current. + + + + + + + + + + + + + + + + + + Calculation of the persistent sodium current. + + + + + + + i_p_Na + + g_pna + + 1.0 + + 1.0 + + + + + V + 52.0 + + 8.0 + + + + + + + V + E_Na + + + + + + + + + + + + The background sodium current. + + + + + + + + + + + + + + + + + + + Calculation of the sodium background current. + + + + + + + i_b_Na + + g_bna + + V + E_Na + + + + + + + + + + + + + This component describes an inward ionic current which is the sum + of calcium, sodium and potassium ions through the membrane channel. + The channel has one activation gate (d) and two inactivation gates + (f and f2 (or f2ds in the diadic space)). A fraction of these channels + (ICaLfract) open into the diadic subspace, with the remainder being + evenly distributed throughout the membrane area. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The calcium ion component of the total current through the channel into + the bulk myoplasm. + + + + + + + i_Ca_L_Ca + + + 1.0 + ICaLfract + + 4.0 + P_ca + d + f + f2 + + + + V + 50.0 + + + + R + T + + F + + + + 1.0 + + + + + V + 50.0 + + + + + R + T + + + 2.0 + F + + + + + + + + + Ca_i + + + 50.0 + + + R + T + + + 2.0 + F + + + + + + + Ca_o + + + + + V + 50.0 + + + + + R + T + + + 2.0 + F + + + + + + + + 1.0 + + ACh + + ACh + K_AChICaL + + + + + + + + + + + The potassium ion component of the total current through the channel into + the bulk myoplasm. + + + + + + + i_Ca_L_K + + + 1.0 + ICaLfract + + P_caK + P_ca + d + f + f2 + + + K_i + + + 50.0 + + + R + T + + F + + + + + + K_o + + + + + V + 50.0 + + + + + R + T + + F + + + + + + + 1.0 + + ACh + + ACh + K_AChICaL + + + + + + + + + + + The sodium ion component of the total current through the channel into + the bulk myoplasm. + + + + + + + i_Ca_L_Na + + + 1.0 + ICaLfract + + P_caNa + P_ca + d + f + f2 + + + Na_i + + + 50.0 + + + R + T + + F + + + + + + Na_o + + + + + V + 50.0 + + + + + R + T + + F + + + + + + + 1.0 + + ACh + + ACh + K_AChICaL + + + + + + + + + + + The calcium ion component of the total current through the channel into + the diadic subspace. + + + + + + + i_Ca_L_Ca_ds + + ICaLfract + 4.0 + P_ca + d + f + f2ds + + + + V + 50.0 + + + + R + T + + F + + + + 1.0 + + + + + V + 50.0 + + + + + R + T + + + 2.0 + F + + + + + + + + + Ca_ds + + + 50.0 + + + R + T + + + 2.0 + F + + + + + + + Ca_o + + + + + V + 50.0 + + + + + R + T + + + 2.0 + F + + + + + + + + 1.0 + + ACh + + ACh + K_AChICaL + + + + + + + + + + + The potassium ion component of the total current through the channel into + the diadic subspace. + + + + + + + i_Ca_L_K_ds + + ICaLfract + P_caK + P_ca + d + f + f2ds + + + K_i + + + 50.0 + + + R + T + + F + + + + + + K_o + + + + + V + 50.0 + + + + + R + T + + F + + + + + + + 1.0 + + ACh + + ACh + K_AChICaL + + + + + + + + + + + The sodium ion component of the total current through the channel into + the diadic subspace. + + + + + + + i_Ca_L_Na_ds + + ICaLfract + P_caNa + P_ca + d + f + f2ds + + + Na_i + + + 50.0 + + + R + T + + F + + + + + + Na_o + + + + + V + 50.0 + + + + + R + T + + F + + + + + + + 1.0 + + ACh + + ACh + K_AChICaL + + + + + + + + + + + + + + The activation gate of the L-type calcium channel. + + + + + + + + + + + + + + + + + The gating kinetics for the activation gate. + + + + + + + + time + d + + + + alpha + + 1.0 + d + + + + beta + d + + + + + + + + + The opening rate for the activation gate. + + + + + + + alpha + + + 0.36 + + + + V + 19.0 + + + 1.0e-3 + + + + + + 0.09 + + V + 19.0 + + + + 1.0 + + + + + V + 19.0 + + + 4.0 + + + + + + + + + + + + + The closing rate for the activation gate. + + + + + + + beta + + + 0.36 + + + + V + 19.0 + + + 1.0e-3 + + + + + + -0.036 + + V + 19.0 + + + + 1.0 + + + + V + 19.0 + + 10.0 + + + + + + + + + + + + + + + + The first inactivation gate for the L-type calcium channel. + + + + + + + + + + + + + + + + + + + The gating kinetics for the first inactivation gate. + + + + + + + + time + f + + + + alpha + + 1.0 + f + + + + beta + f + + + + + + + + + The opening rate for the inactivation gate. + + + + + + + alpha + + + 0.0075 + + + + V + 34.0 + + + 1.0e-3 + + + + + -0.001875 + + + V + 34.0 + + + 1.0 + + + + V + 34.0 + + 4.0 + + + + + + + + + + + + + + The closing rate for the inactivation gate. + + + + + + + beta + + 0.0036 + + 1.0 + + + + + V + 34.0 + + 4.0 + + + + + + + + + + + + + + + The second inactivation gate for L-type calcium channels in the + membrane outside the diadic subspace. + + + + + + + + + + + + + + + + + + + The gating kinetics for the inactivation gate. + + + + + + + + time + f2 + + + CaInact + + 1.0 + + + Ca_i + + K_cachoff + Ca_i + + + f2 + + + + + + + + + + + + + The second inactivation gate for L-type calcium channels in the + membrane when open into the diadic subspace. + + + + + + + + + + + + + + + + + + The gating kinetics for the inactivation gate. + + + + + + + + time + f2ds + + + CaInactDS + + 1.0 + + + Ca_ds + + K_dsoff + Ca_ds + + + f2ds + + + + + + + + + + + + + The background calcium current. + + + + + + + + + + + + + + + + + + Calculation of the background calcium current. + + + + + + + i_b_Ca + + g_bca + + V + E_Ca + + + + + + + + + + + + The doubly gated transient outward current. + + + + + + + + + + + + + + + + + + + + + + + Evaluation of the transient outward current. + + + + + + + i_to + + g_to + + g_tos + + s + + 1.0 + g_tos + + + + r + + V + E_K + + + + + + + + + + + + The first gate of the transient outward current. + + + + + + + + + + + + + + The gating kinetics. + + + + + + + + time + s + + + + 0.000033 + + + + V + + 17.0 + + + + 1.0 + s + + + + + 0.033 + + 1.0 + + + + + V + 10.0 + + + 8.0 + + + + + s + + + + + + + + + + + + The second of the two gates for the transient outward current. + + + + + + + + + + + + + + + The gating kinetics for the r gate. + + + + + + + + time + r + + + 0.333 + + r_ss + r + + + + + + + + + Calculation of the steady-state component of the gating kinetics + for the r gate. + + + + + + + r_ss + + 1.0 + + 1.0 + + + -0.2 + + V + 4.0 + + + + + + + + + + + + + + + Acetylcholine (ACh) dependent potassium current. Once more, + this current has been included for completeness with respect + to the original publication but is usually left out of simulations. + It is useful for simulating specific cellular conditions, but + this formulation has not been tested. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Evaluation of the ACh dependent potassium current. + + + + + + + i_K_ACh + + g_KACh + + K_o + + K_o + K_KACh + + + x_ACh1 + x_ACh2 + + + ACh + 1.4969 + + + + ACh + 1.4969 + + + K_ACh + 1.4969 + + + + + + V + E_K + + + 1.0 + + + + 0.4 + + V + + E_K + 140.0 + + + + + + R + T + + F + + + + + + + + + + + + + + + + The first of two gates for the ACh dependent potassium current. + + + + + + + + + + + + + + + Gating kinetics for the first gate. + + + + + + + + time + x_ACh1 + + + + alpha_ACh + + 1.0 + x_ACh1 + + + + + 0.00582 + + 1.0 + + + + + V + 50.0 + + 15.0 + + + + + + x_ACh1 + + + + + + + + + + + + The second of the two gates for the ACh dependent potassium current. + + + + + + + + + + + + + + + Gating kinetics for the second gate. + + + + + + + + time + x_ACh2 + + + + alpha_ACh + + 1.0 + x_ACh2 + + + + + 0.12 + + 1.0 + + + + + V + 50.0 + + 15.0 + + + + + + x_ACh2 + + + + + + + + + + + + The sodium potassium pump. + + + + + + + + + + + + + + + + + + + + Calculation of the sodium potassium pump current. + + + + + + + i_NaK + + i_NaK_max + + K_o + + K_o + K_mk + + + + Na_i + + Na_i + K_mNa + + + + + + + + + + + + + The sodium calcium exchanger. A fraction of the Na-Ca exchangers + (INaCaFract) are assumed to emmpty into the diadic subspace, while + the remainder of the channels open into the bulk cytosol. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculation of the sodium calcium exchanger current for the channels + exposed to the bulk myoplasm. + + + + + + + i_NaCa + + + 1.0 + INaCaFract + + K_NaCa + + + + + + gamma + + V + + + R + T + + F + + + + + + Na_i + 3.0 + + Ca_o + + + + + + gamma + 1.0 + + + V + + + R + T + + F + + + + + + Na_o + 3.0 + + Ca_i + + + + 1.0 + + d_NaCa + + + Ca_i + + Na_o + 3.0 + + + + Ca_o + + Na_i + 3.0 + + + + + + + + 1.0 + + 1.0 + + Ca_i + 0.0069 + + + + + + + + + + + Calculation of the sodium calcium exchanger current for the channels + opening into the diadic subspace. + + + + + + + i_NaCa_ds + + INaCaFract + K_NaCa + + + + + + gamma + + V + + + R + T + + F + + + + + + Na_i + 3.0 + + Ca_o + + + + + + gamma + 1.0 + + + V + + + R + T + + F + + + + + + Na_o + 3.0 + + Ca_ds + + + + 1.0 + + d_NaCa + + + Ca_ds + + Na_o + 3.0 + + + + Ca_o + + Na_i + 3.0 + + + + + + + + 1.0 + + 1.0 + + Ca_ds + 0.0069 + + + + + + + + + + + + + + The sarcoplasmic reticulum calcium pump which transports calcium + from the bulk myoplasm into the network SR. + + + + + + + + + + + + + + + + + + + + Calculation of the calcium uptake flux. + + + + + + + i_up + + + + 0.0004 + Ca_i + + + 0.00003 + Ca_up + + + K_cyca + K_xcs + + K_srca + + + + + Ca_i + + Ca_up + + + K_cyca + K_xcs + + K_srca + + + + K_cyca + K_xcs + + K_cyca + + + + + + + + + + + + Diffusion down the concentration gradient to transfer calcium from + the uptake stores in the network SR to the release stores in the + junctional SR. + + + + + + + + + + + + + + + + Calculation of the transfer flux between the uptake and release + calcium stores. + + + + + + + i_tr + + 0.05 + + Ca_up + Ca_rel + + + + + + + + + + + + This component describes the addition of + length dependence to the Noble models. However, in this implementation + of the model, it is unused - sarcomere length (SL) is a constant 0, + resulting in the removal of length dependence from the model. + + + + + + + + + + + + + + + + + Calculation of the scaling factor for the stretch activated currents + based on the change in length from the reference state. + + + + + + + f_stretch + + 1.0 + + 1.0 + + + -2.0 + gamma_SAC_SL + + SL + SLRef + + + + + + + + + + + + + + + The length dependent leakage of calcium from the junctional + SR into the cytolsol. + + + + + + + + + + + + + + + + i_leak + + + + gamma_SR_SL + SL + + + alpha_SRleak + Ca_rel + + + + + + + + + + + Description of the diffusion of calcium out of the diadic + subspace into the bulk cytosol. + + + + + + + + + + + + + + + + Calculation of the flux of calcium out of the diadic subspace. + + + + + + + i_decay + + alpha_ca_ds_decay + Ca_ds + + + + + + + + + + + The calcium induced calcium release from the junctional SR into + the bulk myoplasm. Assumed that activation of calcium release sites + by the diadic subspace calcium triggers calcium release in the whole + cytosol. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The fraction of release sites in the open state. + + + + + + + OpenReleaseChannelFract + + + ActivatorFract + + ActivatorFract + 0.25 + + + 2.0 + + + + + + + + Calculation of the calcium release flux from the JSR into the cytosol. + + + + + + + i_rel + + alpha_rel + OpenReleaseChannelFract + Ca_rel + + + + + + + + Regulatory binding sites. + + + + + + + RegulatoryBindingSite + + + + Ca_i + + Ca_i + K_mca + + + + + 1.0 + + Ca_i + + Ca_i + K_mca + + + + + Ca_ds + + Ca_ds + K_mca_ds + + + + + 2.0 + + + + + + + + Fraction of release channels in the precursor state. + + + + + + + PrecursorFract + + 1.0 + + ActivatorFract + ProductFract + + + + + + + alpha_act + + 0.5 + RegulatoryBindingSite + + + + + + alpha_inact + + 0.06 + + 0.5 + RegulatoryBindingSite + + + + + + + SR_speed_factor + + + 5.0 + + V + -50.0 + + + + 1.0 + + + + + + + + + time + + ActivatorFract + + + SR_speed_factor + + + alpha_act + PrecursorFract + + + alpha_inact + ActivatorFract + + + + + + + + + + time + + ProductFract + + + SR_speed_factor + + + alpha_inact + ActivatorFract + + + 0.001 + ProductFract + + + + + + + + + + + + + A stretch activated calcium current. Unused and untested in this + implementation, but included for completeness. + + + + + + + + + + + + + + + + + + + Calculation of the current. + + + + + + + i_Ca_stretch + + g_Ca_stretch + f_stretch + + V + E_Ca + + + + + + + + + + + + Stretch activated potassium current - unused and untested, but + included for completeness. + + + + + + + + + + + + + + + + + + + Calculation of the current. + + + + + + + i_K_stretch + + g_K_stretch + f_stretch + + V + E_K + + + + + + + + + + + + A stretch activated sodium current - unused and untested, but + included for completeness. + + + + + + + + + + + + + + + + + + + Calculation of the current. + + + + + + + i_Na_stretch + + g_Na_stretch + f_stretch + + V + E_Na + + + + + + + + + + + + A non-specific stretch activated current. Not used and untested, but + included for completeness. + + + + + + + + + + + + + + + + + + + Calculation of the current. + + + + + + + i_Ns_stretch + + g_Ns_stretch + f_stretch + + V + E_Ns_stretch + + + + + + + + + + + + A anion specific stretch ativated current - unused and untested, but + included for completeness. + + + + + + + + + + + + + + + + + + + Calculation of the current. + + + + + + + i_An_stretch + + g_An_stretch + f_stretch + + V + E_An_stretch + + + + + + + + + + + + A convenient grouping of all the ionic concentration differential + equations. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The rate of change of intracellular sodium concentration. + + + + + + + + time + Na_i + + + + + Am + + V_i + F + + + + + i_Na + i_p_Na + + i_b_Na + + Na_o + 140.0 + + + + i_NaK + 3.0 + + + i_NaCa + 3.0 + + + i_NaCa_ds + 3.0 + + i_Ca_L_Na + i_Ca_L_Na_ds + i_Na_stretch + + + + + + + + + The rate of change of intracellular potassium concentration. + + + + + + + + time + K_i + + + + + Am + + V_i + F + + + + + + i_K1 + i_to + i_b_K + i_K + i_K_stretch + i_Ca_L_K + i_Ca_L_K_ds + i_K_ACh + i_K_ATP + + + i_NaK + 2.0 + + + + + + + + + + The rate of change of intracellular calcium concentration. + + + + + + + + time + Ca_i + + + + + + + Am + + 2.0 + V_i + F + + + + + + i_Ca_L_Ca + i_b_Ca + i_Ca_stretch + + + i_NaCa + 2.0 + + + + + i_rel + + V_rel + V_i + + + + i_leak + + V_rel + V_i + + + + i_decay + + V_ds + V_i + + + + + i_up + dy_Ca_calmod + dy_Ca_troponin + + + + + + + + + The rate of change of calcium concentration in the diadic subspace. + + + + + + + + time + Ca_ds + + + + + + Am + + 2.0 + V_ds + F + + + + + i_Ca_L_Ca_ds + + i_NaCa_ds + 2.0 + + + + i_decay + + + + + + + + The rate of change of calcium concentration in the network SR + uptake store. + + + + + + + + time + Ca_up + + + + + V_i + V_up + + i_up + + i_tr + + + + + + + + The rate of change of calcium concentration in the junctional SR + release store. + + + + + + + + time + Ca_rel + + + + + V_up + V_rel + + i_tr + + + i_rel + i_leak + + + + + + + + + The rate of change of calcium bound to calmodulin. + + + + + + + dy_Ca_calmod + + + 100.0 + Ca_i + + CALM + Ca_calmod + + + + 0.05 + Ca_calmod + + + + + + + + time + Ca_calmod + + dy_Ca_calmod + + + + + + + The rate of change of calcium bound to troponin. + + + + + + + dy_Ca_troponin + + + alpha_trop + Ca_i + + TROP + Ca_troponin + + + + beta_trop + Ca_troponin + + + + + + + + time + Ca_troponin + + dy_Ca_troponin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/ClassicalField/Poisson/AnalyticNonlinearPoisson/CMakeLists.txt b/ClassicalField/Poisson/AnalyticNonlinearPoisson/CMakeLists.txt new file mode 100644 index 00000000..1e32d288 --- /dev/null +++ b/ClassicalField/Poisson/AnalyticNonlinearPoisson/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(analytic.x src/AnalyticNonlinearPoissonExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(analytic.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(analytic.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Poisson COMMAND analytic.x) +add_opencmiss_environment(Poisson) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Poisson/AnalyticNonlinearPoisson/Makefile b/ClassicalField/Poisson/AnalyticNonlinearPoisson/Makefile deleted file mode 100644 index d961bce2..00000000 --- a/ClassicalField/Poisson/AnalyticNonlinearPoisson/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Poisson/ - -EXAMPLE_NAME = AnalyticNonlinearPoisson - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Poisson/CMakeLists.txt b/ClassicalField/Poisson/CMakeLists.txt new file mode 100644 index 00000000..9f1e21a7 --- /dev/null +++ b/ClassicalField/Poisson/CMakeLists.txt @@ -0,0 +1,35 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(AnalyticNonlinearPoisson) + add_subdirectory(ExtracellularBidomain/Fortran) + add_subdirectory(NonlinearPoisson) +endif() diff --git a/ClassicalField/Poisson/ExtracellularBidomain/Fortran/CMakeLists.txt b/ClassicalField/Poisson/ExtracellularBidomain/Fortran/CMakeLists.txt new file mode 100644 index 00000000..383680e1 --- /dev/null +++ b/ClassicalField/Poisson/ExtracellularBidomain/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(extra_cellular.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(extra_cellular.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(extra_cellular.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Poisson COMMAND extra_cellular.x) +add_opencmiss_environment(Poisson) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Poisson/ExtracellularBidomain/Fortran/Makefile b/ClassicalField/Poisson/ExtracellularBidomain/Fortran/Makefile deleted file mode 100644 index f90acba0..00000000 --- a/ClassicalField/Poisson/ExtracellularBidomain/Fortran/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Poisson/ExtracellularBidomain/ - -EXAMPLE_NAME = Fortran - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/Poisson/NonlinearPoisson/CMakeLists.txt b/ClassicalField/Poisson/NonlinearPoisson/CMakeLists.txt new file mode 100644 index 00000000..e069367f --- /dev/null +++ b/ClassicalField/Poisson/NonlinearPoisson/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(nonlinear.x src/NonlinearPoissonExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(nonlinear.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(nonlinear.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Poisson COMMAND nonlinear.x) +add_opencmiss_environment(Poisson) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/Poisson/NonlinearPoisson/Makefile b/ClassicalField/Poisson/NonlinearPoisson/Makefile deleted file mode 100644 index 8fce2aed..00000000 --- a/ClassicalField/Poisson/NonlinearPoisson/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/Poisson/ - -EXAMPLE_NAME = NonlinearPoisson - -include $(GLOBAL_ROOT)/ExampleMakefile - From 2bb3abdc643d5d8ee3fe03b5cc992861928d07e4 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 14:15:30 +1300 Subject: [PATCH 14/28] Added CMake support for ClassicalField/ReactionDiffusion examples --- .../ReactionDiffusion/CMakeLists.txt | 35 ++++++++++ .../CMakeLists.txt | 50 +++++++++++++ .../CellMLSplitReactionDiffusion1D/Makefile | 70 ------------------- .../CMakeLists.txt | 50 +++++++++++++ .../Makefile | 70 ------------------- .../CMakeLists.txt | 50 +++++++++++++ .../ReactionDiffusionNoSource1D/Makefile | 70 ------------------- 7 files changed, 185 insertions(+), 210 deletions(-) create mode 100644 ClassicalField/ReactionDiffusion/CMakeLists.txt create mode 100644 ClassicalField/ReactionDiffusion/CellMLSplitReactionDiffusion1D/CMakeLists.txt delete mode 100755 ClassicalField/ReactionDiffusion/CellMLSplitReactionDiffusion1D/Makefile create mode 100644 ClassicalField/ReactionDiffusion/ReactionDiffusionConstantSource1D/CMakeLists.txt delete mode 100755 ClassicalField/ReactionDiffusion/ReactionDiffusionConstantSource1D/Makefile create mode 100644 ClassicalField/ReactionDiffusion/ReactionDiffusionNoSource1D/CMakeLists.txt delete mode 100755 ClassicalField/ReactionDiffusion/ReactionDiffusionNoSource1D/Makefile diff --git a/ClassicalField/ReactionDiffusion/CMakeLists.txt b/ClassicalField/ReactionDiffusion/CMakeLists.txt new file mode 100644 index 00000000..0ec3fc72 --- /dev/null +++ b/ClassicalField/ReactionDiffusion/CMakeLists.txt @@ -0,0 +1,35 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(CellMLSplitReactionDiffusion1D) + add_subdirectory(ReactionDiffusionConstantSource1D) + add_subdirectory(ReactionDiffusionNoSource1D) +endif() diff --git a/ClassicalField/ReactionDiffusion/CellMLSplitReactionDiffusion1D/CMakeLists.txt b/ClassicalField/ReactionDiffusion/CellMLSplitReactionDiffusion1D/CMakeLists.txt new file mode 100644 index 00000000..1051acdf --- /dev/null +++ b/ClassicalField/ReactionDiffusion/CellMLSplitReactionDiffusion1D/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(react_diff.x src/CellMLSplitReactionDiffusion1DExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(react_diff.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(react_diff.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME ReactionDiffusion COMMAND react_diff.x) +add_opencmiss_environment(ReactionDiffusion) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/ReactionDiffusion/CellMLSplitReactionDiffusion1D/Makefile b/ClassicalField/ReactionDiffusion/CellMLSplitReactionDiffusion1D/Makefile deleted file mode 100755 index 4ef2447f..00000000 --- a/ClassicalField/ReactionDiffusion/CellMLSplitReactionDiffusion1D/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/ReactionDiffusion/ - -EXAMPLE_NAME = CellMLSplitReactionDiffusion1D - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/ReactionDiffusion/ReactionDiffusionConstantSource1D/CMakeLists.txt b/ClassicalField/ReactionDiffusion/ReactionDiffusionConstantSource1D/CMakeLists.txt new file mode 100644 index 00000000..525bc432 --- /dev/null +++ b/ClassicalField/ReactionDiffusion/ReactionDiffusionConstantSource1D/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(react_diff_constant.x src/ReactionDiffusionConstantSource1DExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(react_diff_constant.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(react_diff_constant.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME ReactionDiffusion COMMAND react_diff_constant.x) +add_opencmiss_environment(ReactionDiffusion) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/ReactionDiffusion/ReactionDiffusionConstantSource1D/Makefile b/ClassicalField/ReactionDiffusion/ReactionDiffusionConstantSource1D/Makefile deleted file mode 100755 index 679badf4..00000000 --- a/ClassicalField/ReactionDiffusion/ReactionDiffusionConstantSource1D/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/ReactionDiffusion/ - -EXAMPLE_NAME = ReactionDiffusionConstantSource1D - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/ClassicalField/ReactionDiffusion/ReactionDiffusionNoSource1D/CMakeLists.txt b/ClassicalField/ReactionDiffusion/ReactionDiffusionNoSource1D/CMakeLists.txt new file mode 100644 index 00000000..c6f7b726 --- /dev/null +++ b/ClassicalField/ReactionDiffusion/ReactionDiffusionNoSource1D/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(react_diff_nosource.x src/ReactionDiffusionNoSource1DExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(react_diff_nosource.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(react_diff_nosource.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME ReactionDiffusion COMMAND react_diff_nosource.x) +add_opencmiss_environment(ReactionDiffusion) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/ClassicalField/ReactionDiffusion/ReactionDiffusionNoSource1D/Makefile b/ClassicalField/ReactionDiffusion/ReactionDiffusionNoSource1D/Makefile deleted file mode 100755 index 8dff5de8..00000000 --- a/ClassicalField/ReactionDiffusion/ReactionDiffusionNoSource1D/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=ClassicalField/ReactionDiffusion/ - -EXAMPLE_NAME = ReactionDiffusionNoSource1D - -include $(GLOBAL_ROOT)/ExampleMakefile - From ec00df1b35e5bfe7a07fcfffbced25668b31856a Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 15:46:55 +1300 Subject: [PATCH 15/28] added CMake support for DataProjection examples --- .../1DRectangularCartesian/CMakeLists.txt | 50 +++++++++++++++++++ .../2DRectangularCartesian/CMakeLists.txt | 50 +++++++++++++++++++ .../3DRectangularCartesian/CMakeLists.txt | 50 +++++++++++++++++++ DataProjection/CMakeLists.txt | 35 +++++++++++++ 4 files changed, 185 insertions(+) create mode 100644 DataProjection/1DRectangularCartesian/CMakeLists.txt create mode 100644 DataProjection/2DRectangularCartesian/CMakeLists.txt create mode 100644 DataProjection/3DRectangularCartesian/CMakeLists.txt create mode 100644 DataProjection/CMakeLists.txt diff --git a/DataProjection/1DRectangularCartesian/CMakeLists.txt b/DataProjection/1DRectangularCartesian/CMakeLists.txt new file mode 100644 index 00000000..1002e865 --- /dev/null +++ b/DataProjection/1DRectangularCartesian/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cart_1D.x src/1DRectangularCartesianExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cart_1D.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cart_1D.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME RectangularCartesian COMMAND cart_1D.x) +add_opencmiss_environment(RectangularCartesian) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/DataProjection/2DRectangularCartesian/CMakeLists.txt b/DataProjection/2DRectangularCartesian/CMakeLists.txt new file mode 100644 index 00000000..de677eba --- /dev/null +++ b/DataProjection/2DRectangularCartesian/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cart_2D.x src/2DRectangularCartesianExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cart_2D.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cart_2D.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME RectangularCartesian COMMAND cart_2D.x) +add_opencmiss_environment(RectangularCartesian) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/DataProjection/3DRectangularCartesian/CMakeLists.txt b/DataProjection/3DRectangularCartesian/CMakeLists.txt new file mode 100644 index 00000000..474e1602 --- /dev/null +++ b/DataProjection/3DRectangularCartesian/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cart_3D.x src/3DRectangularCartesianExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cart_3D.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cart_3D.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME RectangularCartesian COMMAND cart_3D.x) +add_opencmiss_environment(RectangularCartesian) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/DataProjection/CMakeLists.txt b/DataProjection/CMakeLists.txt new file mode 100644 index 00000000..467305aa --- /dev/null +++ b/DataProjection/CMakeLists.txt @@ -0,0 +1,35 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(1DRectangularCartesian) + add_subdirectory(2DRectangularCartesian) + add_subdirectory(3DRectangularCartesian) +endif() From e250a7f4a9963cfa065aaa1e60c0e506d247c1ee Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 15:48:13 +1300 Subject: [PATCH 16/28] Added CMake support for EmbeddedMesh examples --- EmbeddedMesh/CMakeLists.txt | 33 ++++++++++++ EmbeddedMesh/EmbeddedMeshBasic/CMakeLists.txt | 50 +++++++++++++++++++ .../EmbeddedMeshBasicWithMap/CMakeLists.txt | 50 +++++++++++++++++++ 3 files changed, 133 insertions(+) create mode 100644 EmbeddedMesh/CMakeLists.txt create mode 100644 EmbeddedMesh/EmbeddedMeshBasic/CMakeLists.txt create mode 100644 EmbeddedMesh/EmbeddedMeshBasicWithMap/CMakeLists.txt diff --git a/EmbeddedMesh/CMakeLists.txt b/EmbeddedMesh/CMakeLists.txt new file mode 100644 index 00000000..c255c999 --- /dev/null +++ b/EmbeddedMesh/CMakeLists.txt @@ -0,0 +1,33 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(EmbeddedMeshBasic) +endif() diff --git a/EmbeddedMesh/EmbeddedMeshBasic/CMakeLists.txt b/EmbeddedMesh/EmbeddedMeshBasic/CMakeLists.txt new file mode 100644 index 00000000..655a726e --- /dev/null +++ b/EmbeddedMesh/EmbeddedMeshBasic/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(embed.x src/EmbeddedMeshBasicExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(embed.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(embed.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Embedded COMMAND embed.x) +add_opencmiss_environment(Embedded) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/EmbeddedMesh/EmbeddedMeshBasicWithMap/CMakeLists.txt b/EmbeddedMesh/EmbeddedMeshBasicWithMap/CMakeLists.txt new file mode 100644 index 00000000..00a5d9b2 --- /dev/null +++ b/EmbeddedMesh/EmbeddedMeshBasicWithMap/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(embed_map.x src/EmbeddedMeshBasicWithMapExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(embed_map.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(embed_map.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Embedded COMMAND embed_map.x) +add_opencmiss_environment(Embedded) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# From 99df08b7bf98ed7bfff16c7d30660a9f9506f658 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 15:49:23 +1300 Subject: [PATCH 17/28] added CMake support for LinearElasticity example --- .../CMakeLists.txt | 50 +++++++++++++++++++ .../3DExtensionHermiteBasis/CMakeLists.txt | 50 +++++++++++++++++++ .../3DExtensionLagrangeBasis/CMakeLists.txt | 50 +++++++++++++++++++ .../Analytic/CantileverBeam/CMakeLists.txt | 50 +++++++++++++++++++ .../Analytic/Extension/CMakeLists.txt | 50 +++++++++++++++++++ LinearElasticity/CMakeLists.txt | 35 +++++++++++++ 6 files changed, 285 insertions(+) create mode 100644 LinearElasticity/2DExtensionPlaneStressLagrangeBasis/CMakeLists.txt create mode 100644 LinearElasticity/3DExtensionHermiteBasis/CMakeLists.txt create mode 100644 LinearElasticity/3DExtensionLagrangeBasis/CMakeLists.txt create mode 100644 LinearElasticity/Analytic/CantileverBeam/CMakeLists.txt create mode 100644 LinearElasticity/Analytic/Extension/CMakeLists.txt create mode 100644 LinearElasticity/CMakeLists.txt diff --git a/LinearElasticity/2DExtensionPlaneStressLagrangeBasis/CMakeLists.txt b/LinearElasticity/2DExtensionPlaneStressLagrangeBasis/CMakeLists.txt new file mode 100644 index 00000000..1ae83d19 --- /dev/null +++ b/LinearElasticity/2DExtensionPlaneStressLagrangeBasis/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(stress_plane_2d.x src/2DExtensionPlaneStressLagrangeBasisExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(stress_plane_2d.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(stress_plane_2d.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME PlaneStress COMMAND stress_plane_2d.x) +add_opencmiss_environment(PlaneStress) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/LinearElasticity/3DExtensionHermiteBasis/CMakeLists.txt b/LinearElasticity/3DExtensionHermiteBasis/CMakeLists.txt new file mode 100644 index 00000000..669377a7 --- /dev/null +++ b/LinearElasticity/3DExtensionHermiteBasis/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(hermite_3d src/3DExtensionHermiteBasisExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(hermite_3d PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(hermite_3d PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME PlaneStress COMMAND hermite_3d) +add_opencmiss_environment(PlaneStress) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/LinearElasticity/3DExtensionLagrangeBasis/CMakeLists.txt b/LinearElasticity/3DExtensionLagrangeBasis/CMakeLists.txt new file mode 100644 index 00000000..6794f8c3 --- /dev/null +++ b/LinearElasticity/3DExtensionLagrangeBasis/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(lagrange_3d.x src/3DExtensionLagrangeBasisExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(lagrange_3d.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(lagrange_3d.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME PlaneStress COMMAND lagrange_3d.x) +add_opencmiss_environment(PlaneStress) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/LinearElasticity/Analytic/CantileverBeam/CMakeLists.txt b/LinearElasticity/Analytic/CantileverBeam/CMakeLists.txt new file mode 100644 index 00000000..531c72ad --- /dev/null +++ b/LinearElasticity/Analytic/CantileverBeam/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cantilever.x src/CantileverBeamExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cantilever.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cantilever.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME AnalyticStress COMMAND cantilever.x) +add_opencmiss_environment(AnalyticStress) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/LinearElasticity/Analytic/Extension/CMakeLists.txt b/LinearElasticity/Analytic/Extension/CMakeLists.txt new file mode 100644 index 00000000..fdec146b --- /dev/null +++ b/LinearElasticity/Analytic/Extension/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(extension.x src/ExtensionExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(extension.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(extension.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME AnalyticStress COMMAND extension.x) +add_opencmiss_environment(AnalyticStress) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/LinearElasticity/CMakeLists.txt b/LinearElasticity/CMakeLists.txt new file mode 100644 index 00000000..17b5fbdb --- /dev/null +++ b/LinearElasticity/CMakeLists.txt @@ -0,0 +1,35 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(2DExtensionPlaneStressLagrangeBasis) + add_subdirectory(3DExtensionHermiteBasis) + add_subdirectory(3DExtensionLagrangeBasis) +endif() From 17b4fc891192870d48b79c407836d88f16378369 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 17 Oct 2016 16:45:42 +1300 Subject: [PATCH 18/28] Added CMake support for DataAssimilation, TwoRegions, define-geometry and simple-field-manipulation examples --- DataAssimilation/CMakeLists.txt | 35 +++++++++++++++ .../CMakeLists.txt | 24 +++++++++++ .../CMakeLists.txt | 24 +++++++++++ .../CMakeLists.txt | 11 +++++ TwoRegions/CMakeLists.txt | 43 +++++++++++++++++++ define-geometry-and-export/CMakeLists.txt | 43 +++++++++++++++++++ .../CMakeLists.txt | 43 +++++++++++++++++++ 7 files changed, 223 insertions(+) create mode 100644 DataAssimilation/CMakeLists.txt create mode 100644 DataAssimilation/DataAssimilationConstantSystem/CMakeLists.txt create mode 100644 DataAssimilation/DataAssimilationInflationGuccione/CMakeLists.txt create mode 100644 DataAssimilation/DataAssimilationUniExtension/CMakeLists.txt create mode 100644 TwoRegions/CMakeLists.txt create mode 100644 define-geometry-and-export/CMakeLists.txt create mode 100644 simple-field-manipulation-direct-access/CMakeLists.txt diff --git a/DataAssimilation/CMakeLists.txt b/DataAssimilation/CMakeLists.txt new file mode 100644 index 00000000..e030fd83 --- /dev/null +++ b/DataAssimilation/CMakeLists.txt @@ -0,0 +1,35 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES CXX) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(DataAssimilationConstantSystem) + add_subdirectory(DataAssimilationInflationGuccione) + add_subdirectory(DataAssimilationUniExtension) +endif() diff --git a/DataAssimilation/DataAssimilationConstantSystem/CMakeLists.txt b/DataAssimilation/DataAssimilationConstantSystem/CMakeLists.txt new file mode 100644 index 00000000..1fd5bc34 --- /dev/null +++ b/DataAssimilation/DataAssimilationConstantSystem/CMakeLists.txt @@ -0,0 +1,24 @@ +# Add example executable +add_executable(data_assim_constant.x src/data_assimilation_test01.cpp) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(data_assim_constant.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME DataAssimilation COMMAND data_assim_constant.x) +add_opencmiss_environment(DataAssimilation) + diff --git a/DataAssimilation/DataAssimilationInflationGuccione/CMakeLists.txt b/DataAssimilation/DataAssimilationInflationGuccione/CMakeLists.txt new file mode 100644 index 00000000..8062d136 --- /dev/null +++ b/DataAssimilation/DataAssimilationInflationGuccione/CMakeLists.txt @@ -0,0 +1,24 @@ +# Add example executable +add_executable(data_assim_inflate.x src/DataAssimilationInflationGuccioneExample.f90) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(data_assim_inflate.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME DataAssimilation COMMAND data_assim_inflate.x) +add_opencmiss_environment(DataAssimilation) + diff --git a/DataAssimilation/DataAssimilationUniExtension/CMakeLists.txt b/DataAssimilation/DataAssimilationUniExtension/CMakeLists.txt new file mode 100644 index 00000000..babfdb91 --- /dev/null +++ b/DataAssimilation/DataAssimilationUniExtension/CMakeLists.txt @@ -0,0 +1,11 @@ +# Add example executable +add_executable(data_assim_uni1.x src/data_assimilation_uniextension.cpp) +target_link_libraries(data_assim_uni1.x PRIVATE opencmiss) + +# Add example executable +add_executable(data_assim_uni2.x src/data_assimilation_uniextension_OpenCMISS_test.cpp) +target_link_libraries(data_assim_uni2.x PRIVATE opencmiss) + +# Add example executable +add_executable(data_assim_uni3.x src/UniAxialExtensionExample.f90) +target_link_libraries(data_assim_uni3.x PRIVATE opencmiss) diff --git a/TwoRegions/CMakeLists.txt b/TwoRegions/CMakeLists.txt new file mode 100644 index 00000000..fba61140 --- /dev/null +++ b/TwoRegions/CMakeLists.txt @@ -0,0 +1,43 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +add_executable(two_regions.x src/TwoRegionsExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() + +target_compile_options(two_regions.x PRIVATE ${PROC_OPT}) +target_link_libraries(two_regions.x PRIVATE opencmiss) +add_test(NAME TwoRegion COMMAND two_regions.x) +add_opencmiss_environment(TwoRegion) diff --git a/define-geometry-and-export/CMakeLists.txt b/define-geometry-and-export/CMakeLists.txt new file mode 100644 index 00000000..cd052b20 --- /dev/null +++ b/define-geometry-and-export/CMakeLists.txt @@ -0,0 +1,43 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +add_executable(define.x src/define-geometry-and-exportExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() + +target_compile_options(define.x PRIVATE ${PROC_OPT}) +target_link_libraries(define.x PRIVATE opencmiss) +add_test(NAME DefineGeometry COMMAND define.x) +add_opencmiss_environment(DefineGeometry) diff --git a/simple-field-manipulation-direct-access/CMakeLists.txt b/simple-field-manipulation-direct-access/CMakeLists.txt new file mode 100644 index 00000000..bc14d3fc --- /dev/null +++ b/simple-field-manipulation-direct-access/CMakeLists.txt @@ -0,0 +1,43 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +add_executable(simple_field.x src/simple-field-manipulation-direct-accessExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() + +target_compile_options(simple_field.x PRIVATE ${PROC_OPT}) +target_link_libraries(simple_field.x PRIVATE opencmiss) +add_test(NAME SimpleFieldManipulation COMMAND simple_field.x) +add_opencmiss_environment(SimpleFieldManipulation) From ef8e7ccf993210af85df2d2fce74e0334e8080e0 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Tue, 18 Oct 2016 11:06:34 +1300 Subject: [PATCH 19/28] Added CMake support for the FiniteElasticity examples --- .../ActiveContraction/CMakeLists.txt | 50 +++++++++++++ FiniteElasticity/ActiveContraction/Makefile | 70 ------------------ FiniteElasticity/CMakeLists.txt | 57 +++++++++++++++ .../Cantilever/Fortran/CMakeLists.txt | 50 +++++++++++++ FiniteElasticity/Cantilever/Fortran/Makefile | 70 ------------------ .../Cantilever/Python/CantileverExample.py | 6 +- .../CantileverGrowthExample.py | 7 +- .../CellMLGrowthLaw/CellMLGrowthExample.py | 7 +- FiniteElasticity/CuboidGeneric/CMakeLists.txt | 50 +++++++++++++ FiniteElasticity/CuboidGeneric/Makefile | 70 ------------------ .../CylinderInflation/CMakeLists.txt | 50 +++++++++++++ FiniteElasticity/CylinderInflation/Makefile | 70 ------------------ .../DofConstraints/DofConstraintsExample.py | 8 ++- .../HermiteProlateSpheroidExample.py | 8 ++- .../prolate_spheroid_geometry.py | 2 +- .../HomogeneousPipeAxialExtension.py | 8 ++- .../LVContraction/Python/LVContraction.py | 4 +- FiniteElasticity/LVContraction/Python/lib.py | 2 +- .../LVInflation/Python/LVInflation.py | 4 +- FiniteElasticity/LVInflation/Python/lib.py | 2 +- .../Fortran/CMakeLists.txt | 50 +++++++++++++ .../LargeUniAxialExtension/Fortran/Makefile | 70 ------------------ .../Python/LargeUniAxialExtensionExample.py | 7 +- .../MeasureStrain/MeasureStrainExample.py | 8 ++- .../MembraneExtension2DSpace/CMakeLists.txt | 50 +++++++++++++ .../MembraneExtension2DSpace/Makefile | 70 ------------------ .../CMakeLists.txt | 50 +++++++++++++ .../MembraneExtension3DSpaceFlat/Makefile | 72 ------------------- .../CMakeLists.txt | 50 +++++++++++++ .../MembraneExtension3DSpaceTilted/Makefile | 72 ------------------- .../MixedBoundaryConditions/CMakeLists.txt | 50 +++++++++++++ .../MixedBoundaryConditions/Makefile | 70 ------------------ .../MooneyRivlinInCellML/CMakeLists.txt | 50 +++++++++++++ .../MooneyRivlinInCellML/Makefile | 70 ------------------ .../QuadraticEllipsoid/CMakeLists.txt | 50 +++++++++++++ FiniteElasticity/QuadraticEllipsoid/Makefile | 70 ------------------ .../QuadraticEllipsoidCosta/CMakeLists.txt | 50 +++++++++++++ .../QuadraticEllipsoidCosta/Makefile | 71 ------------------ .../CMakeLists.txt | 50 +++++++++++++ .../QuadraticEllipsoidCostaReadIn/Makefile | 70 ------------------ .../RightBiceps/Fortran/CMakeLists.txt | 50 +++++++++++++ FiniteElasticity/RightBiceps/Fortran/Makefile | 70 ------------------ .../SimpleShear/Fortran/CMakeLists.txt | 22 ++++++ FiniteElasticity/SimpleShear/Fortran/Makefile | 70 ------------------ .../LargeQuadraticTet/CMakeLists.txt | 50 +++++++++++++ .../LargeQuadraticTet/Makefile | 70 ------------------ .../SimplexElements/LinearTet/CMakeLists.txt | 50 +++++++++++++ .../SimplexElements/LinearTet/Makefile | 70 ------------------ .../QuadraticTet/CMakeLists.txt | 50 +++++++++++++ .../SimplexElements/QuadraticTet/Makefile | 70 ------------------ .../TriCubicAxialExtension/CMakeLists.txt | 50 +++++++++++++ .../TriCubicAxialExtension/Makefile | 70 ------------------ .../TriQuadraticCube/CMakeLists.txt | 50 +++++++++++++ FiniteElasticity/TriQuadraticCube/Makefile | 70 ------------------ .../UniAxialExtension/Fortran/CMakeLists.txt | 50 +++++++++++++ .../UniAxialExtension/Fortran/Makefile | 70 ------------------ .../Python/UniAxialExtensionExample.py | 6 +- .../CMakeLists.txt | 50 +++++++++++++ .../UniAxialExtensionCompressible/Makefile | 70 ------------------ .../CMakeLists.txt | 51 +++++++++++++ .../UniAxialExtensionLoadIncrements/Makefile | 70 ------------------ .../CMakeLists.txt | 50 +++++++++++++ .../UniAxialExtensionOrthotropic/Makefile | 70 ------------------ FiniteElasticity/testingPoints/CMakeLists.txt | 50 +++++++++++++ FiniteElasticity/testingPoints/Makefile | 70 ------------------ 65 files changed, 1335 insertions(+), 1779 deletions(-) create mode 100644 FiniteElasticity/ActiveContraction/CMakeLists.txt delete mode 100644 FiniteElasticity/ActiveContraction/Makefile create mode 100644 FiniteElasticity/CMakeLists.txt create mode 100644 FiniteElasticity/Cantilever/Fortran/CMakeLists.txt delete mode 100644 FiniteElasticity/Cantilever/Fortran/Makefile create mode 100644 FiniteElasticity/CuboidGeneric/CMakeLists.txt delete mode 100644 FiniteElasticity/CuboidGeneric/Makefile create mode 100644 FiniteElasticity/CylinderInflation/CMakeLists.txt delete mode 100644 FiniteElasticity/CylinderInflation/Makefile create mode 100644 FiniteElasticity/LargeUniAxialExtension/Fortran/CMakeLists.txt delete mode 100644 FiniteElasticity/LargeUniAxialExtension/Fortran/Makefile create mode 100644 FiniteElasticity/Membrane/MembraneExtension2DSpace/CMakeLists.txt delete mode 100644 FiniteElasticity/Membrane/MembraneExtension2DSpace/Makefile create mode 100644 FiniteElasticity/Membrane/MembraneExtension3DSpaceFlat/CMakeLists.txt delete mode 100644 FiniteElasticity/Membrane/MembraneExtension3DSpaceFlat/Makefile create mode 100644 FiniteElasticity/Membrane/MembraneExtension3DSpaceTilted/CMakeLists.txt delete mode 100644 FiniteElasticity/Membrane/MembraneExtension3DSpaceTilted/Makefile create mode 100644 FiniteElasticity/MixedBoundaryConditions/CMakeLists.txt delete mode 100644 FiniteElasticity/MixedBoundaryConditions/Makefile create mode 100644 FiniteElasticity/MooneyRivlinInCellML/CMakeLists.txt delete mode 100644 FiniteElasticity/MooneyRivlinInCellML/Makefile create mode 100644 FiniteElasticity/QuadraticEllipsoid/CMakeLists.txt delete mode 100644 FiniteElasticity/QuadraticEllipsoid/Makefile create mode 100644 FiniteElasticity/QuadraticEllipsoidCosta/CMakeLists.txt delete mode 100644 FiniteElasticity/QuadraticEllipsoidCosta/Makefile create mode 100644 FiniteElasticity/QuadraticEllipsoidCostaReadIn/CMakeLists.txt delete mode 100644 FiniteElasticity/QuadraticEllipsoidCostaReadIn/Makefile create mode 100644 FiniteElasticity/RightBiceps/Fortran/CMakeLists.txt delete mode 100644 FiniteElasticity/RightBiceps/Fortran/Makefile create mode 100644 FiniteElasticity/SimpleShear/Fortran/CMakeLists.txt delete mode 100644 FiniteElasticity/SimpleShear/Fortran/Makefile create mode 100644 FiniteElasticity/SimplexElements/LargeQuadraticTet/CMakeLists.txt delete mode 100644 FiniteElasticity/SimplexElements/LargeQuadraticTet/Makefile create mode 100644 FiniteElasticity/SimplexElements/LinearTet/CMakeLists.txt delete mode 100644 FiniteElasticity/SimplexElements/LinearTet/Makefile create mode 100644 FiniteElasticity/SimplexElements/QuadraticTet/CMakeLists.txt delete mode 100644 FiniteElasticity/SimplexElements/QuadraticTet/Makefile create mode 100644 FiniteElasticity/TriCubicAxialExtension/CMakeLists.txt delete mode 100644 FiniteElasticity/TriCubicAxialExtension/Makefile create mode 100644 FiniteElasticity/TriQuadraticCube/CMakeLists.txt delete mode 100644 FiniteElasticity/TriQuadraticCube/Makefile create mode 100644 FiniteElasticity/UniAxialExtension/Fortran/CMakeLists.txt delete mode 100644 FiniteElasticity/UniAxialExtension/Fortran/Makefile create mode 100644 FiniteElasticity/UniAxialExtensionCompressible/CMakeLists.txt delete mode 100644 FiniteElasticity/UniAxialExtensionCompressible/Makefile create mode 100644 FiniteElasticity/UniAxialExtensionLoadIncrements/CMakeLists.txt delete mode 100644 FiniteElasticity/UniAxialExtensionLoadIncrements/Makefile create mode 100644 FiniteElasticity/UniAxialExtensionOrthotropic/CMakeLists.txt delete mode 100644 FiniteElasticity/UniAxialExtensionOrthotropic/Makefile create mode 100644 FiniteElasticity/testingPoints/CMakeLists.txt delete mode 100644 FiniteElasticity/testingPoints/Makefile diff --git a/FiniteElasticity/ActiveContraction/CMakeLists.txt b/FiniteElasticity/ActiveContraction/CMakeLists.txt new file mode 100644 index 00000000..b1cf8368 --- /dev/null +++ b/FiniteElasticity/ActiveContraction/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(active.x src/ActiveContractionExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(active.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(active.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME ActiveContraction COMMAND active.x) +add_opencmiss_environment(ActiveContraction) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/ActiveContraction/Makefile b/FiniteElasticity/ActiveContraction/Makefile deleted file mode 100644 index ba3a57ed..00000000 --- a/FiniteElasticity/ActiveContraction/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = ActiveContraction - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/CMakeLists.txt b/FiniteElasticity/CMakeLists.txt new file mode 100644 index 00000000..9d2a51c1 --- /dev/null +++ b/FiniteElasticity/CMakeLists.txt @@ -0,0 +1,57 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(ActiveContraction) + add_subdirectory(Cantilever/Fortran) + add_subdirectory(CuboidGeneric) + add_subdirectory(CylinderInflation) + add_subdirectory(LargeUniAxialExtension/Fortran) + add_subdirectory(Membrane/MembraneExtension2DSpace) + add_subdirectory(Membrane/MembraneExtension3DSpaceFlat) + add_subdirectory(Membrane/MembraneExtension3DSpaceTilted) + add_subdirectory(MixedBoundaryConditions) + add_subdirectory(MooneyRivlinInCellML) + add_subdirectory(QuadraticEllipsoid) + add_subdirectory(QuadraticEllipsoidCosta) + add_subdirectory(QuadraticEllipsoidCostaReadIn) + add_subdirectory(RightBiceps/Fortran) + add_subdirectory(SimpleShear/Fortran) + add_subdirectory(SimplexElements/LargeQuadraticTet) + add_subdirectory(SimplexElements/LinearTet) + add_subdirectory(SimplexElements/QuadraticTet) + add_subdirectory(testingPoints) + add_subdirectory(TriCubicAxialExtension) + add_subdirectory(TriQuadraticCube) + add_subdirectory(UniAxialExtension/Fortran) + add_subdirectory(UniAxialExtensionCompressible) + add_subdirectory(UniAxialExtensionLoadIncrements) + add_subdirectory(UniAxialExtensionOrthotropic) +endif() diff --git a/FiniteElasticity/Cantilever/Fortran/CMakeLists.txt b/FiniteElasticity/Cantilever/Fortran/CMakeLists.txt new file mode 100644 index 00000000..3c812b03 --- /dev/null +++ b/FiniteElasticity/Cantilever/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cantilever.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cantilever.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cantilever.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Cantilever COMMAND cantilever.x) +add_opencmiss_environment(Cantilever) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/Cantilever/Fortran/Makefile b/FiniteElasticity/Cantilever/Fortran/Makefile deleted file mode 100644 index 4e59e10b..00000000 --- a/FiniteElasticity/Cantilever/Fortran/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/Cantilever/ - -EXAMPLE_NAME = Fortran - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/Cantilever/Python/CantileverExample.py b/FiniteElasticity/Cantilever/Python/CantileverExample.py index 7bd58056..6ba29394 100755 --- a/FiniteElasticity/Cantilever/Python/CantileverExample.py +++ b/FiniteElasticity/Cantilever/Python/CantileverExample.py @@ -52,10 +52,12 @@ # Add Python bindings directory to PATH import sys, os -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) # Intialise OpenCMISS-Iron -from opencmiss import iron +from opencmiss.iron import iron # Set problem parameters diff --git a/FiniteElasticity/CantileverGrowth/CantileverGrowthExample.py b/FiniteElasticity/CantileverGrowth/CantileverGrowthExample.py index 82bdfb35..e0cefb81 100644 --- a/FiniteElasticity/CantileverGrowth/CantileverGrowthExample.py +++ b/FiniteElasticity/CantileverGrowth/CantileverGrowthExample.py @@ -44,11 +44,12 @@ #> Main script # Add Python bindings directory to PATH import sys, os - -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron # Set the physical size of the cantilever length = 5.0 diff --git a/FiniteElasticity/CellMLGrowthLaw/CellMLGrowthExample.py b/FiniteElasticity/CellMLGrowthLaw/CellMLGrowthExample.py index 0819ffd2..48043181 100644 --- a/FiniteElasticity/CellMLGrowthLaw/CellMLGrowthExample.py +++ b/FiniteElasticity/CellMLGrowthLaw/CellMLGrowthExample.py @@ -44,11 +44,12 @@ #> Main script # Add Python bindings directory to PATH import sys, os - -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron # Set problem parameters height = 1.0 diff --git a/FiniteElasticity/CuboidGeneric/CMakeLists.txt b/FiniteElasticity/CuboidGeneric/CMakeLists.txt new file mode 100644 index 00000000..d36f5943 --- /dev/null +++ b/FiniteElasticity/CuboidGeneric/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cuboid.x src/CuboidGenericExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cuboid.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cuboid.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME CuboidGeneric COMMAND cuboid.x) +add_opencmiss_environment(CuboidGeneric) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/CuboidGeneric/Makefile b/FiniteElasticity/CuboidGeneric/Makefile deleted file mode 100644 index 8946c818..00000000 --- a/FiniteElasticity/CuboidGeneric/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = CuboidGeneric - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/CylinderInflation/CMakeLists.txt b/FiniteElasticity/CylinderInflation/CMakeLists.txt new file mode 100644 index 00000000..3c9db959 --- /dev/null +++ b/FiniteElasticity/CylinderInflation/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cylinder.x src/CylinderInflationExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cylinder.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cylinder.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME CylinderInflation COMMAND cylinder.x) +add_opencmiss_environment(CylinderInflation) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/CylinderInflation/Makefile b/FiniteElasticity/CylinderInflation/Makefile deleted file mode 100644 index 41348e2a..00000000 --- a/FiniteElasticity/CylinderInflation/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = CylinderInflation - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/DofConstraints/DofConstraintsExample.py b/FiniteElasticity/DofConstraints/DofConstraintsExample.py index c6e92e00..93e52fbf 100755 --- a/FiniteElasticity/DofConstraints/DofConstraintsExample.py +++ b/FiniteElasticity/DofConstraints/DofConstraintsExample.py @@ -47,7 +47,13 @@ ## constrained so that the end remains oriented in the y-z plane. #< -from opencmiss import iron +# Add Python bindings directory to PATH +import sys, os +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) + +from opencmiss.iron import iron # Problem parameters: density = 9.0e-4 # in g mm^-3 diff --git a/FiniteElasticity/HermiteProlateSpheroid/HermiteProlateSpheroidExample.py b/FiniteElasticity/HermiteProlateSpheroid/HermiteProlateSpheroidExample.py index fbc631ee..933a2404 100755 --- a/FiniteElasticity/HermiteProlateSpheroid/HermiteProlateSpheroidExample.py +++ b/FiniteElasticity/HermiteProlateSpheroid/HermiteProlateSpheroidExample.py @@ -48,8 +48,14 @@ ## \li Linux GNU Build #< +# Add Python bindings directory to PATH +import sys, os +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) + from numpy import pi -from opencmiss import iron +from opencmiss.iron import iron import prolate_spheroid_geometry diff --git a/FiniteElasticity/HermiteProlateSpheroid/prolate_spheroid_geometry.py b/FiniteElasticity/HermiteProlateSpheroid/prolate_spheroid_geometry.py index cd99e857..af62c281 100644 --- a/FiniteElasticity/HermiteProlateSpheroid/prolate_spheroid_geometry.py +++ b/FiniteElasticity/HermiteProlateSpheroid/prolate_spheroid_geometry.py @@ -9,7 +9,7 @@ import numpy as np from numpy import pi, sin, cos, sinh, cosh -from opencmiss import iron +from opencmiss.iron import iron class ProlateSpheroid(object): diff --git a/FiniteElasticity/HomogeneousPipeAxialExtension/HomogeneousPipeAxialExtension.py b/FiniteElasticity/HomogeneousPipeAxialExtension/HomogeneousPipeAxialExtension.py index ee6510a7..c6d2e001 100755 --- a/FiniteElasticity/HomogeneousPipeAxialExtension/HomogeneousPipeAxialExtension.py +++ b/FiniteElasticity/HomogeneousPipeAxialExtension/HomogeneousPipeAxialExtension.py @@ -1,9 +1,11 @@ #!/usr/bin/env python #DOC-START imports +# Add Python bindings directory to PATH import sys, os, exfile -# Make sure $OPENCMISS_ROOT/cm/bindings/python is first in our PYTHONPATH. -sys.path.insert(1, os.path.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) #DOC-END imports #DOC-START load exfile @@ -18,7 +20,7 @@ numberOfXi = 3 # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron # Set problem parameters #Use pressure to enforce incompressibililty constraint diff --git a/FiniteElasticity/LVContraction/Python/LVContraction.py b/FiniteElasticity/LVContraction/Python/LVContraction.py index 1dbc169d..04821860 100644 --- a/FiniteElasticity/LVContraction/Python/LVContraction.py +++ b/FiniteElasticity/LVContraction/Python/LVContraction.py @@ -67,7 +67,9 @@ import math from collections import OrderedDict -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'], 'cm', 'bindings', 'python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) # Initialise OpenCMISS from lib import * diff --git a/FiniteElasticity/LVContraction/Python/lib.py b/FiniteElasticity/LVContraction/Python/lib.py index 3520f170..373fe9a8 100644 --- a/FiniteElasticity/LVContraction/Python/lib.py +++ b/FiniteElasticity/LVContraction/Python/lib.py @@ -12,7 +12,7 @@ # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++# -from opencmiss import iron +from opencmiss.iron import iron import numpy import math # =================================================================================# diff --git a/FiniteElasticity/LVInflation/Python/LVInflation.py b/FiniteElasticity/LVInflation/Python/LVInflation.py index 49eef074..04cee0ce 100644 --- a/FiniteElasticity/LVInflation/Python/LVInflation.py +++ b/FiniteElasticity/LVInflation/Python/LVInflation.py @@ -67,7 +67,9 @@ import math from collections import OrderedDict -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'], 'cm', 'bindings', 'python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) # Initialise OpenCMISS from lib import * diff --git a/FiniteElasticity/LVInflation/Python/lib.py b/FiniteElasticity/LVInflation/Python/lib.py index 9c56bbf1..2bcca634 100644 --- a/FiniteElasticity/LVInflation/Python/lib.py +++ b/FiniteElasticity/LVInflation/Python/lib.py @@ -12,7 +12,7 @@ # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++# -from opencmiss import iron +from opencmiss.iron import iron import numpy import math diff --git a/FiniteElasticity/LargeUniAxialExtension/Fortran/CMakeLists.txt b/FiniteElasticity/LargeUniAxialExtension/Fortran/CMakeLists.txt new file mode 100644 index 00000000..4584184c --- /dev/null +++ b/FiniteElasticity/LargeUniAxialExtension/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(large_uni_axial.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(large_uni_axial.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(large_uni_axial.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME LargeUniAxial COMMAND large_uni_axial.x) +add_opencmiss_environment(LargeUniAxial) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/LargeUniAxialExtension/Fortran/Makefile b/FiniteElasticity/LargeUniAxialExtension/Fortran/Makefile deleted file mode 100644 index af313c75..00000000 --- a/FiniteElasticity/LargeUniAxialExtension/Fortran/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/LargeUniAxialExtension/ - -EXAMPLE_NAME = Fortran - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/LargeUniAxialExtension/Python/LargeUniAxialExtensionExample.py b/FiniteElasticity/LargeUniAxialExtension/Python/LargeUniAxialExtensionExample.py index e9df8268..802cf057 100755 --- a/FiniteElasticity/LargeUniAxialExtension/Python/LargeUniAxialExtensionExample.py +++ b/FiniteElasticity/LargeUniAxialExtension/Python/LargeUniAxialExtensionExample.py @@ -51,11 +51,12 @@ #> Main script # Add Python bindings directory to PATH import sys, os - -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) # Intialise OpenCMISS-Iron -from opencmiss import iron +from opencmiss.iron import iron # Set problem parameters height = 1.0 diff --git a/FiniteElasticity/MeasureStrain/MeasureStrainExample.py b/FiniteElasticity/MeasureStrain/MeasureStrainExample.py index 4df635f0..df196ae1 100755 --- a/FiniteElasticity/MeasureStrain/MeasureStrainExample.py +++ b/FiniteElasticity/MeasureStrain/MeasureStrainExample.py @@ -49,7 +49,13 @@ from __future__ import print_function import numpy as np -from opencmiss import iron +import sys, os + +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) + +from opencmiss.iron import iron # Problem parameters: diff --git a/FiniteElasticity/Membrane/MembraneExtension2DSpace/CMakeLists.txt b/FiniteElasticity/Membrane/MembraneExtension2DSpace/CMakeLists.txt new file mode 100644 index 00000000..89f10f7b --- /dev/null +++ b/FiniteElasticity/Membrane/MembraneExtension2DSpace/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(membrane.x src/MembraneExtension2DSpaceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(membrane.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(membrane.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MembraneExtension COMMAND membrane.x) +add_opencmiss_environment(MembraneExtension) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/Membrane/MembraneExtension2DSpace/Makefile b/FiniteElasticity/Membrane/MembraneExtension2DSpace/Makefile deleted file mode 100644 index d33c76fc..00000000 --- a/FiniteElasticity/Membrane/MembraneExtension2DSpace/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/Membrane/ - -EXAMPLE_NAME = MembraneExtension2DSpace - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/Membrane/MembraneExtension3DSpaceFlat/CMakeLists.txt b/FiniteElasticity/Membrane/MembraneExtension3DSpaceFlat/CMakeLists.txt new file mode 100644 index 00000000..404d1c56 --- /dev/null +++ b/FiniteElasticity/Membrane/MembraneExtension3DSpaceFlat/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(membrane_3d_flat.x src/MembraneExtension3DSpaceFlatExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(membrane_3d_flat.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(membrane_3d_flat.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MembraneExtension COMMAND membrane_3d_flat.x) +add_opencmiss_environment(MembraneExtension) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/Membrane/MembraneExtension3DSpaceFlat/Makefile b/FiniteElasticity/Membrane/MembraneExtension3DSpaceFlat/Makefile deleted file mode 100644 index 790e11e5..00000000 --- a/FiniteElasticity/Membrane/MembraneExtension3DSpaceFlat/Makefile +++ /dev/null @@ -1,72 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/Membrane/ - -EXAMPLE_NAME = MembraneExtension3DSpaceFlat - -include $(GLOBAL_ROOT)/ExampleMakefile - - - diff --git a/FiniteElasticity/Membrane/MembraneExtension3DSpaceTilted/CMakeLists.txt b/FiniteElasticity/Membrane/MembraneExtension3DSpaceTilted/CMakeLists.txt new file mode 100644 index 00000000..77acd345 --- /dev/null +++ b/FiniteElasticity/Membrane/MembraneExtension3DSpaceTilted/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(membrane_3d_tilted.x src/MembraneExtension3DSpaceTiltedExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(membrane_3d_tilted.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(membrane_3d_tilted.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MembraneExtension COMMAND membrane_3d_tilted.x) +add_opencmiss_environment(MembraneExtension) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/Membrane/MembraneExtension3DSpaceTilted/Makefile b/FiniteElasticity/Membrane/MembraneExtension3DSpaceTilted/Makefile deleted file mode 100644 index 5fedff69..00000000 --- a/FiniteElasticity/Membrane/MembraneExtension3DSpaceTilted/Makefile +++ /dev/null @@ -1,72 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/Membrane/ - -EXAMPLE_NAME = MembraneExtension3DSpaceTilted - -include $(GLOBAL_ROOT)/ExampleMakefile - - - diff --git a/FiniteElasticity/MixedBoundaryConditions/CMakeLists.txt b/FiniteElasticity/MixedBoundaryConditions/CMakeLists.txt new file mode 100644 index 00000000..5c374084 --- /dev/null +++ b/FiniteElasticity/MixedBoundaryConditions/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(mixed_BCs.x src/MixedBoundaryConditionsExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(mixed_BCs.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(mixed_BCs.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MixedBoundaryConditions COMMAND mixed_BCs.x) +add_opencmiss_environment(MixedBoundaryConditions) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/MixedBoundaryConditions/Makefile b/FiniteElasticity/MixedBoundaryConditions/Makefile deleted file mode 100644 index 570c0fc4..00000000 --- a/FiniteElasticity/MixedBoundaryConditions/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = MixedBoundaryConditions - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/MooneyRivlinInCellML/CMakeLists.txt b/FiniteElasticity/MooneyRivlinInCellML/CMakeLists.txt new file mode 100644 index 00000000..60104581 --- /dev/null +++ b/FiniteElasticity/MooneyRivlinInCellML/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(mooney.x src/MooneyRivlinInCellMLExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(mooney.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(mooney.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MooneyRivlin COMMAND mooney.x) +add_opencmiss_environment(MooneyRivlin) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/MooneyRivlinInCellML/Makefile b/FiniteElasticity/MooneyRivlinInCellML/Makefile deleted file mode 100644 index 68836e2c..00000000 --- a/FiniteElasticity/MooneyRivlinInCellML/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = MooneyRivlinInCellML - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/QuadraticEllipsoid/CMakeLists.txt b/FiniteElasticity/QuadraticEllipsoid/CMakeLists.txt new file mode 100644 index 00000000..22cf8c33 --- /dev/null +++ b/FiniteElasticity/QuadraticEllipsoid/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(quad_ellipsoid.x src/QuadraticEllipsoidExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(quad_ellipsoid.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(quad_ellipsoid.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME QuadraticEllipsoid COMMAND quad_ellipsoid.x) +add_opencmiss_environment(QuadraticEllipsoid) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/QuadraticEllipsoid/Makefile b/FiniteElasticity/QuadraticEllipsoid/Makefile deleted file mode 100644 index af0aabce..00000000 --- a/FiniteElasticity/QuadraticEllipsoid/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = QuadraticEllipsoid - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/QuadraticEllipsoidCosta/CMakeLists.txt b/FiniteElasticity/QuadraticEllipsoidCosta/CMakeLists.txt new file mode 100644 index 00000000..1765c654 --- /dev/null +++ b/FiniteElasticity/QuadraticEllipsoidCosta/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(quad_ellipsoid_costa.x src/QuadraticEllipsoidCostaExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(quad_ellipsoid_costa.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(quad_ellipsoid_costa.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME QuadraticEllipsoidCosta COMMAND quad_ellipsoid_costa.x) +add_opencmiss_environment(QuadraticEllipsoidCosta) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/QuadraticEllipsoidCosta/Makefile b/FiniteElasticity/QuadraticEllipsoidCosta/Makefile deleted file mode 100644 index 433ec5c8..00000000 --- a/FiniteElasticity/QuadraticEllipsoidCosta/Makefile +++ /dev/null @@ -1,71 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - - -EXAMPLE_NAME = QuadraticEllipsoidCosta - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/QuadraticEllipsoidCostaReadIn/CMakeLists.txt b/FiniteElasticity/QuadraticEllipsoidCostaReadIn/CMakeLists.txt new file mode 100644 index 00000000..1532e19e --- /dev/null +++ b/FiniteElasticity/QuadraticEllipsoidCostaReadIn/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(quad_ellipsoid_costa_readin.x src/QuadraticEllipsoidCostaReadInExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(quad_ellipsoid_costa_readin.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(quad_ellipsoid_costa_readin.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME QuadraticEllipsoidCostaReadIn COMMAND quad_ellipsoid_costa_readin.x) +add_opencmiss_environment(QuadraticEllipsoidCostaReadIn) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/QuadraticEllipsoidCostaReadIn/Makefile b/FiniteElasticity/QuadraticEllipsoidCostaReadIn/Makefile deleted file mode 100644 index 19034f39..00000000 --- a/FiniteElasticity/QuadraticEllipsoidCostaReadIn/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = QuadraticEllipsoidCostaReadIn - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/RightBiceps/Fortran/CMakeLists.txt b/FiniteElasticity/RightBiceps/Fortran/CMakeLists.txt new file mode 100644 index 00000000..f980e116 --- /dev/null +++ b/FiniteElasticity/RightBiceps/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(bicep.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(bicep.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(bicep.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME RightBicep COMMAND bicep.x) +add_opencmiss_environment(RightBicep) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/RightBiceps/Fortran/Makefile b/FiniteElasticity/RightBiceps/Fortran/Makefile deleted file mode 100644 index 11cf403c..00000000 --- a/FiniteElasticity/RightBiceps/Fortran/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/RightBiceps/ - -EXAMPLE_NAME = Fortran - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/SimpleShear/Fortran/CMakeLists.txt b/FiniteElasticity/SimpleShear/Fortran/CMakeLists.txt new file mode 100644 index 00000000..ceacf9a0 --- /dev/null +++ b/FiniteElasticity/SimpleShear/Fortran/CMakeLists.txt @@ -0,0 +1,22 @@ +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() + +# Add first example executable +add_executable(shear_ex1.x src/FortranExample.f90) +target_compile_options(shear_ex1.x PRIVATE ${PROC_OPT}) +target_link_libraries(shear_ex1.x PRIVATE opencmiss) + +# Add second example executable +add_executable(shear_ex2.x src/FortranExample_incomp.f90) +target_compile_options(shear_ex2.x PRIVATE ${PROC_OPT}) +target_link_libraries(shear_ex2.x PRIVATE opencmiss) + +# Add third example executable +add_executable(shear_ex3.x src/FortranExample_nearly.f90) +target_compile_options(shear_ex3.x PRIVATE ${PROC_OPT}) +target_link_libraries(shear_ex3.x PRIVATE opencmiss) + diff --git a/FiniteElasticity/SimpleShear/Fortran/Makefile b/FiniteElasticity/SimpleShear/Fortran/Makefile deleted file mode 100644 index a3fa653e..00000000 --- a/FiniteElasticity/SimpleShear/Fortran/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/SimpleShear/ - -EXAMPLE_NAME = Fortran - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/SimplexElements/LargeQuadraticTet/CMakeLists.txt b/FiniteElasticity/SimplexElements/LargeQuadraticTet/CMakeLists.txt new file mode 100644 index 00000000..1ad5e289 --- /dev/null +++ b/FiniteElasticity/SimplexElements/LargeQuadraticTet/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(large_quad_tet.x src/LargeQuadraticTetExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(large_quad_tet.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(large_quad_tet.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME LargeQuadraticTet COMMAND large_quad_tet.x) +add_opencmiss_environment(LargeQuadraticTet) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/SimplexElements/LargeQuadraticTet/Makefile b/FiniteElasticity/SimplexElements/LargeQuadraticTet/Makefile deleted file mode 100644 index b2049d30..00000000 --- a/FiniteElasticity/SimplexElements/LargeQuadraticTet/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/SimplexElements/ - -EXAMPLE_NAME = LargeQuadraticTet - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/SimplexElements/LinearTet/CMakeLists.txt b/FiniteElasticity/SimplexElements/LinearTet/CMakeLists.txt new file mode 100644 index 00000000..f48e150c --- /dev/null +++ b/FiniteElasticity/SimplexElements/LinearTet/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(linear_tet.x src/LinearTetExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(linear_tet.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(linear_tet.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME LinearTet COMMAND linear_tet.x) +add_opencmiss_environment(LinearTet) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/SimplexElements/LinearTet/Makefile b/FiniteElasticity/SimplexElements/LinearTet/Makefile deleted file mode 100644 index 7e007297..00000000 --- a/FiniteElasticity/SimplexElements/LinearTet/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/SimplexElements/ - -EXAMPLE_NAME = LinearTet - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/SimplexElements/QuadraticTet/CMakeLists.txt b/FiniteElasticity/SimplexElements/QuadraticTet/CMakeLists.txt new file mode 100644 index 00000000..74286349 --- /dev/null +++ b/FiniteElasticity/SimplexElements/QuadraticTet/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(quad_tet.x src/QuadraticTetExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(quad_tet.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(quad_tet.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME QuadraticTet COMMAND quad_tet.x) +add_opencmiss_environment(QuadraticTet) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/SimplexElements/QuadraticTet/Makefile b/FiniteElasticity/SimplexElements/QuadraticTet/Makefile deleted file mode 100644 index aa74abd2..00000000 --- a/FiniteElasticity/SimplexElements/QuadraticTet/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/SimplexElements/ - -EXAMPLE_NAME = QuadraticTet - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/TriCubicAxialExtension/CMakeLists.txt b/FiniteElasticity/TriCubicAxialExtension/CMakeLists.txt new file mode 100644 index 00000000..ed38adcc --- /dev/null +++ b/FiniteElasticity/TriCubicAxialExtension/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(tri_cubic_axial_ext.x src/TriCubicAxialExtensionExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(tri_cubic_axial_ext.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(tri_cubic_axial_ext.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME TriCubicAxialExtension COMMAND tri_cubic_axial_ext.x) +add_opencmiss_environment(TriCubicAxialExtension) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/TriCubicAxialExtension/Makefile b/FiniteElasticity/TriCubicAxialExtension/Makefile deleted file mode 100644 index 7f1e1bab..00000000 --- a/FiniteElasticity/TriCubicAxialExtension/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = TriCubicAxialExtension - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/TriQuadraticCube/CMakeLists.txt b/FiniteElasticity/TriQuadraticCube/CMakeLists.txt new file mode 100644 index 00000000..8a743113 --- /dev/null +++ b/FiniteElasticity/TriQuadraticCube/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(tri_quad_cube.x src/TriQuadraticCubeExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(tri_quad_cube.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(tri_quad_cube.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME TriQuadraticCube COMMAND tri_quad_cube.x) +add_opencmiss_environment(TriQuadraticCube) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/TriQuadraticCube/Makefile b/FiniteElasticity/TriQuadraticCube/Makefile deleted file mode 100644 index 50b9bae3..00000000 --- a/FiniteElasticity/TriQuadraticCube/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = TriQuadraticCube - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/UniAxialExtension/Fortran/CMakeLists.txt b/FiniteElasticity/UniAxialExtension/Fortran/CMakeLists.txt new file mode 100644 index 00000000..2f4b51be --- /dev/null +++ b/FiniteElasticity/UniAxialExtension/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(uni_axial_ext.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(uni_axial_ext.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(uni_axial_ext.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME UniAxialExtension COMMAND uni_axial_ext.x) +add_opencmiss_environment(UniAxialExtension) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/UniAxialExtension/Fortran/Makefile b/FiniteElasticity/UniAxialExtension/Fortran/Makefile deleted file mode 100644 index 1f6249a2..00000000 --- a/FiniteElasticity/UniAxialExtension/Fortran/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/UniAxialExtension/ - -EXAMPLE_NAME = Fortran - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/UniAxialExtension/Python/UniAxialExtensionExample.py b/FiniteElasticity/UniAxialExtension/Python/UniAxialExtensionExample.py index 7ad81f86..6f0dc109 100755 --- a/FiniteElasticity/UniAxialExtension/Python/UniAxialExtensionExample.py +++ b/FiniteElasticity/UniAxialExtension/Python/UniAxialExtensionExample.py @@ -52,10 +52,12 @@ # Add Python bindings directory to PATH import sys, os -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron # Set problem parameters height = 1.0 diff --git a/FiniteElasticity/UniAxialExtensionCompressible/CMakeLists.txt b/FiniteElasticity/UniAxialExtensionCompressible/CMakeLists.txt new file mode 100644 index 00000000..ddc83c42 --- /dev/null +++ b/FiniteElasticity/UniAxialExtensionCompressible/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(uni_axial_ext_compress.x src/UniAxialExtensionCompressibleExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(uni_axial_ext_compress.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(uni_axial_ext_compress.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME UniAxialExtensionCompressible COMMAND uni_axial_ext_compress.x) +add_opencmiss_environment(UniAxialExtensionCompressible) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/UniAxialExtensionCompressible/Makefile b/FiniteElasticity/UniAxialExtensionCompressible/Makefile deleted file mode 100644 index 80b89384..00000000 --- a/FiniteElasticity/UniAxialExtensionCompressible/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = UniAxialExtensionCompressible - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/UniAxialExtensionLoadIncrements/CMakeLists.txt b/FiniteElasticity/UniAxialExtensionLoadIncrements/CMakeLists.txt new file mode 100644 index 00000000..adb91985 --- /dev/null +++ b/FiniteElasticity/UniAxialExtensionLoadIncrements/CMakeLists.txt @@ -0,0 +1,51 @@ +# Add example executable +add_executable(uni_axial_ext_increments.x src/UniAxialExtensionLoadIncrementsExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(uni_axial_ext_increments.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(uni_axial_ext_increments.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME UniAxialExtensionLoadIncrements COMMAND uni_axial_ext_increments.x) +add_opencmiss_environment(UniAxialExtensionLoadIncrements) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# + diff --git a/FiniteElasticity/UniAxialExtensionLoadIncrements/Makefile b/FiniteElasticity/UniAxialExtensionLoadIncrements/Makefile deleted file mode 100644 index 690ebcd5..00000000 --- a/FiniteElasticity/UniAxialExtensionLoadIncrements/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = UniAxialExtensionLoadIncrements - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/UniAxialExtensionOrthotropic/CMakeLists.txt b/FiniteElasticity/UniAxialExtensionOrthotropic/CMakeLists.txt new file mode 100644 index 00000000..e56ba5f5 --- /dev/null +++ b/FiniteElasticity/UniAxialExtensionOrthotropic/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(uni_axial_ext_ortho.x src/UniAxialExtensionOrthotropicExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(uni_axial_ext_ortho.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(uni_axial_ext_ortho.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME UniAxialExtensionOrthotropic COMMAND uni_axial_ext_ortho.x) +add_opencmiss_environment(UniAxialExtensionOrthotropic) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/UniAxialExtensionOrthotropic/Makefile b/FiniteElasticity/UniAxialExtensionOrthotropic/Makefile deleted file mode 100644 index d49cd4a0..00000000 --- a/FiniteElasticity/UniAxialExtensionOrthotropic/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - -EXAMPLE_NAME = UniAxialExtensionOrthotropic - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FiniteElasticity/testingPoints/CMakeLists.txt b/FiniteElasticity/testingPoints/CMakeLists.txt new file mode 100644 index 00000000..fd2802f2 --- /dev/null +++ b/FiniteElasticity/testingPoints/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(testing_pts.x src/testingPointsExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(testing_pts.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(testing_pts.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME TestingPoints COMMAND testing_pts.x) +add_opencmiss_environment(TestingPoints) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FiniteElasticity/testingPoints/Makefile b/FiniteElasticity/testingPoints/Makefile deleted file mode 100644 index 64810586..00000000 --- a/FiniteElasticity/testingPoints/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = FiniteElasticity/ - - -EXAMPLE_NAME = testingPoints - -include $(GLOBAL_ROOT)/ExampleMakefile From dceaa69bea9f6c8c79b9214213da997e56121896 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Tue, 18 Oct 2016 11:13:50 +1300 Subject: [PATCH 20/28] modified Fitting example to use current OpenCMISS build structure --- Fitting/CubeToSphere/Python/GeometricFittingExample.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Fitting/CubeToSphere/Python/GeometricFittingExample.py b/Fitting/CubeToSphere/Python/GeometricFittingExample.py index d3443306..946f8ed8 100644 --- a/Fitting/CubeToSphere/Python/GeometricFittingExample.py +++ b/Fitting/CubeToSphere/Python/GeometricFittingExample.py @@ -48,7 +48,9 @@ # Add Python bindings directory to PATH import sys, os -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) import exfile import numpy @@ -57,7 +59,7 @@ import random # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron def writeExdataFile(filename,dataPointLocations,offset): "Writes data points to an exdata file" From a3255a165d213af924e385f4d333f065a3c575c5 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Tue, 18 Oct 2016 15:16:31 +1300 Subject: [PATCH 21/28] added CMake support for the Fluid Dynamics examples --- FluidMechanics/Burgers/Burgers/CMakeLists.txt | 50 +++++++++++++ FluidMechanics/Burgers/Burgers/Makefile | 70 ------------------- .../Burgers/GeneralisedBurgers/CMakeLists.txt | 50 +++++++++++++ .../Burgers/GeneralisedBurgers/Makefile | 70 ------------------- .../Burgers/StaticBurgers/CMakeLists.txt | 50 +++++++++++++ FluidMechanics/Burgers/StaticBurgers/Makefile | 70 ------------------- FluidMechanics/CMakeLists.txt | 36 ++++++++++ .../Python/1DTransientExample.py | 8 ++- .../NavierStokes/LidDrivenCavity/LidDriven.py | 8 +-- .../Matrices/NavierStokesMatrices.py | 8 ++- .../Womersley/WomersleyExample.py | 6 +- .../Womersley/womersleyAnalytic.py | 4 +- .../Poiseuille/Static/CMakeLists.txt | 50 +++++++++++++ FluidMechanics/Poiseuille/Static/Makefile | 70 ------------------- 14 files changed, 258 insertions(+), 292 deletions(-) create mode 100644 FluidMechanics/Burgers/Burgers/CMakeLists.txt delete mode 100755 FluidMechanics/Burgers/Burgers/Makefile create mode 100644 FluidMechanics/Burgers/GeneralisedBurgers/CMakeLists.txt delete mode 100755 FluidMechanics/Burgers/GeneralisedBurgers/Makefile create mode 100644 FluidMechanics/Burgers/StaticBurgers/CMakeLists.txt delete mode 100755 FluidMechanics/Burgers/StaticBurgers/Makefile create mode 100644 FluidMechanics/CMakeLists.txt create mode 100644 FluidMechanics/Poiseuille/Static/CMakeLists.txt delete mode 100644 FluidMechanics/Poiseuille/Static/Makefile diff --git a/FluidMechanics/Burgers/Burgers/CMakeLists.txt b/FluidMechanics/Burgers/Burgers/CMakeLists.txt new file mode 100644 index 00000000..527e6a21 --- /dev/null +++ b/FluidMechanics/Burgers/Burgers/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(burgers.x src/BurgersExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(burgers.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(burgers.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Burgers COMMAND burgers.x) +add_opencmiss_environment(Burgers) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FluidMechanics/Burgers/Burgers/Makefile b/FluidMechanics/Burgers/Burgers/Makefile deleted file mode 100755 index 21a4f410..00000000 --- a/FluidMechanics/Burgers/Burgers/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=FluidMechanics/Burgers/ - -EXAMPLE_NAME = Burgers - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FluidMechanics/Burgers/GeneralisedBurgers/CMakeLists.txt b/FluidMechanics/Burgers/GeneralisedBurgers/CMakeLists.txt new file mode 100644 index 00000000..3a9fa738 --- /dev/null +++ b/FluidMechanics/Burgers/GeneralisedBurgers/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(gen_burgers.x src/GeneralisedBurgersExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(gen_burgers.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(gen_burgers.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Burgers COMMAND gen_burgers.x) +add_opencmiss_environment(Burgers) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FluidMechanics/Burgers/GeneralisedBurgers/Makefile b/FluidMechanics/Burgers/GeneralisedBurgers/Makefile deleted file mode 100755 index dfbccca6..00000000 --- a/FluidMechanics/Burgers/GeneralisedBurgers/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=FluidMechanics/Burgers/ - -EXAMPLE_NAME = GeneralisedBurgers - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FluidMechanics/Burgers/StaticBurgers/CMakeLists.txt b/FluidMechanics/Burgers/StaticBurgers/CMakeLists.txt new file mode 100644 index 00000000..8a7ab40f --- /dev/null +++ b/FluidMechanics/Burgers/StaticBurgers/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(static_burgers.x src/StaticBurgersExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(static_burgers.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(static_burgers.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Burgers COMMAND static_burgers.x) +add_opencmiss_environment(Burgers) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FluidMechanics/Burgers/StaticBurgers/Makefile b/FluidMechanics/Burgers/StaticBurgers/Makefile deleted file mode 100755 index ef13bf10..00000000 --- a/FluidMechanics/Burgers/StaticBurgers/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=FluidMechanics/Burgers/ - -EXAMPLE_NAME = StaticBurgers - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/FluidMechanics/CMakeLists.txt b/FluidMechanics/CMakeLists.txt new file mode 100644 index 00000000..13e733f0 --- /dev/null +++ b/FluidMechanics/CMakeLists.txt @@ -0,0 +1,36 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(Burgers/Burgers) + add_subdirectory(Burgers/GeneralisedBurgers) + add_subdirectory(Burgers/StaticBurgers) + add_subdirectory(Poiseuille/Static) +endif() diff --git a/FluidMechanics/NavierStokes/Coupled1DCellML/Python/1DTransientExample.py b/FluidMechanics/NavierStokes/Coupled1DCellML/Python/1DTransientExample.py index 2b04ee64..69c19a26 100644 --- a/FluidMechanics/NavierStokes/Coupled1DCellML/Python/1DTransientExample.py +++ b/FluidMechanics/NavierStokes/Coupled1DCellML/Python/1DTransientExample.py @@ -112,8 +112,12 @@ from scipy.sparse import linalg from scipy.linalg import inv,eig from scipy.special import jn -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) -from opencmiss import iron + +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) + +from opencmiss.iron import iron # Diagnostics #iron.DiagnosticsSetOn(iron.DiagnosticTypes.ALL,[1,2,3,4,5],"Diagnostics",[""]) diff --git a/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py b/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py index a036d3f9..1323ccf1 100644 --- a/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py +++ b/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py @@ -49,10 +49,10 @@ # Add Python bindings directory to PATH import sys, os -sys.path.append(os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], - 'x86_64_linux/intel-C16.0-intel-F16.0/intel_release/release', - 'python', - 'RELEASE'))) + +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) import math import time diff --git a/FluidMechanics/NavierStokes/Matrices/NavierStokesMatrices.py b/FluidMechanics/NavierStokes/Matrices/NavierStokesMatrices.py index 90c45107..da0b130c 100755 --- a/FluidMechanics/NavierStokes/Matrices/NavierStokesMatrices.py +++ b/FluidMechanics/NavierStokes/Matrices/NavierStokesMatrices.py @@ -49,9 +49,11 @@ import os # Add OpenCMISS python bindings directory to path so we can import it -sys.path.append(os.sep.join(( - os.environ['OPENCMISS_ROOT'], 'cm', 'bindings', 'python'))) -from opencmiss import iron +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) + +from opencmiss.iron import iron # Problem parameters diff --git a/FluidMechanics/NavierStokes/Womersley/WomersleyExample.py b/FluidMechanics/NavierStokes/Womersley/WomersleyExample.py index 260a8d2f..6d09c6e4 100644 --- a/FluidMechanics/NavierStokes/Womersley/WomersleyExample.py +++ b/FluidMechanics/NavierStokes/Womersley/WomersleyExample.py @@ -49,7 +49,9 @@ # Add Python bindings directory to PATH import sys, os -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) import numpy import gzip @@ -60,7 +62,7 @@ import womersleyAnalytic # Intialise OpenCMISS -from opencmiss import iron +from opencmiss.iron import iron @contextlib.contextmanager def ChangeDirectory(path): diff --git a/FluidMechanics/NavierStokes/Womersley/womersleyAnalytic.py b/FluidMechanics/NavierStokes/Womersley/womersleyAnalytic.py index b767de3f..01b0cb9c 100644 --- a/FluidMechanics/NavierStokes/Womersley/womersleyAnalytic.py +++ b/FluidMechanics/NavierStokes/Womersley/womersleyAnalytic.py @@ -1,7 +1,9 @@ #!/usr/bin/env python import sys, os -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) import numpy import cmath diff --git a/FluidMechanics/Poiseuille/Static/CMakeLists.txt b/FluidMechanics/Poiseuille/Static/CMakeLists.txt new file mode 100644 index 00000000..0d512239 --- /dev/null +++ b/FluidMechanics/Poiseuille/Static/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(static_poiseuille.x src/StaticExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(static_poiseuille.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(static_poiseuille.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Poiseuille COMMAND static_poiseuille.x) +add_opencmiss_environment(Poiseuille) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/FluidMechanics/Poiseuille/Static/Makefile b/FluidMechanics/Poiseuille/Static/Makefile deleted file mode 100644 index 6da6b0bd..00000000 --- a/FluidMechanics/Poiseuille/Static/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=FluidMechanics/Poiseuille/ - -EXAMPLE_NAME = Static - -include $(GLOBAL_ROOT)/ExampleMakefile - From e4b99e6e40bc7dd23bfb08c44c49f8e95f61869f Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Tue, 18 Oct 2016 15:59:33 +1300 Subject: [PATCH 22/28] added CMake support for the Interface examples --- InterfaceExamples/CMakeLists.txt | 35 +++++++++++++ .../CoupledFluidSolid/Fortran/CMakeLists.txt | 50 +++++++++++++++++++ .../Python/CoupledFluidSolidExample.py | 6 ++- .../CoupledLaplace/CMakeLists.txt | 50 +++++++++++++++++++ .../UnCoupledLaplace/CMakeLists.txt | 50 +++++++++++++++++++ 5 files changed, 189 insertions(+), 2 deletions(-) create mode 100644 InterfaceExamples/CMakeLists.txt create mode 100644 InterfaceExamples/CoupledFluidSolid/Fortran/CMakeLists.txt create mode 100644 InterfaceExamples/CoupledLaplace/CMakeLists.txt create mode 100644 InterfaceExamples/UnCoupledLaplace/CMakeLists.txt diff --git a/InterfaceExamples/CMakeLists.txt b/InterfaceExamples/CMakeLists.txt new file mode 100644 index 00000000..483682f0 --- /dev/null +++ b/InterfaceExamples/CMakeLists.txt @@ -0,0 +1,35 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(CoupledFluidSolid/Fortran) + add_subdirectory(CoupledLaplace) + add_subdirectory(UnCoupledLaplace) +endif() diff --git a/InterfaceExamples/CoupledFluidSolid/Fortran/CMakeLists.txt b/InterfaceExamples/CoupledFluidSolid/Fortran/CMakeLists.txt new file mode 100644 index 00000000..02032bca --- /dev/null +++ b/InterfaceExamples/CoupledFluidSolid/Fortran/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cpl_fluid_solid.x src/FortranExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cpl_fluid_solid.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cpl_fluid_solid.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME InterfaceExamples COMMAND cpl_fluid_solid.x) +add_opencmiss_environment(InterfaceExamples) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/InterfaceExamples/CoupledFluidSolid/Python/CoupledFluidSolidExample.py b/InterfaceExamples/CoupledFluidSolid/Python/CoupledFluidSolidExample.py index ad58625a..49cdfc9c 100644 --- a/InterfaceExamples/CoupledFluidSolid/Python/CoupledFluidSolidExample.py +++ b/InterfaceExamples/CoupledFluidSolid/Python/CoupledFluidSolidExample.py @@ -144,8 +144,10 @@ # Import the libraries (OpenCMISS,python,numpy,scipy) import numpy,csv,time,sys,os,pdb -sys.path.append(os.sep.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python'))) -from opencmiss import iron +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) +sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], + 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) +from opencmiss.iron import iron # Diagnostics #iron.DiagnosticsSetOn(iron.DiagnosticTypes.ALL,[1,2,3,4,5],"Diagnostics",[""]) diff --git a/InterfaceExamples/CoupledLaplace/CMakeLists.txt b/InterfaceExamples/CoupledLaplace/CMakeLists.txt new file mode 100644 index 00000000..3451ea8e --- /dev/null +++ b/InterfaceExamples/CoupledLaplace/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cpl_laplace.x src/CoupledLaplaceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cpl_laplace.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cpl_laplace.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME InterfaceExamples COMMAND cpl_laplace.x) +add_opencmiss_environment(InterfaceExamples) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/InterfaceExamples/UnCoupledLaplace/CMakeLists.txt b/InterfaceExamples/UnCoupledLaplace/CMakeLists.txt new file mode 100644 index 00000000..4c6a3579 --- /dev/null +++ b/InterfaceExamples/UnCoupledLaplace/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(ucpl_laplace.x src/UnCoupledLaplaceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(ucpl_laplace.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(ucpl_laplace.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME InterfaceExamples COMMAND ucpl_laplace.x) +add_opencmiss_environment(InterfaceExamples) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# From dd773a9f9d6bf2131ce50e0db7ed330d5bf39e7f Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Tue, 18 Oct 2016 16:35:04 +1300 Subject: [PATCH 23/28] added CMake support for Meshes examples --- Meshes/1DCubicHermite/CMakeLists.txt | 50 +++++++++++++ Meshes/1DCubicHermite/Makefile | 70 ------------------- Meshes/CMakeLists.txt | 44 ++++++++++++ Meshes/LagrangeSimplexMesh/CMakeLists.txt | 50 +++++++++++++ Meshes/LagrangeSimplexMesh/Makefile | 69 ------------------ Meshes/MoreComplexMesh/CMakeLists.txt | 50 +++++++++++++ Meshes/MoreComplexMesh/Makefile | 70 ------------------- Meshes/MoreComplexMeshC/CMakeLists.txt | 25 +++++++ Meshes/MoreComplexMeshC/Makefile | 70 ------------------- Meshes/MultipleMeshComponents/CMakeLists.txt | 50 +++++++++++++ Meshes/MultipleMeshComponents/Makefile | 70 ------------------- .../Simplex/Tetrahedral/Cubic/CMakeLists.txt | 50 +++++++++++++ Meshes/Simplex/Tetrahedral/Cubic/Makefile | 70 ------------------- .../Simplex/Tetrahedral/Linear/CMakeLists.txt | 50 +++++++++++++ Meshes/Simplex/Tetrahedral/Linear/Makefile | 70 ------------------- .../Tetrahedral/Quadratic/CMakeLists.txt | 50 +++++++++++++ Meshes/Simplex/Tetrahedral/Quadratic/Makefile | 70 ------------------- .../Simplex/Triangular/Cubic/CMakeLists.txt | 50 +++++++++++++ Meshes/Simplex/Triangular/Cubic/Makefile | 70 ------------------- .../Simplex/Triangular/Linear/CMakeLists.txt | 50 +++++++++++++ Meshes/Simplex/Triangular/Linear/Makefile | 70 ------------------- .../Triangular/Quadratic/CMakeLists.txt | 50 +++++++++++++ Meshes/Simplex/Triangular/Quadratic/Makefile | 70 ------------------- Meshes/Versions3DLaplace/CMakeLists.txt | 50 +++++++++++++ Meshes/Versions3DLaplace/Makefile | 70 ------------------- 25 files changed, 619 insertions(+), 839 deletions(-) create mode 100644 Meshes/1DCubicHermite/CMakeLists.txt delete mode 100755 Meshes/1DCubicHermite/Makefile create mode 100644 Meshes/CMakeLists.txt create mode 100644 Meshes/LagrangeSimplexMesh/CMakeLists.txt delete mode 100644 Meshes/LagrangeSimplexMesh/Makefile create mode 100644 Meshes/MoreComplexMesh/CMakeLists.txt delete mode 100755 Meshes/MoreComplexMesh/Makefile create mode 100644 Meshes/MoreComplexMeshC/CMakeLists.txt delete mode 100755 Meshes/MoreComplexMeshC/Makefile create mode 100644 Meshes/MultipleMeshComponents/CMakeLists.txt delete mode 100755 Meshes/MultipleMeshComponents/Makefile create mode 100644 Meshes/Simplex/Tetrahedral/Cubic/CMakeLists.txt delete mode 100755 Meshes/Simplex/Tetrahedral/Cubic/Makefile create mode 100644 Meshes/Simplex/Tetrahedral/Linear/CMakeLists.txt delete mode 100755 Meshes/Simplex/Tetrahedral/Linear/Makefile create mode 100644 Meshes/Simplex/Tetrahedral/Quadratic/CMakeLists.txt delete mode 100755 Meshes/Simplex/Tetrahedral/Quadratic/Makefile create mode 100644 Meshes/Simplex/Triangular/Cubic/CMakeLists.txt delete mode 100755 Meshes/Simplex/Triangular/Cubic/Makefile create mode 100644 Meshes/Simplex/Triangular/Linear/CMakeLists.txt delete mode 100755 Meshes/Simplex/Triangular/Linear/Makefile create mode 100644 Meshes/Simplex/Triangular/Quadratic/CMakeLists.txt delete mode 100755 Meshes/Simplex/Triangular/Quadratic/Makefile create mode 100644 Meshes/Versions3DLaplace/CMakeLists.txt delete mode 100644 Meshes/Versions3DLaplace/Makefile diff --git a/Meshes/1DCubicHermite/CMakeLists.txt b/Meshes/1DCubicHermite/CMakeLists.txt new file mode 100644 index 00000000..7f85bdcb --- /dev/null +++ b/Meshes/1DCubicHermite/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(1d_cubic_hermite.x src/1DCubicHermiteExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(1d_cubic_hermite.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(1d_cubic_hermite.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND 1d_cubic_hermite.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/1DCubicHermite/Makefile b/Meshes/1DCubicHermite/Makefile deleted file mode 100755 index ff23e944..00000000 --- a/Meshes/1DCubicHermite/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=Meshes/ - -EXAMPLE_NAME = 1DCubicHermite - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/CMakeLists.txt b/Meshes/CMakeLists.txt new file mode 100644 index 00000000..8932fd65 --- /dev/null +++ b/Meshes/CMakeLists.txt @@ -0,0 +1,44 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(1DCubicHermite) + add_subdirectory(LagrangeSimplexMesh) + add_subdirectory(MoreComplexMesh) + add_subdirectory(MoreComplexMeshC) + add_subdirectory(MultipleMeshComponents) + add_subdirectory(Simplex/Tetrahedral/Linear) + add_subdirectory(Simplex/Tetrahedral/Quadratic) + add_subdirectory(Simplex/Tetrahedral/Cubic) + add_subdirectory(Simplex/Triangular/Linear) + add_subdirectory(Simplex/Triangular/Quadratic) + add_subdirectory(Simplex/Triangular/Cubic) + add_subdirectory(Versions3DLaplace) +endif() diff --git a/Meshes/LagrangeSimplexMesh/CMakeLists.txt b/Meshes/LagrangeSimplexMesh/CMakeLists.txt new file mode 100644 index 00000000..f737e80b --- /dev/null +++ b/Meshes/LagrangeSimplexMesh/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(lagrange_simplex.x src/LagrangeSimplexMeshExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(lagrange_simplex.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(lagrange_simplex.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND lagrange_simplex.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/LagrangeSimplexMesh/Makefile b/Meshes/LagrangeSimplexMesh/Makefile deleted file mode 100644 index 9907cd3f..00000000 --- a/Meshes/LagrangeSimplexMesh/Makefile +++ /dev/null @@ -1,69 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=Meshes/ - -EXAMPLE_NAME = LagrangeSimplexMesh - -include $(GLOBAL_ROOT)/ExampleMakefile diff --git a/Meshes/MoreComplexMesh/CMakeLists.txt b/Meshes/MoreComplexMesh/CMakeLists.txt new file mode 100644 index 00000000..a91859f3 --- /dev/null +++ b/Meshes/MoreComplexMesh/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(complex_mesh.x src/MoreComplexMeshExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(complex_mesh.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(complex_mesh.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND complex_mesh.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/MoreComplexMesh/Makefile b/Meshes/MoreComplexMesh/Makefile deleted file mode 100755 index cefa079d..00000000 --- a/Meshes/MoreComplexMesh/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=Meshes/ - -EXAMPLE_NAME = MoreComplexMesh - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/MoreComplexMeshC/CMakeLists.txt b/Meshes/MoreComplexMeshC/CMakeLists.txt new file mode 100644 index 00000000..53fdd86b --- /dev/null +++ b/Meshes/MoreComplexMeshC/CMakeLists.txt @@ -0,0 +1,25 @@ +# Add example executable +add_executable(complex_mesh_c.x src/MoreComplexMeshCExample.c) + + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(complex_mesh_c.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND complex_mesh_c.x) +add_opencmiss_environment(Meshes) + diff --git a/Meshes/MoreComplexMeshC/Makefile b/Meshes/MoreComplexMeshC/Makefile deleted file mode 100755 index 1b330767..00000000 --- a/Meshes/MoreComplexMeshC/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../ - GLOBAL_ROOT := $(CURDIR)/../../../../ -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=Meshes/ - -EXAMPLE_NAME = MoreComplexMeshC - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/MultipleMeshComponents/CMakeLists.txt b/Meshes/MultipleMeshComponents/CMakeLists.txt new file mode 100644 index 00000000..9cd1f632 --- /dev/null +++ b/Meshes/MultipleMeshComponents/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(multi_comp_mesh.x src/MultipleMeshComponentsExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(multi_comp_mesh.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(multi_comp_mesh.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND multi_comp_mesh.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/MultipleMeshComponents/Makefile b/Meshes/MultipleMeshComponents/Makefile deleted file mode 100755 index ad139af0..00000000 --- a/Meshes/MultipleMeshComponents/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=Meshes/ - -EXAMPLE_NAME = MultipleMeshComponents - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/Simplex/Tetrahedral/Cubic/CMakeLists.txt b/Meshes/Simplex/Tetrahedral/Cubic/CMakeLists.txt new file mode 100644 index 00000000..947df04d --- /dev/null +++ b/Meshes/Simplex/Tetrahedral/Cubic/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(simplex_cubic.x src/CubicExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(simplex_cubic.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(simplex_cubic.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND simplex_cubic.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/Simplex/Tetrahedral/Cubic/Makefile b/Meshes/Simplex/Tetrahedral/Cubic/Makefile deleted file mode 100755 index eabbf933..00000000 --- a/Meshes/Simplex/Tetrahedral/Cubic/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Meshes/Simplex/Tetrahedral/ - -EXAMPLE_NAME = Cubic - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/Simplex/Tetrahedral/Linear/CMakeLists.txt b/Meshes/Simplex/Tetrahedral/Linear/CMakeLists.txt new file mode 100644 index 00000000..63f95d41 --- /dev/null +++ b/Meshes/Simplex/Tetrahedral/Linear/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(simplex_linear.x src/LinearExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(simplex_linear.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(simplex_linear.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND simplex_linear.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/Simplex/Tetrahedral/Linear/Makefile b/Meshes/Simplex/Tetrahedral/Linear/Makefile deleted file mode 100755 index 881cb943..00000000 --- a/Meshes/Simplex/Tetrahedral/Linear/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Meshes/Simplex/Tetrahedral/ - -EXAMPLE_NAME = Linear - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/Simplex/Tetrahedral/Quadratic/CMakeLists.txt b/Meshes/Simplex/Tetrahedral/Quadratic/CMakeLists.txt new file mode 100644 index 00000000..5917aca3 --- /dev/null +++ b/Meshes/Simplex/Tetrahedral/Quadratic/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(simplex_quad.x src/QuadraticExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(simplex_quad.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(simplex_quad.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND simplex_quad.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/Simplex/Tetrahedral/Quadratic/Makefile b/Meshes/Simplex/Tetrahedral/Quadratic/Makefile deleted file mode 100755 index b10e5cc8..00000000 --- a/Meshes/Simplex/Tetrahedral/Quadratic/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Meshes/Simplex/Tetrahedral/ - -EXAMPLE_NAME = Quadratic - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/Simplex/Triangular/Cubic/CMakeLists.txt b/Meshes/Simplex/Triangular/Cubic/CMakeLists.txt new file mode 100644 index 00000000..ff79c316 --- /dev/null +++ b/Meshes/Simplex/Triangular/Cubic/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(simplex_tri_cubic.x src/CubicExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(simplex_tri_cubic.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(simplex_tri_cubic.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND simplex_tri_cubic.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/Simplex/Triangular/Cubic/Makefile b/Meshes/Simplex/Triangular/Cubic/Makefile deleted file mode 100755 index d56de781..00000000 --- a/Meshes/Simplex/Triangular/Cubic/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Meshes/Simplex/Triangular/ - -EXAMPLE_NAME = Cubic - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/Simplex/Triangular/Linear/CMakeLists.txt b/Meshes/Simplex/Triangular/Linear/CMakeLists.txt new file mode 100644 index 00000000..85ff406d --- /dev/null +++ b/Meshes/Simplex/Triangular/Linear/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(simplex_tri_linear.x src/LinearExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(simplex_tri_linear.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(simplex_tri_linear.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND simplex_tri_linear.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/Simplex/Triangular/Linear/Makefile b/Meshes/Simplex/Triangular/Linear/Makefile deleted file mode 100755 index 1d741ded..00000000 --- a/Meshes/Simplex/Triangular/Linear/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Meshes/Simplex/Triangular/ - -EXAMPLE_NAME = Linear - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/Simplex/Triangular/Quadratic/CMakeLists.txt b/Meshes/Simplex/Triangular/Quadratic/CMakeLists.txt new file mode 100644 index 00000000..929f7204 --- /dev/null +++ b/Meshes/Simplex/Triangular/Quadratic/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(simplex_tri_quadratic.x src/QuadraticExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(simplex_tri_quadratic.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(simplex_tri_quadratic.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND simplex_tri_quadratic.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/Simplex/Triangular/Quadratic/Makefile b/Meshes/Simplex/Triangular/Quadratic/Makefile deleted file mode 100755 index 2e136379..00000000 --- a/Meshes/Simplex/Triangular/Quadratic/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Meshes/Simplex/Triangular/ - -EXAMPLE_NAME = Quadratic - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/Meshes/Versions3DLaplace/CMakeLists.txt b/Meshes/Versions3DLaplace/CMakeLists.txt new file mode 100644 index 00000000..795cb1cd --- /dev/null +++ b/Meshes/Versions3DLaplace/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(mesh_laplace_versions.x src/Versions3DLaplaceExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(mesh_laplace_versions.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(mesh_laplace_versions.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME Meshes COMMAND mesh_laplace_versions.x) +add_opencmiss_environment(Meshes) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/Meshes/Versions3DLaplace/Makefile b/Meshes/Versions3DLaplace/Makefile deleted file mode 100644 index 6e863e9d..00000000 --- a/Meshes/Versions3DLaplace/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = Meshes/ - -EXAMPLE_NAME = Versions3DLaplace - -include $(GLOBAL_ROOT)/ExampleMakefile - From 1a0ff23a99cf2a2d9d2aabade9c5712840655e7f Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Wed, 19 Oct 2016 08:38:07 +1300 Subject: [PATCH 24/28] added CMake support for Multiphysics examples --- .../simple_geometry/CMakeLists.txt | 50 +++++++++++ .../simple_geometry/Makefile | 72 --------------- .../src/simple_geometryExample.f90 | 4 +- .../titin_10/CMakeLists.txt | 50 +++++++++++ .../titin_10/Makefile | 72 --------------- .../titin_10/src/titin_10Example.f90 | 18 +--- .../while_loop/CMakeLists.txt | 50 +++++++++++ .../while_loop/Makefile | 72 --------------- .../while_loop/src/while_loopExample.f90 | 14 +-- .../CMakeLists.txt | 50 +++++++++++ .../Makefile | 72 --------------- MultiPhysics/CMakeLists.txt | 43 +++++++++ .../CMakeLists.txt | 50 +++++++++++ .../CylinderInflationDrivenDarcy/Makefile | 70 --------------- .../CMakeLists.txt | 50 +++++++++++ .../Makefile | 70 --------------- .../CMakeLists.txt | 50 +++++++++++ .../Makefile | 87 ------------------- .../CMakeLists.txt | 50 +++++++++++ .../QuadraticEllipsoidDrivenDarcy/Makefile | 70 --------------- .../CMakeLists.txt | 50 +++++++++++ .../Makefile | 70 --------------- .../Cantilever/CMakeLists.txt | 50 +++++++++++ .../Cantilever/Makefile | 71 --------------- .../StaticExtension/CMakeLists.txt | 50 +++++++++++ .../StaticExtension/Makefile | 70 --------------- 26 files changed, 596 insertions(+), 829 deletions(-) create mode 100644 MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/CMakeLists.txt delete mode 100644 MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/Makefile create mode 100644 MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/CMakeLists.txt delete mode 100644 MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/Makefile create mode 100644 MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/CMakeLists.txt delete mode 100644 MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/Makefile create mode 100644 MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticitySameMesh/CMakeLists.txt delete mode 100644 MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticitySameMesh/Makefile create mode 100644 MultiPhysics/CMakeLists.txt create mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenDarcy/CMakeLists.txt delete mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenDarcy/Makefile create mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenMultiCompDarcy/CMakeLists.txt delete mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenMultiCompDarcy/Makefile create mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/IncompressibleElasticityDrivenDarcy/CMakeLists.txt delete mode 100755 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/IncompressibleElasticityDrivenDarcy/Makefile create mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenDarcy/CMakeLists.txt delete mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenDarcy/Makefile create mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenMultiCompDarcy/CMakeLists.txt delete mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenMultiCompDarcy/Makefile create mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/Cantilever/CMakeLists.txt delete mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/Cantilever/Makefile create mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/StaticExtension/CMakeLists.txt delete mode 100644 MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/StaticExtension/Makefile diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/CMakeLists.txt b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/CMakeLists.txt new file mode 100644 index 00000000..bc1f47aa --- /dev/null +++ b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(simple_geometry.x src/simple_geometryExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(simple_geometry.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(simple_geometry.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND simple_geometry.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/Makefile b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/Makefile deleted file mode 100644 index 9bf671a7..00000000 --- a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/Makefile +++ /dev/null @@ -1,72 +0,0 @@ -# -#-*- makefile -*- -# -# For use with GNU make. -# -# $Id: Makefile -1 $ -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/ - -EXAMPLE_NAME = simple_geometry - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/src/simple_geometryExample.f90 b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/src/simple_geometryExample.f90 index b9db7045..3fd91b7d 100644 --- a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/src/simple_geometryExample.f90 +++ b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry/src/simple_geometryExample.f90 @@ -364,9 +364,7 @@ PROGRAM SIMPLE_GEOMETRYEXAMPLE !################################################################################################################################## ! fast_twitch=.true. ! if(fast_twitch) then - filename= & - &"/home/heidlauf/OpenCMISS/OpenCMISS/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/fast_2012_07_23.xml" -! &"/home/heidlauf/OpenCMISS/opencmiss/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/shorten_mod_2011_07_04.xml" + filename = "cellModelFiles/fast_2012_07_23.xml" STIM_VALUE=1200.0_CMISSRP ! STIM_VALUE=8000.0_CMISSRP ! else !slow twitch diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/CMakeLists.txt b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/CMakeLists.txt new file mode 100644 index 00000000..30c3ff40 --- /dev/null +++ b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(titin10_geometry.x src/titin_10Example.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(titin10_geometry.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(titin10_geometry.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND titin10_geometry.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/Makefile b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/Makefile deleted file mode 100644 index d8a38fad..00000000 --- a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/Makefile +++ /dev/null @@ -1,72 +0,0 @@ -# -#-*- makefile -*- -# -# For use with GNU make. -# -# $Id: Makefile -1 $ -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/ - -EXAMPLE_NAME = titin_10 - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/src/titin_10Example.f90 b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/src/titin_10Example.f90 index a74a5f24..339c8f6d 100644 --- a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/src/titin_10Example.f90 +++ b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10/src/titin_10Example.f90 @@ -371,24 +371,8 @@ PROGRAM simple_geometryEXAMPLE & NumberOfNodesInXi2*NumberOfNodesInXi3 !################################################################################################################################## -! fast_twitch=.true. -! if(fast_twitch) then - filename= & -! &"data/homes/heidlauf/OpenCMISS/OpenCMISS/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/fast_2012_07_23.xml" -! "/data/home/heidlauf/OpenCMISS/OpenCMISS/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/fast_2012_07_23.xml" -! "/home/heidlauf/OpenCMISS/OpenCMISS/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/slow_2014_11_28.xml" -! "/home/heidlauf/OpenCMISS/OpenCMISS/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/slow_TK_2014_12_08.xml" -! "/home/heidlauf/OpenCMISS/OpenCMISS/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/slow_TK_2015_02_13.xml" - "/home/heidlauf/OpenCMISS/OpenCMISS/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/slow_TK_2015_06_25.xml" -! &"/home/heidlauf/OpenCMISS/opencmiss/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/shorten_mod_2011_07_04.xml" + filename = "cellModelFiles/slow_TK_2015_06_25.xml" STIM_VALUE=1200.0_CMISSRP -! else !slow twitch -! filename2= & -! &"/home/heidlauf/OpenCMISS/opencmiss/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/fast_stim_2012_07_23.xml" -! &"/home/heidlauf/OpenCMISS/opencmiss/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/slow_2012_07_23.xml_0.401" -! &"/home/heidlauf/OpenCMISS/opencmiss/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/slow_twitch_2012_01_27.xml" -! STIM_VALUE=2000.0_CMISSRP -! endif !################################################################################################################################## diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/CMakeLists.txt b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/CMakeLists.txt new file mode 100644 index 00000000..5c7e15db --- /dev/null +++ b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(while_loop.x src/while_loopExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(while_loop.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(while_loop.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND while_loop.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/Makefile b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/Makefile deleted file mode 100644 index 4e39bebc..00000000 --- a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/Makefile +++ /dev/null @@ -1,72 +0,0 @@ -# -#-*- makefile -*- -# -# For use with GNU make. -# -# $Id: Makefile -1 $ -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/ - -EXAMPLE_NAME = while_loop - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/src/while_loopExample.f90 b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/src/while_loopExample.f90 index 7af4b617..ed415d54 100644 --- a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/src/while_loopExample.f90 +++ b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop/src/while_loopExample.f90 @@ -338,20 +338,8 @@ PROGRAM WHILE_LOOPEXAMPLE & NumberOfNodesInXi2*NumberOfNodesInXi3 !################################################################################################################################## -! fast_twitch=.true. -! if(fast_twitch) then - filename= & - &"/home/heidlauf/OpenCMISS/OpenCMISS/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/fast_2014_03_25.xml" -! &"/home/heidlauf/OpenCMISS/opencmiss/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/shorten_mod_2011_07_04.xml" + filename = "cellModelFiles/fast_2014_03_25.xml" STIM_VALUE=1200.0_CMISSRP -! STIM_VALUE=8000.0_CMISSRP -! else !slow twitch -! filename2= & -! &"/home/heidlauf/OpenCMISS/opencmiss/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/fast_stim_2012_07_23.xml" -! &"/home/heidlauf/OpenCMISS/opencmiss/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/slow_2012_07_23.xml_0.401" -! &"/home/heidlauf/OpenCMISS/opencmiss/examples/MultiPhysics/BioelectricFiniteElasticity/cellModelFiles/slow_twitch_2012_01_27.xml" -! STIM_VALUE=2000.0_CMISSRP -! endif !################################################################################################################################## diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticitySameMesh/CMakeLists.txt b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticitySameMesh/CMakeLists.txt new file mode 100644 index 00000000..4a2de98e --- /dev/null +++ b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticitySameMesh/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(same_geometry.x src/GudunovMonodomainElasticitySameMeshExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(same_geometry.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(same_geometry.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND same_geometry.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticitySameMesh/Makefile b/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticitySameMesh/Makefile deleted file mode 100644 index 74a0b759..00000000 --- a/MultiPhysics/BioelectricFiniteElasticity/GudunovMonodomainElasticitySameMesh/Makefile +++ /dev/null @@ -1,72 +0,0 @@ -# -#-*- makefile -*- -# -# For use with GNU make. -# -# $Id: Makefile -1 $ -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling OpenCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/BioelectricFiniteElasticity/ - -EXAMPLE_NAME = GudunovMonodomainElasticitySameMesh - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/MultiPhysics/CMakeLists.txt b/MultiPhysics/CMakeLists.txt new file mode 100644 index 00000000..798a099e --- /dev/null +++ b/MultiPhysics/CMakeLists.txt @@ -0,0 +1,43 @@ +# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) +# is a mathematical modelling environment that enables the application of finite element +# analysis techniques to a variety of complex bioengineering problems. +# +# The OpenCMISS project website can be found at http://www.opencmiss.org +# For more information see http://www.opencmiss.org/documentation + +# Include the OpenCMISS initalisation & macro definition file. +include(../OpenCMISS.cmake) + +# Project setup +# ------------- +cmake_minimum_required(VERSION 3.3 FATAL_ERROR) +project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) +enable_testing() + +# Find OpenCMISS +# -------------- +# +# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. +# Currently available OpenCMISS package components: Iron Zinc +# Requiring Iron will also include the iron_c bindings target if available. +# +# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. +# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include +# paths needed! +find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) + +# CMake application code +# ---------------------- +if (CMAKE_Fortran_COMPILER) + add_subdirectory(BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/simple_geometry) + add_subdirectory(BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/titin_10) + add_subdirectory(BioelectricFiniteElasticity/GudunovMonodomainElasticity1D3DMesh/while_loop) + add_subdirectory(BioelectricFiniteElasticity/GudunovMonodomainElasticitySameMesh) + add_subdirectory(Poroelasticity/FiniteElasticityFluidPressure/Cantilever) + add_subdirectory(Poroelasticity/FiniteElasticityFluidPressure/StaticExtension) + add_subdirectory(Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenDarcy) + add_subdirectory(Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenMultiCompDarcy) + add_subdirectory(Poroelasticity/FiniteElasticityDarcy/IncompressibleElasticityDrivenDarcy) + add_subdirectory(Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenDarcy) + add_subdirectory(Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenMultiCompDarcy) +endif() diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenDarcy/CMakeLists.txt b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenDarcy/CMakeLists.txt new file mode 100644 index 00000000..37ef22d9 --- /dev/null +++ b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenDarcy/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cylinder_infate.x src/CylinderInflationDrivenDarcyExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cylinder_infate.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cylinder_infate.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND cylinder_infate.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenDarcy/Makefile b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenDarcy/Makefile deleted file mode 100644 index 11b6f74b..00000000 --- a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenDarcy/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/Poroelasticity/FiniteElasticityDarcy/ - -EXAMPLE_NAME = CylinderInflationDrivenDarcy - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenMultiCompDarcy/CMakeLists.txt b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenMultiCompDarcy/CMakeLists.txt new file mode 100644 index 00000000..3b61f377 --- /dev/null +++ b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenMultiCompDarcy/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cylinder_inflate_multicomp.x src/CylinderInflationDrivenMultiCompDarcyExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cylinder_inflate_multicomp.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cylinder_inflate_multicomp.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND cylinder_inflate_multicomp.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenMultiCompDarcy/Makefile b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenMultiCompDarcy/Makefile deleted file mode 100644 index 84f3e8f9..00000000 --- a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/CylinderInflationDrivenMultiCompDarcy/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/Poroelasticity/FiniteElasticityDarcy/ - -EXAMPLE_NAME = CylinderInflationDrivenMultiCompDarcy - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/IncompressibleElasticityDrivenDarcy/CMakeLists.txt b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/IncompressibleElasticityDrivenDarcy/CMakeLists.txt new file mode 100644 index 00000000..aa1188dc --- /dev/null +++ b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/IncompressibleElasticityDrivenDarcy/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(incompress_elastic.x src/IncompressibleElasticityDrivenDarcyExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(incompress_elastic.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(incompress_elastic.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND incompress_elastic.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/IncompressibleElasticityDrivenDarcy/Makefile b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/IncompressibleElasticityDrivenDarcy/Makefile deleted file mode 100755 index a18c976b..00000000 --- a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/IncompressibleElasticityDrivenDarcy/Makefile +++ /dev/null @@ -1,87 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../.. - GLOBAL_ROOT := $(CURDIR)/../../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH=MultiPhysics/Poroelasticity/FiniteElasticityDarcy/ - -EXAMPLE_NAME = IncompressibleElasticityDrivenDarcy - -include $(GLOBAL_ROOT)/ExampleMakefile - -# let's assume fluid_mechanics_IO_routines has been built in main_object, copy them over -# redefine preliminaries -preliminaries: $(OBJECT_DIR) $(EXE_DIR) - cp $(MAIN_OBJECT_DIR)/fluid_mechanics_IO_routines.o $(OBJECT_DIR) - cp $(MAIN_OBJECT_DIR)/fluid_mechanics_io_routines.mod $(OBJECT_DIR) - -info: - @echo "OBJECTS:" - @echo $(OBJECTS) - @echo "OBJECT_DIR:" - @echo $(OBJECT_DIR) - @echo "MAIN_OBJECT_DIR:" - @echo $(MAIN_OBJECT_DIR) - @echo "EXAMPLE_SOURCE_DIR:" - @echo $(EXAMPLE_SOURCE_DIR) - @echo "MAIN_SOURCE_DIR:" - @echo $(MAIN_SOURCE_DIR) diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenDarcy/CMakeLists.txt b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenDarcy/CMakeLists.txt new file mode 100644 index 00000000..4edb5cb1 --- /dev/null +++ b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenDarcy/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(quad_ellipsoid.x src/QuadraticEllipsoidDrivenDarcyExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(quad_ellipsoid.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(quad_ellipsoid.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND quad_ellipsoid.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenDarcy/Makefile b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenDarcy/Makefile deleted file mode 100644 index 5c7e71ba..00000000 --- a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenDarcy/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/Poroelasticity/FiniteElasticityDarcy/ - -EXAMPLE_NAME = QuadraticEllipsoidDrivenDarcy - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenMultiCompDarcy/CMakeLists.txt b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenMultiCompDarcy/CMakeLists.txt new file mode 100644 index 00000000..af16c006 --- /dev/null +++ b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenMultiCompDarcy/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(quad_ellipsoid_multicomp.x src/QuadraticEllipsoidDrivenMultiCompDarcyExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(quad_ellipsoid_multicomp.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(quad_ellipsoid_multicomp.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND quad_ellipsoid_multicomp.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenMultiCompDarcy/Makefile b/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenMultiCompDarcy/Makefile deleted file mode 100644 index d073d6cc..00000000 --- a/MultiPhysics/Poroelasticity/FiniteElasticityDarcy/QuadraticEllipsoidDrivenMultiCompDarcy/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/Poroelasticity/FiniteElasticityDarcy/ - -EXAMPLE_NAME = QuadraticEllipsoidDrivenMultiCompDarcy - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/Cantilever/CMakeLists.txt b/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/Cantilever/CMakeLists.txt new file mode 100644 index 00000000..f7e88514 --- /dev/null +++ b/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/Cantilever/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(cantilever.x src/CantileverExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(cantilever.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(cantilever.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND cantilever.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/Cantilever/Makefile b/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/Cantilever/Makefile deleted file mode 100644 index 323ae200..00000000 --- a/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/Cantilever/Makefile +++ /dev/null @@ -1,71 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# $Id: Makefile 27 2007-07-24 16:52:51Z cpb $ -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/ - -EXAMPLE_NAME = Cantilever - -include $(GLOBAL_ROOT)/ExampleMakefile - diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/StaticExtension/CMakeLists.txt b/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/StaticExtension/CMakeLists.txt new file mode 100644 index 00000000..9ebf633f --- /dev/null +++ b/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/StaticExtension/CMakeLists.txt @@ -0,0 +1,50 @@ +# Add example executable +add_executable(static_ext.x src/StaticExtensionExample.f90) + +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(static_ext.x PRIVATE ${PROC_OPT}) + +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(static_ext.x PRIVATE opencmiss) + +# Add a simple test that runs the executable +add_test(NAME MultiPhysics COMMAND static_ext.x) +add_opencmiss_environment(MultiPhysics) + +################### +# Developer notice! +# +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. +# diff --git a/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/StaticExtension/Makefile b/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/StaticExtension/Makefile deleted file mode 100644 index e204c38b..00000000 --- a/MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/StaticExtension/Makefile +++ /dev/null @@ -1,70 +0,0 @@ -# -*- makefile -*- -# -# For use with GNU make. -# -# -#---------------------------------------------------------------------------------------------------------------------------------- -# Makefile for compiling openCMISS examples -# -# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson -# Changes: -# -#---------------------------------------------------------------------------------------------------------------------------------- -# -# LICENSE -# -# Version: MPL 1.1/GPL 2.0/LGPL 2.1 -# -# The contents of this file are subject to the Mozilla Public License -# Version 1.1 (the "License"); you may not use this file except in -# compliance with the License. You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is openCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../.. - GLOBAL_ROOT := $(CURDIR)/../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- - -EXAMPLE_PATH = MultiPhysics/Poroelasticity/FiniteElasticityFluidPressure/ - -EXAMPLE_NAME = StaticExtension - -include $(GLOBAL_ROOT)/ExampleMakefile - From 91bfd179c15bba002e034764af4945a74a3d60a7 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Thu, 20 Oct 2016 14:39:17 +1300 Subject: [PATCH 25/28] moved input files for Laplace and Monodomain example to central directories --- Bioelectrics/CMakeLists.txt | 2 +- Bioelectrics/Monodomain/CMakeLists.txt | 75 +- .../Monodomain/Fortran/CMakeLists.txt | 50 - Bioelectrics/Monodomain/Fortran/input/n98.xml | 5799 ----------------- .../Monodomain/Python/Monodomain2DSquare.py | 12 +- Bioelectrics/Monodomain/Python/n98.xml | 5799 ----------------- Bioelectrics/MonodomainCUDA/FHN.xml | 355 - Bioelectrics/MonodomainCUDA/LRd.xml | 1960 ------ Bioelectrics/MonodomainCUDA/jrw-1998.xml | 5332 --------------- Bioelectrics/MonodomainCUDA/n98.xml | 5799 ----------------- .../Monodomain_Shiqiang/input/FHN.xml | 355 - .../Monodomain_Shiqiang/input/LRd.xml | 4320 ------------ .../Monodomain_Shiqiang/input/jrw-1998.xml | 5332 --------------- .../lindblad_murphey_clark_giles_1996.xml | 3779 ----------- .../input/maltsev_rate_modulation.xml | 4487 ------------- .../Monodomain_Shiqiang/input/n98.xml | 5799 ----------------- .../{MonodomainCUDA => input}/Atlas_Mesh.vtk | 0 .../{MonodomainCUDA => input}/LRd2.xml | 0 ClassicalField/Laplace/CMakeLists.txt | 4 +- ClassicalField/Laplace/Laplace/CMakeLists.txt | 19 + .../Laplace/Laplace/Fortran/CMakeLists.txt | 50 - 21 files changed, 73 insertions(+), 49255 deletions(-) delete mode 100644 Bioelectrics/Monodomain/Fortran/CMakeLists.txt delete mode 100644 Bioelectrics/Monodomain/Fortran/input/n98.xml delete mode 100644 Bioelectrics/Monodomain/Python/n98.xml delete mode 100644 Bioelectrics/MonodomainCUDA/FHN.xml delete mode 100644 Bioelectrics/MonodomainCUDA/LRd.xml delete mode 100644 Bioelectrics/MonodomainCUDA/jrw-1998.xml delete mode 100644 Bioelectrics/MonodomainCUDA/n98.xml delete mode 100644 Bioelectrics/Monodomain_Shiqiang/input/FHN.xml delete mode 100644 Bioelectrics/Monodomain_Shiqiang/input/LRd.xml delete mode 100644 Bioelectrics/Monodomain_Shiqiang/input/jrw-1998.xml delete mode 100644 Bioelectrics/Monodomain_Shiqiang/input/lindblad_murphey_clark_giles_1996.xml delete mode 100644 Bioelectrics/Monodomain_Shiqiang/input/maltsev_rate_modulation.xml delete mode 100644 Bioelectrics/Monodomain_Shiqiang/input/n98.xml rename Bioelectrics/{MonodomainCUDA => input}/Atlas_Mesh.vtk (100%) rename Bioelectrics/{MonodomainCUDA => input}/LRd2.xml (100%) create mode 100644 ClassicalField/Laplace/Laplace/CMakeLists.txt delete mode 100644 ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt diff --git a/Bioelectrics/CMakeLists.txt b/Bioelectrics/CMakeLists.txt index 35e27f44..54f881c2 100644 --- a/Bioelectrics/CMakeLists.txt +++ b/Bioelectrics/CMakeLists.txt @@ -30,7 +30,7 @@ find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) # ---------------------- if (CMAKE_Fortran_COMPILER) add_subdirectory(Bidomain) - add_subdirectory(Monodomain/Fortran) + add_subdirectory(Monodomain) add_subdirectory(Monodomain_Shiqiang) add_subdirectory(MonodomainTP06) add_subdirectory(MonodomainBuenoOrovio) diff --git a/Bioelectrics/Monodomain/CMakeLists.txt b/Bioelectrics/Monodomain/CMakeLists.txt index 65d54ffe..0b523b2a 100644 --- a/Bioelectrics/Monodomain/CMakeLists.txt +++ b/Bioelectrics/Monodomain/CMakeLists.txt @@ -1,37 +1,50 @@ -# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification) -# is a mathematical modelling environment that enables the application of finite element -# analysis techniques to a variety of complex bioengineering problems. -# -# The OpenCMISS project website can be found at http://www.opencmiss.org -# For more information see http://www.opencmiss.org/documentation +# Add example executable +add_executable(monodomain.x Fortran/src/FortranExample.f90) -# Include the OpenCMISS initalisation & macro definition file. -include(../../OpenCMISS.cmake) - -# Project setup -# ------------- -cmake_minimum_required(VERSION 3.3 FATAL_ERROR) -project(OpenCMISS-Example VERSION 1.0 LANGUAGES Fortran C) -enable_testing() +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() +target_compile_options(monodomain.x PRIVATE ${PROC_OPT}) -message(STATUS "FORTRAN Compiler: ${CMAKE_Fortran_COMPILER}") -message(STATUS "MPI: ${MPI}") +# Link to opencmiss +# ----------------- +# +# This simply uses the opencmiss target created by OC_INIT() above. +# +# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly +# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. +# +# If required, add any other required link libraries (cellml, petsc ..) here, too. +# For example, if you needed PetSC functionality, issue +# +# find_package(PETSC REQUIRED) +# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) +# +# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. +target_link_libraries(monodomain.x PRIVATE opencmiss) +# Add a simple test that runs the executable +add_test(NAME MonoDomain COMMAND monodomain.x) +add_opencmiss_environment(MonoDomain) -# Find OpenCMISS -# -------------- +################### +# Developer notice! # -# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. -# Currently available OpenCMISS package components: Iron Zinc -# Requiring Iron will also include the iron_c bindings target if available. +# If you write Fortran code and use MPI, you need to use the following MPI directives: +# +# #ifndef NOMPIMOD +# USE MPI +# #endif +# [...] +# IMPLICIT NONE +# [...] +# #ifdef NOMPIMOD +# #include "mpif.h" +# #endif +# +# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make +# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. # -# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components. -# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include -# paths needed! -find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) - -# CMake application code -# ---------------------- -if (CMAKE_Fortran_COMPILER) - add_subdirectory(Fortran) -endif() diff --git a/Bioelectrics/Monodomain/Fortran/CMakeLists.txt b/Bioelectrics/Monodomain/Fortran/CMakeLists.txt deleted file mode 100644 index 2244a375..00000000 --- a/Bioelectrics/Monodomain/Fortran/CMakeLists.txt +++ /dev/null @@ -1,50 +0,0 @@ -# Add example executable -add_executable(monodomain.x src/FortranExample.f90) - -# Turn on Fortran preprocessing (#include directives) -if (MSVC) - set(PROC_OPT "/fpp") -else() - set(PROC_OPT "-cpp") -endif() -target_compile_options(monodomain.x PRIVATE ${PROC_OPT}) - -# Link to opencmiss -# ----------------- -# -# This simply uses the opencmiss target created by OC_INIT() above. -# -# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly -# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. -# -# If required, add any other required link libraries (cellml, petsc ..) here, too. -# For example, if you needed PetSC functionality, issue -# -# find_package(PETSC REQUIRED) -# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) -# -# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. -target_link_libraries(monodomain.x PRIVATE opencmiss) - -# Add a simple test that runs the executable -add_test(NAME MonoDomain COMMAND monodomain.x) -add_opencmiss_environment(MonoDomain) - -################### -# Developer notice! -# -# If you write Fortran code and use MPI, you need to use the following MPI directives: -# -# #ifndef NOMPIMOD -# USE MPI -# #endif -# [...] -# IMPLICIT NONE -# [...] -# #ifdef NOMPIMOD -# #include "mpif.h" -# #endif -# -# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make -# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. -# diff --git a/Bioelectrics/Monodomain/Fortran/input/n98.xml b/Bioelectrics/Monodomain/Fortran/input/n98.xml deleted file mode 100644 index 2945739a..00000000 --- a/Bioelectrics/Monodomain/Fortran/input/n98.xml +++ /dev/null @@ -1,5799 +0,0 @@ - - - - - - - - - - - - - - - - Lloyd - Catherine - May - - - c.lloyd@auckland.ac.nz - - - - The University of Auckland - The Bioengineering Research Group - - - - - - 2001-12-18 - - - - - - Added more metadata. - - - - Lloyd - Catherine - May - - - - 2002-07-22 - - - - - Corrected units. - - - - Lloyd - Catherine - May - - - - 2002-03-01 - - - - - Corrected several equations. - - - - Lloyd - Catherine - May - - - - 2002-02-26 - - - - - Corrected the i_K1 and i_K_ACh calculations. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Updated metadata to conform to the 16/1/02 CellML Metadata 1.0 - Specification. - - - - Cuellar - Autumn - A. - - - - 2002-01-21 - - - - - Altered some of the connections. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Added some initial values from Penny Noble's documentation. Removed - the blocked h_gate component from the fast sodium current as it - belongs to a separate model which considers the effect of drugs. - - - - Lloyd - Catherine - May - - - - 2002-05-06 - - - - - Fixed up the CellML/MathML to enable the model to be solved in CMISS. The - model is no longer a direct translation of the Noble 1998 article, but - I believe it accurately represents the intent of the model. - - - - Nickerson - David - P - - - - 2003-04-05 - - - - - - Bioengineering Institute, The University of Auckland. - - - - - - - - The Noble 1998 Improved Guinea-Pig Ventricular Cell Model - - - - - - This is the CellML description of Noble's 1998 improved guinea-pig - ventricular cell model. It incorporates a diadic space, rapid and - slow potassium currents and length- and tension-dependent processes. - - - - Catherine Lloyd - - - - Guinea-Pig - - Ventricular Myocyte - - - - 9487284 - - - - - - - Noble - Denis - - - - - - - Varghese - Anthony - - - - - - - Kohl - Peter - - - - - - - Noble - Penny - - - - - - - Improved guinea-pig ventricular cell model incorporating a diadic - space, IKr and IKs, and length- and tension-dependent processes - - - 1998 - - - Canadian Journal of Cardiology - - 14 - 123 - 134 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This component is used to declare variables that are used by - all or most of the other components, in this case just `time'. - - - - - - - - - - - - - This component is the `root' node of our model. - It defines the action potential variable `V'. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A dummy equation used to get the total stimulus current into CMISS. - - - - - - - IStimC - IStim - - - - - - - - The ODE governing the membrane potential -- given by the summation of the - ionic currents and an applied stimulus. - - - - - - - - time - V - - - - IStim - - i_K1 - i_to - i_K - i_K_ATP - i_b_K - i_NaK - i_Na - i_b_Na - i_p_Na - i_NaCa - i_NaCa_ds - i_Ca_L_Ca - i_Ca_L_Ca_ds - i_Ca_L_K - i_Ca_L_K_ds - i_Ca_L_Na - i_Ca_L_Na_ds - i_b_Ca - i_Na_stretch - i_K_stretch - i_Ca_stretch - i_Ns_stretch - i_An_stretch - i_K_ACh - - - Cm - - - - - - - - - - - A component that conveniently keeps the reversal potential calculations - together. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the sodium reversal potential from the current intra- and - extracellular concentration of sodium ions. - - - - - - - E_Na - - - - R - T - - F - - - - Na_o - Na_i - - - - - - - - - - Calculation of the potassium reversal potential from the current intra- and - extracellular concentration of potassium ions. - - - - - - - E_K - - - - R - T - - F - - - - K_o - K_i - - - - - - - - - - Calculation of the potassium reversal potential for the slow component of - the delayed rectifier. - - - - - - - E_Ks - - - - R - T - - F - - - - - K_o - - P_kna - Na_o - - - - K_i - - P_kna - Na_i - - - - - - - - - - - - Calculation of the calcium reversal potential. - - - - - - - E_Ca - - 0.5 - - - R - T - - F - - - - Ca_o - Ca_i - - - - - - - - - - Calculation of the reversal potential for the fast sodium channel. - - - - - - - E_mh - - - - R - T - - F - - - - - Na_o - - P_nak - K_o - - - - Na_i - - P_nak - K_i - - - - - - - - - - - - - - - Description of the time independent inward potassium current. - - - - - - - - - - - - - - - - - - - - - - - Calculation of the time independent potassium current. - - - - - - - i_K1 - - g_K1 - - K_o - - K_o - K_mk1 - - - - - V - E_K - - - 1.0 - - - - 1.25 - - V - - E_K - 10.0 - - - - - - R - T - - F - - - - - - - - - - - - - - - - A component to group the potassium currents. - - - - - - - - - - - - - - - Simple summation of the individual potassium currents into a - single current. - - - - - - - i_K - - i_Kr - i_Ks - i_KNa - - - - - - - - - - - The rapid component of the delayed rectifier current. - - - - - - - - - - - - - - - - - - - - - - Calculation of the rapid component of the delayed rectifier current. - - - - - - - i_Kr - - - - g_Kr1 - Xr1 - - - g_Kr2 - Xr2 - - - - 1.0 - - 1.0 - - - - V - 9.0 - - 22.4 - - - - - - V - E_K - - - - - - - - - - - - The fast activation gate for the rapid component of the delayed - rectifier. - - - - - - - - - - - - - - The gating kinetics for the fast gate of the rapid component - of the delayed rectifier. - - - - - - - - time - Xr1 - - - - - 0.05 - - 1.0 - - - - - V - 5.0 - - - 9.0 - - - - - - 1.0 - Xr1 - - - - 0.00005 - - - - - V - 20.0 - - 15.0 - - - - Xr1 - - - - - - - - - - - - The slow gate of the rapid component of the delayed rectifier. - - - - - - - - - - - - - - Gating kinetics for the slow gate of the rapid component of - the delayed rectifier. - - - - - - - - time - Xr2 - - - - - 0.05 - - 1.0 - - - - - V - 5.0 - - - 9.0 - - - - - - 1.0 - Xr2 - - - - 0.0004 - - - - - - V - 30.0 - - 30.0 - - 3.0 - - - - Xr2 - - - - - - - - - - - - The slow component of the delayed rectifier current. - - - - - - - - - - - - - - - - - - - - Calculation of the slow component current of the delayed rectifier. - - - - - - - i_Ks - - - g_Ks - - Xs - 2.0 - - - - V - E_Ks - - - - - - - - - - - - The gate for the slow component of the delayed rectifier current. - - - - - - - - - - - - - - The gating kinetics for the slow component of the delayed - rectifier current. - - - - - - - - time - Xs - - - - - 0.014 - - 1.0 - - - - - V - 40.0 - - - 9.0 - - - - - - 1.0 - Xs - - - - Xs - 0.001 - - - - V - - 45.0 - - - - - - - - - - - - - - Background potassium current. - - - - - - - - - - - - - - - - - - Calculation of the background potassium current. - - - - - - - i_b_K - - g_bk - - V - E_K - - - - - - - - - - - - An ATP dependent potassium current. Included here for completeness, but - this current is only used when modelling ischaemia - and this version - of the model has not been tested for this. - - - - - - - - - - - - - - - - - - - Calculation of the ATP dependent potassium current. - - - - - - - i_K_ATP - - - g_K_ATP - - V - 80.0 - - - - 1.0 - - - ATP - K_ATP - - 2.0 - - - - - - - - - - - - - A sodium activated potassium current. Again, included for completeness - but generally not used and untested. - - - - - - - - - - - - - - - - - - - - Calculation of the sodium activated potassium current. - - - - - - - i_KNa - - g_K_Na - - Na_i - - Na_i - K_kna - - - - V - E_K - - - - - - - - - - - - The fast sodium current - the driving force of the upstroke of the - cardiac action potential. - - - - - - - - - - - - - - - - - - - - - Calculation of the fast sodium current. - - - - - - - i_Na - - g_Na - - m - 3.0 - - h - - V - E_mh - - - - - - - - - - - - The activation gate for the fast sodium current. - - - - - - - - - - - - - - - - - The gating kinetics for the activation gate of the fast sodium current. - - - - - - - - time - m - - - - alpha - - 1.0 - m - - - - beta - m - - - - - - - - - Calculation of the opening rate of the activation gate for the fast - sodium current. - - - - - - - alpha - - - 2.0 - - - - V - 41.0 - - - 0.1e-4 - - - - - - 0.2 - - V - 41.0 - - - - 1.0 - - - -0.1 - - V - 41.0 - - - - - - - - - - - - - - Calculation of the closing rate of the activation gate for the fast - sodium current. - - - - - - - beta - - 8.0 - - - -0.055556 - - V - 66.0 - - - - - - - - - - - - - - The inactivation gate for the fast sodium current. - - - - - - - - - - - - - - The gating kinetics for the inactivation gate of the fast sodium - current. - - - - - - - - time - h - - - - - 0.02 - - - -0.125 - - V - 75.0 - - - - - - 1.0 - h - - - - h - - 2.0 - - 1.0 - - 320.0 - - - -0.1 - - V - 75.0 - - - - - - - - - - - - - - - - - - The persistent sodium current. - - - - - - - - - - - - - - - - - - Calculation of the persistent sodium current. - - - - - - - i_p_Na - - g_pna - - 1.0 - - 1.0 - - - - - V - 52.0 - - 8.0 - - - - - - - V - E_Na - - - - - - - - - - - - The background sodium current. - - - - - - - - - - - - - - - - - - - Calculation of the sodium background current. - - - - - - - i_b_Na - - g_bna - - V - E_Na - - - - - - - - - - - - - This component describes an inward ionic current which is the sum - of calcium, sodium and potassium ions through the membrane channel. - The channel has one activation gate (d) and two inactivation gates - (f and f2 (or f2ds in the diadic space)). A fraction of these channels - (ICaLfract) open into the diadic subspace, with the remainder being - evenly distributed throughout the membrane area. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The calcium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_Ca - - - 1.0 - ICaLfract - - 4.0 - P_ca - d - f - f2 - - - - V - 50.0 - - - - R - T - - F - - - - 1.0 - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - - Ca_i - - - 50.0 - - - R - T - - - 2.0 - F - - - - - - - Ca_o - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The potassium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_K - - - 1.0 - ICaLfract - - P_caK - P_ca - d - f - f2 - - - K_i - - - 50.0 - - - R - T - - F - - - - - - K_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The sodium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_Na - - - 1.0 - ICaLfract - - P_caNa - P_ca - d - f - f2 - - - Na_i - - - 50.0 - - - R - T - - F - - - - - - Na_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The calcium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_Ca_ds - - ICaLfract - 4.0 - P_ca - d - f - f2ds - - - - V - 50.0 - - - - R - T - - F - - - - 1.0 - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - - Ca_ds - - - 50.0 - - - R - T - - - 2.0 - F - - - - - - - Ca_o - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The potassium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_K_ds - - ICaLfract - P_caK - P_ca - d - f - f2ds - - - K_i - - - 50.0 - - - R - T - - F - - - - - - K_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The sodium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_Na_ds - - ICaLfract - P_caNa - P_ca - d - f - f2ds - - - Na_i - - - 50.0 - - - R - T - - F - - - - - - Na_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - - - - The activation gate of the L-type calcium channel. - - - - - - - - - - - - - - - - - The gating kinetics for the activation gate. - - - - - - - - time - d - - - - alpha - - 1.0 - d - - - - beta - d - - - - - - - - - The opening rate for the activation gate. - - - - - - - alpha - - - 0.36 - - - - V - 19.0 - - - 1.0e-3 - - - - - - 0.09 - - V - 19.0 - - - - 1.0 - - - - - V - 19.0 - - - 4.0 - - - - - - - - - - - - - The closing rate for the activation gate. - - - - - - - beta - - - 0.36 - - - - V - 19.0 - - - 1.0e-3 - - - - - - -0.036 - - V - 19.0 - - - - 1.0 - - - - V - 19.0 - - 10.0 - - - - - - - - - - - - - - - - The first inactivation gate for the L-type calcium channel. - - - - - - - - - - - - - - - - - - - The gating kinetics for the first inactivation gate. - - - - - - - - time - f - - - - alpha - - 1.0 - f - - - - beta - f - - - - - - - - - The opening rate for the inactivation gate. - - - - - - - alpha - - - 0.0075 - - - - V - 34.0 - - - 1.0e-3 - - - - - -0.001875 - - - V - 34.0 - - - 1.0 - - - - V - 34.0 - - 4.0 - - - - - - - - - - - - - - The closing rate for the inactivation gate. - - - - - - - beta - - 0.0036 - - 1.0 - - - - - V - 34.0 - - 4.0 - - - - - - - - - - - - - - - The second inactivation gate for L-type calcium channels in the - membrane outside the diadic subspace. - - - - - - - - - - - - - - - - - - - The gating kinetics for the inactivation gate. - - - - - - - - time - f2 - - - CaInact - - 1.0 - - - Ca_i - - K_cachoff - Ca_i - - - f2 - - - - - - - - - - - - - The second inactivation gate for L-type calcium channels in the - membrane when open into the diadic subspace. - - - - - - - - - - - - - - - - - - The gating kinetics for the inactivation gate. - - - - - - - - time - f2ds - - - CaInactDS - - 1.0 - - - Ca_ds - - K_dsoff - Ca_ds - - - f2ds - - - - - - - - - - - - - The background calcium current. - - - - - - - - - - - - - - - - - - Calculation of the background calcium current. - - - - - - - i_b_Ca - - g_bca - - V - E_Ca - - - - - - - - - - - - The doubly gated transient outward current. - - - - - - - - - - - - - - - - - - - - - - - Evaluation of the transient outward current. - - - - - - - i_to - - g_to - - g_tos - - s - - 1.0 - g_tos - - - - r - - V - E_K - - - - - - - - - - - - The first gate of the transient outward current. - - - - - - - - - - - - - - The gating kinetics. - - - - - - - - time - s - - - - 0.000033 - - - - V - - 17.0 - - - - 1.0 - s - - - - - 0.033 - - 1.0 - - - - - V - 10.0 - - - 8.0 - - - - - s - - - - - - - - - - - - The second of the two gates for the transient outward current. - - - - - - - - - - - - - - - The gating kinetics for the r gate. - - - - - - - - time - r - - - 0.333 - - r_ss - r - - - - - - - - - Calculation of the steady-state component of the gating kinetics - for the r gate. - - - - - - - r_ss - - 1.0 - - 1.0 - - - -0.2 - - V - 4.0 - - - - - - - - - - - - - - - Acetylcholine (ACh) dependent potassium current. Once more, - this current has been included for completeness with respect - to the original publication but is usually left out of simulations. - It is useful for simulating specific cellular conditions, but - this formulation has not been tested. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Evaluation of the ACh dependent potassium current. - - - - - - - i_K_ACh - - g_KACh - - K_o - - K_o - K_KACh - - - x_ACh1 - x_ACh2 - - - ACh - 1.4969 - - - - ACh - 1.4969 - - - K_ACh - 1.4969 - - - - - - V - E_K - - - 1.0 - - - - 0.4 - - V - - E_K - 140.0 - - - - - - R - T - - F - - - - - - - - - - - - - - - - The first of two gates for the ACh dependent potassium current. - - - - - - - - - - - - - - - Gating kinetics for the first gate. - - - - - - - - time - x_ACh1 - - - - alpha_ACh - - 1.0 - x_ACh1 - - - - - 0.00582 - - 1.0 - - - - - V - 50.0 - - 15.0 - - - - - - x_ACh1 - - - - - - - - - - - - The second of the two gates for the ACh dependent potassium current. - - - - - - - - - - - - - - - Gating kinetics for the second gate. - - - - - - - - time - x_ACh2 - - - - alpha_ACh - - 1.0 - x_ACh2 - - - - - 0.12 - - 1.0 - - - - - V - 50.0 - - 15.0 - - - - - - x_ACh2 - - - - - - - - - - - - The sodium potassium pump. - - - - - - - - - - - - - - - - - - - - Calculation of the sodium potassium pump current. - - - - - - - i_NaK - - i_NaK_max - - K_o - - K_o - K_mk - - - - Na_i - - Na_i - K_mNa - - - - - - - - - - - - - The sodium calcium exchanger. A fraction of the Na-Ca exchangers - (INaCaFract) are assumed to emmpty into the diadic subspace, while - the remainder of the channels open into the bulk cytosol. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the sodium calcium exchanger current for the channels - exposed to the bulk myoplasm. - - - - - - - i_NaCa - - - 1.0 - INaCaFract - - K_NaCa - - - - - - gamma - - V - - - R - T - - F - - - - - - Na_i - 3.0 - - Ca_o - - - - - - gamma - 1.0 - - - V - - - R - T - - F - - - - - - Na_o - 3.0 - - Ca_i - - - - 1.0 - - d_NaCa - - - Ca_i - - Na_o - 3.0 - - - - Ca_o - - Na_i - 3.0 - - - - - - - - 1.0 - - 1.0 - - Ca_i - 0.0069 - - - - - - - - - - - Calculation of the sodium calcium exchanger current for the channels - opening into the diadic subspace. - - - - - - - i_NaCa_ds - - INaCaFract - K_NaCa - - - - - - gamma - - V - - - R - T - - F - - - - - - Na_i - 3.0 - - Ca_o - - - - - - gamma - 1.0 - - - V - - - R - T - - F - - - - - - Na_o - 3.0 - - Ca_ds - - - - 1.0 - - d_NaCa - - - Ca_ds - - Na_o - 3.0 - - - - Ca_o - - Na_i - 3.0 - - - - - - - - 1.0 - - 1.0 - - Ca_ds - 0.0069 - - - - - - - - - - - - - - The sarcoplasmic reticulum calcium pump which transports calcium - from the bulk myoplasm into the network SR. - - - - - - - - - - - - - - - - - - - - Calculation of the calcium uptake flux. - - - - - - - i_up - - - - 0.0004 - Ca_i - - - 0.00003 - Ca_up - - - K_cyca - K_xcs - - K_srca - - - - - Ca_i - - Ca_up - - - K_cyca - K_xcs - - K_srca - - - - K_cyca - K_xcs - - K_cyca - - - - - - - - - - - - Diffusion down the concentration gradient to transfer calcium from - the uptake stores in the network SR to the release stores in the - junctional SR. - - - - - - - - - - - - - - - - Calculation of the transfer flux between the uptake and release - calcium stores. - - - - - - - i_tr - - 0.05 - - Ca_up - Ca_rel - - - - - - - - - - - - This component describes the addition of - length dependence to the Noble models. However, in this implementation - of the model, it is unused - sarcomere length (SL) is a constant 0, - resulting in the removal of length dependence from the model. - - - - - - - - - - - - - - - - - Calculation of the scaling factor for the stretch activated currents - based on the change in length from the reference state. - - - - - - - f_stretch - - 1.0 - - 1.0 - - - -2.0 - gamma_SAC_SL - - SL - SLRef - - - - - - - - - - - - - - - The length dependent leakage of calcium from the junctional - SR into the cytolsol. - - - - - - - - - - - - - - - - i_leak - - - - gamma_SR_SL - SL - - - alpha_SRleak - Ca_rel - - - - - - - - - - - Description of the diffusion of calcium out of the diadic - subspace into the bulk cytosol. - - - - - - - - - - - - - - - - Calculation of the flux of calcium out of the diadic subspace. - - - - - - - i_decay - - alpha_ca_ds_decay - Ca_ds - - - - - - - - - - - The calcium induced calcium release from the junctional SR into - the bulk myoplasm. Assumed that activation of calcium release sites - by the diadic subspace calcium triggers calcium release in the whole - cytosol. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The fraction of release sites in the open state. - - - - - - - OpenReleaseChannelFract - - - ActivatorFract - - ActivatorFract - 0.25 - - - 2.0 - - - - - - - - Calculation of the calcium release flux from the JSR into the cytosol. - - - - - - - i_rel - - alpha_rel - OpenReleaseChannelFract - Ca_rel - - - - - - - - Regulatory binding sites. - - - - - - - RegulatoryBindingSite - - - - Ca_i - - Ca_i - K_mca - - - - - 1.0 - - Ca_i - - Ca_i - K_mca - - - - - Ca_ds - - Ca_ds - K_mca_ds - - - - - 2.0 - - - - - - - - Fraction of release channels in the precursor state. - - - - - - - PrecursorFract - - 1.0 - - ActivatorFract - ProductFract - - - - - - - alpha_act - - 0.5 - RegulatoryBindingSite - - - - - - alpha_inact - - 0.06 - - 0.5 - RegulatoryBindingSite - - - - - - - SR_speed_factor - - - 5.0 - - V - -50.0 - - - - 1.0 - - - - - - - - - time - - ActivatorFract - - - SR_speed_factor - - - alpha_act - PrecursorFract - - - alpha_inact - ActivatorFract - - - - - - - - - - time - - ProductFract - - - SR_speed_factor - - - alpha_inact - ActivatorFract - - - 0.001 - ProductFract - - - - - - - - - - - - - A stretch activated calcium current. Unused and untested in this - implementation, but included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ca_stretch - - g_Ca_stretch - f_stretch - - V - E_Ca - - - - - - - - - - - - Stretch activated potassium current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_K_stretch - - g_K_stretch - f_stretch - - V - E_K - - - - - - - - - - - - A stretch activated sodium current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Na_stretch - - g_Na_stretch - f_stretch - - V - E_Na - - - - - - - - - - - - A non-specific stretch activated current. Not used and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ns_stretch - - g_Ns_stretch - f_stretch - - V - E_Ns_stretch - - - - - - - - - - - - A anion specific stretch ativated current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_An_stretch - - g_An_stretch - f_stretch - - V - E_An_stretch - - - - - - - - - - - - A convenient grouping of all the ionic concentration differential - equations. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The rate of change of intracellular sodium concentration. - - - - - - - - time - Na_i - - - - - Am - - V_i - F - - - - - i_Na - i_p_Na - - i_b_Na - - Na_o - 140.0 - - - - i_NaK - 3.0 - - - i_NaCa - 3.0 - - - i_NaCa_ds - 3.0 - - i_Ca_L_Na - i_Ca_L_Na_ds - i_Na_stretch - - - - - - - - - The rate of change of intracellular potassium concentration. - - - - - - - - time - K_i - - - - - Am - - V_i - F - - - - - - i_K1 - i_to - i_b_K - i_K - i_K_stretch - i_Ca_L_K - i_Ca_L_K_ds - i_K_ACh - i_K_ATP - - - i_NaK - 2.0 - - - - - - - - - - The rate of change of intracellular calcium concentration. - - - - - - - - time - Ca_i - - - - - - - Am - - 2.0 - V_i - F - - - - - - i_Ca_L_Ca - i_b_Ca - i_Ca_stretch - - - i_NaCa - 2.0 - - - - - i_rel - - V_rel - V_i - - - - i_leak - - V_rel - V_i - - - - i_decay - - V_ds - V_i - - - - - i_up - dy_Ca_calmod - dy_Ca_troponin - - - - - - - - - The rate of change of calcium concentration in the diadic subspace. - - - - - - - - time - Ca_ds - - - - - - Am - - 2.0 - V_ds - F - - - - - i_Ca_L_Ca_ds - - i_NaCa_ds - 2.0 - - - - i_decay - - - - - - - - The rate of change of calcium concentration in the network SR - uptake store. - - - - - - - - time - Ca_up - - - - - V_i - V_up - - i_up - - i_tr - - - - - - - - The rate of change of calcium concentration in the junctional SR - release store. - - - - - - - - time - Ca_rel - - - - - V_up - V_rel - - i_tr - - - i_rel - i_leak - - - - - - - - - The rate of change of calcium bound to calmodulin. - - - - - - - dy_Ca_calmod - - - 100.0 - Ca_i - - CALM - Ca_calmod - - - - 0.05 - Ca_calmod - - - - - - - - time - Ca_calmod - - dy_Ca_calmod - - - - - - - The rate of change of calcium bound to troponin. - - - - - - - dy_Ca_troponin - - - alpha_trop - Ca_i - - TROP - Ca_troponin - - - - beta_trop - Ca_troponin - - - - - - - - time - Ca_troponin - - dy_Ca_troponin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py b/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py index 6f1aca2e..2e3083b8 100644 --- a/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py +++ b/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py @@ -1,10 +1,12 @@ #!/usr/bin/env python #DOC-START imports -import sys, os, math +#import sys, os, math +import math + # Make required inclusions into PYTHONPATH. -sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/python' ) -sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/x86_64_linux/gnu-C5.4-gnu-F5.4/mpich_release/release/python/RELEASE' ) +#sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/python' ) +#sys.path.append( os.environ['OPENCMISS_INSTALL_DIR'] + '/x86_64_linux/gnu-C5.4-gnu-F5.4/mpich_release/release/python/RELEASE' ) # Intialise OpenCMISS from opencmiss.iron import iron @@ -15,8 +17,8 @@ # 2D domain size height = 1.0 width = 1.0 -numberOfXElements = 25 -numberOfYElements = 25 +numberOfXElements = 50 +numberOfYElements = 50 # Materials parameters Am = 193.6 diff --git a/Bioelectrics/Monodomain/Python/n98.xml b/Bioelectrics/Monodomain/Python/n98.xml deleted file mode 100644 index 2945739a..00000000 --- a/Bioelectrics/Monodomain/Python/n98.xml +++ /dev/null @@ -1,5799 +0,0 @@ - - - - - - - - - - - - - - - - Lloyd - Catherine - May - - - c.lloyd@auckland.ac.nz - - - - The University of Auckland - The Bioengineering Research Group - - - - - - 2001-12-18 - - - - - - Added more metadata. - - - - Lloyd - Catherine - May - - - - 2002-07-22 - - - - - Corrected units. - - - - Lloyd - Catherine - May - - - - 2002-03-01 - - - - - Corrected several equations. - - - - Lloyd - Catherine - May - - - - 2002-02-26 - - - - - Corrected the i_K1 and i_K_ACh calculations. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Updated metadata to conform to the 16/1/02 CellML Metadata 1.0 - Specification. - - - - Cuellar - Autumn - A. - - - - 2002-01-21 - - - - - Altered some of the connections. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Added some initial values from Penny Noble's documentation. Removed - the blocked h_gate component from the fast sodium current as it - belongs to a separate model which considers the effect of drugs. - - - - Lloyd - Catherine - May - - - - 2002-05-06 - - - - - Fixed up the CellML/MathML to enable the model to be solved in CMISS. The - model is no longer a direct translation of the Noble 1998 article, but - I believe it accurately represents the intent of the model. - - - - Nickerson - David - P - - - - 2003-04-05 - - - - - - Bioengineering Institute, The University of Auckland. - - - - - - - - The Noble 1998 Improved Guinea-Pig Ventricular Cell Model - - - - - - This is the CellML description of Noble's 1998 improved guinea-pig - ventricular cell model. It incorporates a diadic space, rapid and - slow potassium currents and length- and tension-dependent processes. - - - - Catherine Lloyd - - - - Guinea-Pig - - Ventricular Myocyte - - - - 9487284 - - - - - - - Noble - Denis - - - - - - - Varghese - Anthony - - - - - - - Kohl - Peter - - - - - - - Noble - Penny - - - - - - - Improved guinea-pig ventricular cell model incorporating a diadic - space, IKr and IKs, and length- and tension-dependent processes - - - 1998 - - - Canadian Journal of Cardiology - - 14 - 123 - 134 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This component is used to declare variables that are used by - all or most of the other components, in this case just `time'. - - - - - - - - - - - - - This component is the `root' node of our model. - It defines the action potential variable `V'. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A dummy equation used to get the total stimulus current into CMISS. - - - - - - - IStimC - IStim - - - - - - - - The ODE governing the membrane potential -- given by the summation of the - ionic currents and an applied stimulus. - - - - - - - - time - V - - - - IStim - - i_K1 - i_to - i_K - i_K_ATP - i_b_K - i_NaK - i_Na - i_b_Na - i_p_Na - i_NaCa - i_NaCa_ds - i_Ca_L_Ca - i_Ca_L_Ca_ds - i_Ca_L_K - i_Ca_L_K_ds - i_Ca_L_Na - i_Ca_L_Na_ds - i_b_Ca - i_Na_stretch - i_K_stretch - i_Ca_stretch - i_Ns_stretch - i_An_stretch - i_K_ACh - - - Cm - - - - - - - - - - - A component that conveniently keeps the reversal potential calculations - together. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the sodium reversal potential from the current intra- and - extracellular concentration of sodium ions. - - - - - - - E_Na - - - - R - T - - F - - - - Na_o - Na_i - - - - - - - - - - Calculation of the potassium reversal potential from the current intra- and - extracellular concentration of potassium ions. - - - - - - - E_K - - - - R - T - - F - - - - K_o - K_i - - - - - - - - - - Calculation of the potassium reversal potential for the slow component of - the delayed rectifier. - - - - - - - E_Ks - - - - R - T - - F - - - - - K_o - - P_kna - Na_o - - - - K_i - - P_kna - Na_i - - - - - - - - - - - - Calculation of the calcium reversal potential. - - - - - - - E_Ca - - 0.5 - - - R - T - - F - - - - Ca_o - Ca_i - - - - - - - - - - Calculation of the reversal potential for the fast sodium channel. - - - - - - - E_mh - - - - R - T - - F - - - - - Na_o - - P_nak - K_o - - - - Na_i - - P_nak - K_i - - - - - - - - - - - - - - - Description of the time independent inward potassium current. - - - - - - - - - - - - - - - - - - - - - - - Calculation of the time independent potassium current. - - - - - - - i_K1 - - g_K1 - - K_o - - K_o - K_mk1 - - - - - V - E_K - - - 1.0 - - - - 1.25 - - V - - E_K - 10.0 - - - - - - R - T - - F - - - - - - - - - - - - - - - - A component to group the potassium currents. - - - - - - - - - - - - - - - Simple summation of the individual potassium currents into a - single current. - - - - - - - i_K - - i_Kr - i_Ks - i_KNa - - - - - - - - - - - The rapid component of the delayed rectifier current. - - - - - - - - - - - - - - - - - - - - - - Calculation of the rapid component of the delayed rectifier current. - - - - - - - i_Kr - - - - g_Kr1 - Xr1 - - - g_Kr2 - Xr2 - - - - 1.0 - - 1.0 - - - - V - 9.0 - - 22.4 - - - - - - V - E_K - - - - - - - - - - - - The fast activation gate for the rapid component of the delayed - rectifier. - - - - - - - - - - - - - - The gating kinetics for the fast gate of the rapid component - of the delayed rectifier. - - - - - - - - time - Xr1 - - - - - 0.05 - - 1.0 - - - - - V - 5.0 - - - 9.0 - - - - - - 1.0 - Xr1 - - - - 0.00005 - - - - - V - 20.0 - - 15.0 - - - - Xr1 - - - - - - - - - - - - The slow gate of the rapid component of the delayed rectifier. - - - - - - - - - - - - - - Gating kinetics for the slow gate of the rapid component of - the delayed rectifier. - - - - - - - - time - Xr2 - - - - - 0.05 - - 1.0 - - - - - V - 5.0 - - - 9.0 - - - - - - 1.0 - Xr2 - - - - 0.0004 - - - - - - V - 30.0 - - 30.0 - - 3.0 - - - - Xr2 - - - - - - - - - - - - The slow component of the delayed rectifier current. - - - - - - - - - - - - - - - - - - - - Calculation of the slow component current of the delayed rectifier. - - - - - - - i_Ks - - - g_Ks - - Xs - 2.0 - - - - V - E_Ks - - - - - - - - - - - - The gate for the slow component of the delayed rectifier current. - - - - - - - - - - - - - - The gating kinetics for the slow component of the delayed - rectifier current. - - - - - - - - time - Xs - - - - - 0.014 - - 1.0 - - - - - V - 40.0 - - - 9.0 - - - - - - 1.0 - Xs - - - - Xs - 0.001 - - - - V - - 45.0 - - - - - - - - - - - - - - Background potassium current. - - - - - - - - - - - - - - - - - - Calculation of the background potassium current. - - - - - - - i_b_K - - g_bk - - V - E_K - - - - - - - - - - - - An ATP dependent potassium current. Included here for completeness, but - this current is only used when modelling ischaemia - and this version - of the model has not been tested for this. - - - - - - - - - - - - - - - - - - - Calculation of the ATP dependent potassium current. - - - - - - - i_K_ATP - - - g_K_ATP - - V - 80.0 - - - - 1.0 - - - ATP - K_ATP - - 2.0 - - - - - - - - - - - - - A sodium activated potassium current. Again, included for completeness - but generally not used and untested. - - - - - - - - - - - - - - - - - - - - Calculation of the sodium activated potassium current. - - - - - - - i_KNa - - g_K_Na - - Na_i - - Na_i - K_kna - - - - V - E_K - - - - - - - - - - - - The fast sodium current - the driving force of the upstroke of the - cardiac action potential. - - - - - - - - - - - - - - - - - - - - - Calculation of the fast sodium current. - - - - - - - i_Na - - g_Na - - m - 3.0 - - h - - V - E_mh - - - - - - - - - - - - The activation gate for the fast sodium current. - - - - - - - - - - - - - - - - - The gating kinetics for the activation gate of the fast sodium current. - - - - - - - - time - m - - - - alpha - - 1.0 - m - - - - beta - m - - - - - - - - - Calculation of the opening rate of the activation gate for the fast - sodium current. - - - - - - - alpha - - - 2.0 - - - - V - 41.0 - - - 0.1e-4 - - - - - - 0.2 - - V - 41.0 - - - - 1.0 - - - -0.1 - - V - 41.0 - - - - - - - - - - - - - - Calculation of the closing rate of the activation gate for the fast - sodium current. - - - - - - - beta - - 8.0 - - - -0.055556 - - V - 66.0 - - - - - - - - - - - - - - The inactivation gate for the fast sodium current. - - - - - - - - - - - - - - The gating kinetics for the inactivation gate of the fast sodium - current. - - - - - - - - time - h - - - - - 0.02 - - - -0.125 - - V - 75.0 - - - - - - 1.0 - h - - - - h - - 2.0 - - 1.0 - - 320.0 - - - -0.1 - - V - 75.0 - - - - - - - - - - - - - - - - - - The persistent sodium current. - - - - - - - - - - - - - - - - - - Calculation of the persistent sodium current. - - - - - - - i_p_Na - - g_pna - - 1.0 - - 1.0 - - - - - V - 52.0 - - 8.0 - - - - - - - V - E_Na - - - - - - - - - - - - The background sodium current. - - - - - - - - - - - - - - - - - - - Calculation of the sodium background current. - - - - - - - i_b_Na - - g_bna - - V - E_Na - - - - - - - - - - - - - This component describes an inward ionic current which is the sum - of calcium, sodium and potassium ions through the membrane channel. - The channel has one activation gate (d) and two inactivation gates - (f and f2 (or f2ds in the diadic space)). A fraction of these channels - (ICaLfract) open into the diadic subspace, with the remainder being - evenly distributed throughout the membrane area. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The calcium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_Ca - - - 1.0 - ICaLfract - - 4.0 - P_ca - d - f - f2 - - - - V - 50.0 - - - - R - T - - F - - - - 1.0 - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - - Ca_i - - - 50.0 - - - R - T - - - 2.0 - F - - - - - - - Ca_o - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The potassium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_K - - - 1.0 - ICaLfract - - P_caK - P_ca - d - f - f2 - - - K_i - - - 50.0 - - - R - T - - F - - - - - - K_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The sodium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_Na - - - 1.0 - ICaLfract - - P_caNa - P_ca - d - f - f2 - - - Na_i - - - 50.0 - - - R - T - - F - - - - - - Na_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The calcium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_Ca_ds - - ICaLfract - 4.0 - P_ca - d - f - f2ds - - - - V - 50.0 - - - - R - T - - F - - - - 1.0 - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - - Ca_ds - - - 50.0 - - - R - T - - - 2.0 - F - - - - - - - Ca_o - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The potassium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_K_ds - - ICaLfract - P_caK - P_ca - d - f - f2ds - - - K_i - - - 50.0 - - - R - T - - F - - - - - - K_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The sodium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_Na_ds - - ICaLfract - P_caNa - P_ca - d - f - f2ds - - - Na_i - - - 50.0 - - - R - T - - F - - - - - - Na_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - - - - The activation gate of the L-type calcium channel. - - - - - - - - - - - - - - - - - The gating kinetics for the activation gate. - - - - - - - - time - d - - - - alpha - - 1.0 - d - - - - beta - d - - - - - - - - - The opening rate for the activation gate. - - - - - - - alpha - - - 0.36 - - - - V - 19.0 - - - 1.0e-3 - - - - - - 0.09 - - V - 19.0 - - - - 1.0 - - - - - V - 19.0 - - - 4.0 - - - - - - - - - - - - - The closing rate for the activation gate. - - - - - - - beta - - - 0.36 - - - - V - 19.0 - - - 1.0e-3 - - - - - - -0.036 - - V - 19.0 - - - - 1.0 - - - - V - 19.0 - - 10.0 - - - - - - - - - - - - - - - - The first inactivation gate for the L-type calcium channel. - - - - - - - - - - - - - - - - - - - The gating kinetics for the first inactivation gate. - - - - - - - - time - f - - - - alpha - - 1.0 - f - - - - beta - f - - - - - - - - - The opening rate for the inactivation gate. - - - - - - - alpha - - - 0.0075 - - - - V - 34.0 - - - 1.0e-3 - - - - - -0.001875 - - - V - 34.0 - - - 1.0 - - - - V - 34.0 - - 4.0 - - - - - - - - - - - - - - The closing rate for the inactivation gate. - - - - - - - beta - - 0.0036 - - 1.0 - - - - - V - 34.0 - - 4.0 - - - - - - - - - - - - - - - The second inactivation gate for L-type calcium channels in the - membrane outside the diadic subspace. - - - - - - - - - - - - - - - - - - - The gating kinetics for the inactivation gate. - - - - - - - - time - f2 - - - CaInact - - 1.0 - - - Ca_i - - K_cachoff - Ca_i - - - f2 - - - - - - - - - - - - - The second inactivation gate for L-type calcium channels in the - membrane when open into the diadic subspace. - - - - - - - - - - - - - - - - - - The gating kinetics for the inactivation gate. - - - - - - - - time - f2ds - - - CaInactDS - - 1.0 - - - Ca_ds - - K_dsoff - Ca_ds - - - f2ds - - - - - - - - - - - - - The background calcium current. - - - - - - - - - - - - - - - - - - Calculation of the background calcium current. - - - - - - - i_b_Ca - - g_bca - - V - E_Ca - - - - - - - - - - - - The doubly gated transient outward current. - - - - - - - - - - - - - - - - - - - - - - - Evaluation of the transient outward current. - - - - - - - i_to - - g_to - - g_tos - - s - - 1.0 - g_tos - - - - r - - V - E_K - - - - - - - - - - - - The first gate of the transient outward current. - - - - - - - - - - - - - - The gating kinetics. - - - - - - - - time - s - - - - 0.000033 - - - - V - - 17.0 - - - - 1.0 - s - - - - - 0.033 - - 1.0 - - - - - V - 10.0 - - - 8.0 - - - - - s - - - - - - - - - - - - The second of the two gates for the transient outward current. - - - - - - - - - - - - - - - The gating kinetics for the r gate. - - - - - - - - time - r - - - 0.333 - - r_ss - r - - - - - - - - - Calculation of the steady-state component of the gating kinetics - for the r gate. - - - - - - - r_ss - - 1.0 - - 1.0 - - - -0.2 - - V - 4.0 - - - - - - - - - - - - - - - Acetylcholine (ACh) dependent potassium current. Once more, - this current has been included for completeness with respect - to the original publication but is usually left out of simulations. - It is useful for simulating specific cellular conditions, but - this formulation has not been tested. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Evaluation of the ACh dependent potassium current. - - - - - - - i_K_ACh - - g_KACh - - K_o - - K_o - K_KACh - - - x_ACh1 - x_ACh2 - - - ACh - 1.4969 - - - - ACh - 1.4969 - - - K_ACh - 1.4969 - - - - - - V - E_K - - - 1.0 - - - - 0.4 - - V - - E_K - 140.0 - - - - - - R - T - - F - - - - - - - - - - - - - - - - The first of two gates for the ACh dependent potassium current. - - - - - - - - - - - - - - - Gating kinetics for the first gate. - - - - - - - - time - x_ACh1 - - - - alpha_ACh - - 1.0 - x_ACh1 - - - - - 0.00582 - - 1.0 - - - - - V - 50.0 - - 15.0 - - - - - - x_ACh1 - - - - - - - - - - - - The second of the two gates for the ACh dependent potassium current. - - - - - - - - - - - - - - - Gating kinetics for the second gate. - - - - - - - - time - x_ACh2 - - - - alpha_ACh - - 1.0 - x_ACh2 - - - - - 0.12 - - 1.0 - - - - - V - 50.0 - - 15.0 - - - - - - x_ACh2 - - - - - - - - - - - - The sodium potassium pump. - - - - - - - - - - - - - - - - - - - - Calculation of the sodium potassium pump current. - - - - - - - i_NaK - - i_NaK_max - - K_o - - K_o - K_mk - - - - Na_i - - Na_i - K_mNa - - - - - - - - - - - - - The sodium calcium exchanger. A fraction of the Na-Ca exchangers - (INaCaFract) are assumed to emmpty into the diadic subspace, while - the remainder of the channels open into the bulk cytosol. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the sodium calcium exchanger current for the channels - exposed to the bulk myoplasm. - - - - - - - i_NaCa - - - 1.0 - INaCaFract - - K_NaCa - - - - - - gamma - - V - - - R - T - - F - - - - - - Na_i - 3.0 - - Ca_o - - - - - - gamma - 1.0 - - - V - - - R - T - - F - - - - - - Na_o - 3.0 - - Ca_i - - - - 1.0 - - d_NaCa - - - Ca_i - - Na_o - 3.0 - - - - Ca_o - - Na_i - 3.0 - - - - - - - - 1.0 - - 1.0 - - Ca_i - 0.0069 - - - - - - - - - - - Calculation of the sodium calcium exchanger current for the channels - opening into the diadic subspace. - - - - - - - i_NaCa_ds - - INaCaFract - K_NaCa - - - - - - gamma - - V - - - R - T - - F - - - - - - Na_i - 3.0 - - Ca_o - - - - - - gamma - 1.0 - - - V - - - R - T - - F - - - - - - Na_o - 3.0 - - Ca_ds - - - - 1.0 - - d_NaCa - - - Ca_ds - - Na_o - 3.0 - - - - Ca_o - - Na_i - 3.0 - - - - - - - - 1.0 - - 1.0 - - Ca_ds - 0.0069 - - - - - - - - - - - - - - The sarcoplasmic reticulum calcium pump which transports calcium - from the bulk myoplasm into the network SR. - - - - - - - - - - - - - - - - - - - - Calculation of the calcium uptake flux. - - - - - - - i_up - - - - 0.0004 - Ca_i - - - 0.00003 - Ca_up - - - K_cyca - K_xcs - - K_srca - - - - - Ca_i - - Ca_up - - - K_cyca - K_xcs - - K_srca - - - - K_cyca - K_xcs - - K_cyca - - - - - - - - - - - - Diffusion down the concentration gradient to transfer calcium from - the uptake stores in the network SR to the release stores in the - junctional SR. - - - - - - - - - - - - - - - - Calculation of the transfer flux between the uptake and release - calcium stores. - - - - - - - i_tr - - 0.05 - - Ca_up - Ca_rel - - - - - - - - - - - - This component describes the addition of - length dependence to the Noble models. However, in this implementation - of the model, it is unused - sarcomere length (SL) is a constant 0, - resulting in the removal of length dependence from the model. - - - - - - - - - - - - - - - - - Calculation of the scaling factor for the stretch activated currents - based on the change in length from the reference state. - - - - - - - f_stretch - - 1.0 - - 1.0 - - - -2.0 - gamma_SAC_SL - - SL - SLRef - - - - - - - - - - - - - - - The length dependent leakage of calcium from the junctional - SR into the cytolsol. - - - - - - - - - - - - - - - - i_leak - - - - gamma_SR_SL - SL - - - alpha_SRleak - Ca_rel - - - - - - - - - - - Description of the diffusion of calcium out of the diadic - subspace into the bulk cytosol. - - - - - - - - - - - - - - - - Calculation of the flux of calcium out of the diadic subspace. - - - - - - - i_decay - - alpha_ca_ds_decay - Ca_ds - - - - - - - - - - - The calcium induced calcium release from the junctional SR into - the bulk myoplasm. Assumed that activation of calcium release sites - by the diadic subspace calcium triggers calcium release in the whole - cytosol. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The fraction of release sites in the open state. - - - - - - - OpenReleaseChannelFract - - - ActivatorFract - - ActivatorFract - 0.25 - - - 2.0 - - - - - - - - Calculation of the calcium release flux from the JSR into the cytosol. - - - - - - - i_rel - - alpha_rel - OpenReleaseChannelFract - Ca_rel - - - - - - - - Regulatory binding sites. - - - - - - - RegulatoryBindingSite - - - - Ca_i - - Ca_i - K_mca - - - - - 1.0 - - Ca_i - - Ca_i - K_mca - - - - - Ca_ds - - Ca_ds - K_mca_ds - - - - - 2.0 - - - - - - - - Fraction of release channels in the precursor state. - - - - - - - PrecursorFract - - 1.0 - - ActivatorFract - ProductFract - - - - - - - alpha_act - - 0.5 - RegulatoryBindingSite - - - - - - alpha_inact - - 0.06 - - 0.5 - RegulatoryBindingSite - - - - - - - SR_speed_factor - - - 5.0 - - V - -50.0 - - - - 1.0 - - - - - - - - - time - - ActivatorFract - - - SR_speed_factor - - - alpha_act - PrecursorFract - - - alpha_inact - ActivatorFract - - - - - - - - - - time - - ProductFract - - - SR_speed_factor - - - alpha_inact - ActivatorFract - - - 0.001 - ProductFract - - - - - - - - - - - - - A stretch activated calcium current. Unused and untested in this - implementation, but included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ca_stretch - - g_Ca_stretch - f_stretch - - V - E_Ca - - - - - - - - - - - - Stretch activated potassium current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_K_stretch - - g_K_stretch - f_stretch - - V - E_K - - - - - - - - - - - - A stretch activated sodium current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Na_stretch - - g_Na_stretch - f_stretch - - V - E_Na - - - - - - - - - - - - A non-specific stretch activated current. Not used and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ns_stretch - - g_Ns_stretch - f_stretch - - V - E_Ns_stretch - - - - - - - - - - - - A anion specific stretch ativated current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_An_stretch - - g_An_stretch - f_stretch - - V - E_An_stretch - - - - - - - - - - - - A convenient grouping of all the ionic concentration differential - equations. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The rate of change of intracellular sodium concentration. - - - - - - - - time - Na_i - - - - - Am - - V_i - F - - - - - i_Na - i_p_Na - - i_b_Na - - Na_o - 140.0 - - - - i_NaK - 3.0 - - - i_NaCa - 3.0 - - - i_NaCa_ds - 3.0 - - i_Ca_L_Na - i_Ca_L_Na_ds - i_Na_stretch - - - - - - - - - The rate of change of intracellular potassium concentration. - - - - - - - - time - K_i - - - - - Am - - V_i - F - - - - - - i_K1 - i_to - i_b_K - i_K - i_K_stretch - i_Ca_L_K - i_Ca_L_K_ds - i_K_ACh - i_K_ATP - - - i_NaK - 2.0 - - - - - - - - - - The rate of change of intracellular calcium concentration. - - - - - - - - time - Ca_i - - - - - - - Am - - 2.0 - V_i - F - - - - - - i_Ca_L_Ca - i_b_Ca - i_Ca_stretch - - - i_NaCa - 2.0 - - - - - i_rel - - V_rel - V_i - - - - i_leak - - V_rel - V_i - - - - i_decay - - V_ds - V_i - - - - - i_up - dy_Ca_calmod - dy_Ca_troponin - - - - - - - - - The rate of change of calcium concentration in the diadic subspace. - - - - - - - - time - Ca_ds - - - - - - Am - - 2.0 - V_ds - F - - - - - i_Ca_L_Ca_ds - - i_NaCa_ds - 2.0 - - - - i_decay - - - - - - - - The rate of change of calcium concentration in the network SR - uptake store. - - - - - - - - time - Ca_up - - - - - V_i - V_up - - i_up - - i_tr - - - - - - - - The rate of change of calcium concentration in the junctional SR - release store. - - - - - - - - time - Ca_rel - - - - - V_up - V_rel - - i_tr - - - i_rel - i_leak - - - - - - - - - The rate of change of calcium bound to calmodulin. - - - - - - - dy_Ca_calmod - - - 100.0 - Ca_i - - CALM - Ca_calmod - - - - 0.05 - Ca_calmod - - - - - - - - time - Ca_calmod - - dy_Ca_calmod - - - - - - - The rate of change of calcium bound to troponin. - - - - - - - dy_Ca_troponin - - - alpha_trop - Ca_i - - TROP - Ca_troponin - - - - beta_trop - Ca_troponin - - - - - - - - time - Ca_troponin - - dy_Ca_troponin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Bioelectrics/MonodomainCUDA/FHN.xml b/Bioelectrics/MonodomainCUDA/FHN.xml deleted file mode 100644 index c01c9d20..00000000 --- a/Bioelectrics/MonodomainCUDA/FHN.xml +++ /dev/null @@ -1,355 +0,0 @@ - - - - -
- - The FitzHugh-Nagumo Simplified Cardiac Myocyte Model - - Catherine - Lloyd - - Bioengineering Institute, University of Auckland - - - -
- Model Status - - This version of the model has been curated by Penny Noble using - COR and is also known to read in to JSim and PCEnv. There is also a PCEnv session file associated with this model. - -
- -Model Structure - - -Often it is not necessary to model the ionic currents of a cell with the accuracy and complexity inherent in the biophysically based models. With a view to investigating phenomena on a larger spatial and temporal scale, several ionic current models have been developed that do not seek to model subcellular processes but only to provide an action potential at a minimal computational cost. - - - -The FitzHugh-Nagumo model (1961) is based on the cubic excitation model (see The Polynomial Model, 1975), but it also includes a recovery variable so both depolarisation and repolarisation can be modelled. In 1994, Rogers and McCulloch modified the original model to generate a more realistic action potential. The velocity of the upstroke was increased and the large hyperpolarisation at the end of the recovery phase was removed. The model parameters were also updated. In 1996, this form of the already modified FitzHugh_Nagumo model was further updated by Aliev and Panfilov. They altered the equation which modelled the change of the recovery variable to provide a more realistic restitution period and to allow for reentrant phenomena. - - - -The complete original paper references are cited below: - - - -Impulses and physiological states in theoretical models of nerve membrane, FitzHugh, R.A., 1961, - Biophys. J. - , 1, 445-466. - - - -An active pulse transmission line simulating nerve axon, Nagumo, J., Animoto, S., Yoshizawa, S., 1962, Proc. Inst. Radio Engineers, 50, 2061-2070. - - - -A collocation-Galerkin finite element model of cardiac action potential propagation, Rogers, J.M., McCulloch, A.D., 1994a, - IEEE Trans. Biomed. Eng. - , 41, 743-757. - - - -A simple two-variable model of cardiac excitation, Aliev, R.R. and Panfilov, A.V., 1996, - Chaos, Solitons and Fractals - , 7, 293-301. PubMed ID: 8796189 - - - -The raw CellML description of the simplified cardiac myocyte models can be downloaded in various formats as described in . For an example of a more complete documentation for an electrophysiological model, see The Hodgkin-Huxley Squid Axon Model, 1952. - - - -
- - - - - - - - - - - - - - - - - - - - - - - t - - v - - - - 1 - - - - - - - v - - - v - alpha - - - - 1 - v - - - w - - I - - - - - - - - - t - - w - - - - 1 - epsilon - - - v - - - gamma - w - - - - - - - - - - - - - - - - - - - - - J - Nagumo - - - - - - - - - - - - - - S - Yoshizawa - - - 1962-10-01 00:00 - - - - - - - - Peter - Villiger - J - - - - An active pulse transmission line simulating nerve axon - 50 - 2061 - - - 2070 - - - J - Nagumo - - - Penny - Noble - J - - - - - - - - - - - - - - - - - - Penny - Noble - - - - 1000 - 10000 - - - - - - - Department of Physiology, Anatomy & Genetics, University of Oxford - - - - - - - Biophysical Journal - - - S - Arimoto - - - - - - - - Impulses and Physiological States in Theoretical Models of Nerve Membrane - 1 - 445 - - - 466 - - - 2005-06-14T00:00:00+00:00 - - - - - - - - keyword - - - simplified model - neuron - electrophysiology - cardiac - Myocyte - - - - - - - - - added metadata - - - - - Units checked, curated. - - - - - - - - - - - 2007-11-29T12:16:16+13:00 - - - - - - Oxford University - The Bioengineering Institute - - - Biophysical Journal - - - - - - Richard - Fitzhugh - A - - - - - - - - - - - penny.noble@physiol.ox.ac.uk - - - 1961-01-01 - - - - - - - 2006-03-31 - - - \ No newline at end of file diff --git a/Bioelectrics/MonodomainCUDA/LRd.xml b/Bioelectrics/MonodomainCUDA/LRd.xml deleted file mode 100644 index 399fbef4..00000000 --- a/Bioelectrics/MonodomainCUDA/LRd.xml +++ /dev/null @@ -1,1960 +0,0 @@ - - - - - -
- - Luo-Rudy Mammalian Ventricular Model I 1991 - - Catherine - Lloyd - - Auckland Bioengineering Institute, The University of Auckland - - - -
- Model Status - - This model has been curated and unit checked and is known to replicate the published results in OpenCell and COR. - -
- -Model Structure - - -In 1991, Ching-hsing Luo and Yoram Rudy published a mathematical model of the ventricular cardiac action potential. This original model is the first of the two Luo-Rudy models, and it has subsequently come to be known as the Luo-Rudy I model. It is a significant update of the Beeler-Reuter mammalian ventricular model (1977) (see the figure below), and like the the Beeler-Reuter model, the Luo-Rudy I model uses Hodgkin-Huxley type equations to calculate ionic currents. - - - -The complete original paper reference is cited below: - - - -A Model of the Ventricular Cardiac Action Potential - Depolarisation, Repolarisation and Their Interaction, Ching-hsing Luo and Yoram Rudy, 1991 Circulation Research, 68, 1501-1526. PubMed ID: 1709839 - - - - - - - cell diagram of the LR-I model showing ionic currents, pumps and exchangers within the sarcolemma - - - - -A schematic diagram describing the current flows across the cell membrane that are captured in the LR-I model. - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - I_stim - - - stim_amplitude - - - - - time - stim_start - - - - time - stim_end - - - - - - - - time - stim_start - - - - - - - - - - time - stim_start - - stim_period - - - stim_period - - - stim_duration - - - - - 0 - - - - - - - - - time - - V - - - - - - - - 1 - - C - - - - I_stim - i_Na - i_si - i_K - i_K1 - i_Kp - i_b - - - - - - - - - - - - - - - - - - - - - - - E_Na - - - - - - - R - T - - F - - - - - - Nao - Nai - - - - - - - i_Na - - - g_Na - - - m - 3 - - h - j - - - V - E_Na - - - - - - - - - - - - - - - alpha_m - - - - - 0.32 - - - V - 47.13 - - - - - 1 - - - - - - - 0.1 - - - - V - 47.13 - - - - - - - - - beta_m - - - 0.08 - - - - - - - V - - 11 - - - - - - - - - - time - - m - - - - - - alpha_m - - - 1 - m - - - - - beta_m - m - - - - - - - - - - - - - - - alpha_h - - - - - 0.135 - - - - - - - 80 - V - - - - 6.8 - - - - - - - V - - - 40 - - - - - 0 - - - - - - beta_h - - - - - - - 3.56 - - - - - 0.079 - V - - - - - - 310000 - - - - - 0.35 - V - - - - - - - V - - - 40 - - - - - - - 1 - - - 0.13 - - - 1 - - - - - - - V - 10.66 - - - - 11.1 - - - - - - - - - - - - - - - time - - h - - - - - - alpha_h - - - 1 - h - - - - - beta_h - h - - - - - - - - - - - - - - - alpha_j - - - - - - - - - - - - - 127140 - - - - - - 0.2444 - V - - - - - - 0.00003474 - - - - - - - 0.04391 - - V - - - - - - - V - 37.78 - - - - - 1 - - - - - 0.311 - - - V - 79.23 - - - - - - - - V - - - 40 - - - - - 0 - - - - - - beta_j - - - - - - - 0.1212 - - - - - - - 0.01052 - - V - - - - - - 1 - - - - - - - 0.1378 - - - - V - 40.14 - - - - - - - - V - - - 40 - - - - - - - - - 0.3 - - - - - - - 0.0000002535 - - V - - - - - - 1 - - - - - - - 0.1 - - - - V - 32 - - - - - - - - - - - - - - time - - j - - - - - - alpha_j - - - 1 - j - - - - - beta_j - j - - - - - - - - - - - - - - - - - E_si - - - 7.7 - - - 13.0287 - - - - - Cai - 1 - - - - - - - - i_si - - - 0.09 - d - f - - - V - E_si - - - - - - - - - - - - - - - alpha_d - - - - - 0.095 - - - - - - - 0.01 - - - - V - 5 - - - - - - - 1 - - - - - - - 0.072 - - - - V - 5 - - - - - - - - - beta_d - - - - - 0.07 - - - - - - - 0.017 - - - - V - 44 - - - - - - - 1 - - - - - 0.05 - - - V - 44 - - - - - - - - - - - - time - - d - - - - - - alpha_d - - - 1 - d - - - - - beta_d - d - - - - - - - - - - - - - - - alpha_f - - - - - 0.012 - - - - - - - 0.008 - - - - V - 28 - - - - - - - 1 - - - - - 0.15 - - - V - 28 - - - - - - - - - beta_f - - - - - 0.0065 - - - - - - - 0.02 - - - - V - 30 - - - - - - - 1 - - - - - - - 0.2 - - - - V - 30 - - - - - - - - - - - - time - - f - - - - - - alpha_f - - - 1 - f - - - - - beta_f - f - - - - - - - - - - - - - - - - - - - - - - - - - g_K - - - 0.282 - - - - - Ko - 5.4 - - - - - - - E_K - - - - - - - R - T - - F - - - - - - - - Ko - - - PR_NaK - Nao - - - - - Ki - - - PR_NaK - Nai - - - - - - - - - i_K - - - g_K - X - Xi - - - V - E_K - - - - - - - - - - - - - - - alpha_X - - - - - 0.0005 - - - - - 0.083 - - - V - 50 - - - - - - - 1 - - - - - 0.057 - - - V - 50 - - - - - - - - - beta_X - - - - - 0.0013 - - - - - - - 0.06 - - - - V - 20 - - - - - - - 1 - - - - - - - 0.04 - - - - V - 20 - - - - - - - - - - - - time - - X - - - - - - alpha_X - - - 1 - X - - - - - beta_X - X - - - - - - - - - - - - - Xi - - - - - - - 2.837 - - - - - - - 0.04 - - - V - 77 - - - - 1 - - - - - - - V - 77 - - - - - - 0.04 - - - V - 35 - - - - - - - - V - - - 100 - - - - - 1 - - - - - - - - - - - - - - - - - - - - g_K1 - - - 0.6047 - - - - - Ko - 5.4 - - - - - - - E_K1 - - - - - - - R - T - - F - - - - - - Ko - Ki - - - - - - - i_K1 - - - g_K1 - K1_infinity - - - V - E_K1 - - - - - - - - - - - - - - - alpha_K1 - - - 1.02 - - - 1 - - - - - 0.2385 - - - - - V - E_K1 - - 59.215 - - - - - - - - - beta_K1 - - - - - - - 0.49124 - - - - - 0.08032 - - - - - V - 5.476 - - E_K1 - - - - - - - 1 - - - - - 0.06175 - - - V - - - E_K1 - 594.31 - - - - - - - - - 1 - - - - - - - 0.5143 - - - - - - V - E_K1 - - 4.753 - - - - - - - - - K1_infinity - - - alpha_K1 - - - alpha_K1 - beta_K1 - - - - - - - - - - - - - - - - E_Kp - E_K1 - - - - Kp - - - 1 - - - 1 - - - - - - - 7.488 - V - - 5.98 - - - - - - - - i_Kp - - - g_Kp - Kp - - - V - E_Kp - - - - - - - - - - - - - - i_b - - - g_b - - - V - E_b - - - - - - - - - - - - - - - - - - - - - - time - - Cai - - - - - - - - - - 0.0001 - - 1 - - i_si - - - - 0.07 - - - 0.0001 - Cai - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Y - Rudy - - - - Added a repeating stimulus protocol using the stimulus duration (2ms) and amplitude (-25.5 microA_per_cm2) used for the original single stimulus. - - - - - - - - - Added a repeating stimulus protocol using the stimulus duration (2ms) and amplitude (-25.5 microA_per_cm2) used for the original single stimulus. - - - - The University of Auckland, Bioengineering Institute - - - - - - - - - - 1709839 - - - - - This is the CellML description of Luo and Rudy's mathematical model of the membrane action potential of the mammalian ventricular cell. It describes six ionic currents and it is a development of the Beeler-Reuter 1977 mammalian ventricular model, using Hodgkin-Huxley type equations. - - - James - Lawson - Richard - - - 2006-03-31 - - - Catherine - Lloyd - May - - - - - - - - James - Lawson - Richard - - - 2008-02-25T11:01:56+13:00 - - - - - - - keyword - - - Ventricular Myocyte - cardiac - electrophysiology - ventricular myocyte - - - - - - - - 2001-09-15T00:00:00+00:00 - - - 1991-01-01 - - - - - - - - - - C - Luo - H - - - Penny - Noble - J - - - - - - - - - - - A Model of the Ventricular Cardiac Action Potential. Depolarization, repolarization and their interaction - 68(6) - 1501 - - - 1526 - - - - - - Circulation Research - - - - Units checked, curated. Some cmeta:id's added to variables to allow referencing by PCEnv session file - - - - - - - 2007-08-17T12:59:52+12:00 - - - Peter - Villiger - J - - - James Lawson - - - - c.lloyd@auckland.ac.nz - - - - This model has had a repeating current stimulus protocol added to allow it to simulate trains of action potentials. This model is known to run in PCEnv and produce the correct output. - - - Catherine Lloyd - - - - added metadata - - - - The University of Auckland - The Bioengineering Institute - - - 2007-08-17T12:59:52+12:00 - - - 10000 - - - - - - diff --git a/Bioelectrics/MonodomainCUDA/jrw-1998.xml b/Bioelectrics/MonodomainCUDA/jrw-1998.xml deleted file mode 100644 index 6a407ee4..00000000 --- a/Bioelectrics/MonodomainCUDA/jrw-1998.xml +++ /dev/null @@ -1,5332 +0,0 @@ - - - - - - - - - - - - - Lloyd - Catherine - May - - - c.lloyd@auckland.ac.nz - - - - The University of Auckland - The Bioengineering Research Group - - - - - - 2001-09-24 - - - - - - Corrected equations. - - - - Lloyd - Catherine - May - - - - 2003-07-30 - - - - - Corrected equations: alpha_j_calculation and beta_j_calculation in - fast_sodium_current_j_gate, alpha_X_calculation and beta_X_calculation in time_dependent_potassium_current_X_gate, and f_NaK_calculation and - i_NaK_calculation in Ca_release_current_from_JSR. - - - - Lloyd - Catherine - May - - - - 2003-06-04 - - - - - Added some initial values from Penny Noble's documentation. - - - - Lloyd - Catherine - May - - - - 2002-05-06 - - - - - Corrected several equations, variable units and their initial values. - - - - Lloyd - Catherine - May - - - - 2002-02-28 - - - - - Corrected several equations. - - - - Lloyd - Catherine - May - - - - 2002-02-25 - - - - - Altered some of the connections. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Changed tau_y_calculation after checking mathml using the validator. - - - - Lloyd - Catherine - May - - - - 2001-12-07 - - - - - Removed document type definition as this is declared as optional - according to the W3C recommendation. - - - - Lloyd - Catherine - May - - - - 2001-10-19 - - - - - - - The University of Auckland, Bioengineering Research Group - - - - - - - - The Jafri-Rice-Winslow Model for Calcium Regulation in the Ventricular - Myocyte, 1997 - - - - - - This is the CellML description of Jafri, Rice and Winslow's - mathematical model for calcium regulation in the ventricular myocyte. - It is based on an accurate model of the membrane currents and adds a - more sophisticated model of calcium handling. The JRW model is based - on the LR-II model for ventricular action potentials, with several - modifications. - - - - Catherine Lloyd - - - - - Mammalia - - Ventricular Myocyte - - - - 9512016 - - - - - - - Jafri - M - Saleet - - - - - - - Rice - John - Jeremy - - - - - - - Winslow - Raimond - L - - - - - - - Cardiac Ca2+ Dynamics: The Roles of Ryanodine Receptor Adaptation - and Sarcoplasmic Reticulum Load - - - 1998-03 - - - Biophysical Journal - - 74 - 1149 - 1168 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The main component of the model which defines the action potential. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The kinetics of the transmembrane potential, defined as the sum of - all the sarcolemmal currents and an applied stimulus current. - - - - - - - - time - V - - - - I_stim - - i_Na - i_Ca_L_Ca - i_Ca_L_K - i_K - i_NaCa - i_K1 - i_Kp - i_p_Ca - i_Na_b - i_Ca_b - i_NaK - i_ns_Ca - - - Cm - - - - - - - - This is a dummy equation that we simply use to make grabbing the - value in CMISS much easier. - - - - - - - - IStimC - I_stim - - - - - - - - - - The fast sodium current component contains the differential - equations governing the influx of sodium ions through the cell - surface membrane into the cell. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the fast sodium current using the three - Hodkin-Huxley type voltage-dependent gating variables m, h, and j. - - - - - - - i_Na - - g_Na - - m - 3.0 - - h - j - - V - E_Na - - - - - - - - - - The sodium reversal potential. - - - - - - - E_Na - - - - R - T - - F - - - - Nao - Nai - - - - - - - - - - - - - - The voltage-dependent activation gate for the fast sodium current - - the m gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the m gate. - - - - - - - alpha_m - - - 0.32 - - V - 47.13 - - - - 1.0 - - - -0.1 - - V - 47.13 - - - - - - - - - - - - - The closing rate of the m gate. - - - - - - - beta_m - - 0.08 - - - - V - - 11.0 - - - - - - - - - - - The kinetics of the m gate. - - - - - - - - time - m - - - - alpha_m - - 1.0 - m - - - - beta_m - m - - - - - - - - - - - - - The voltage-dependent inactivation gate for the fast sodium current - - the h gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the h gate. - - - - - - - alpha_h - - - - 0.135 - - - - 80.0 - V - - -6.8 - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate of the h gate. - - - - - - - beta_h - - - - - 3.56 - - - 0.079 - V - - - - - 310000.0 - - - 0.35 - V - - - - - - V - -40.0 - - - - - 1.0 - - 0.13 - - 1.0 - - - - V - 10.66 - - -11.1 - - - - - - - - - - - - - - - The kinetics of the h gate. - - - - - - - - time - h - - - - alpha_h - - 1.0 - h - - - - beta_h - h - - - - - - - - - - - - - The voltage-dependent slow inactivation gate for the fast sodium - current - the j gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the j gate. - - - - - - - alpha_j - - - - - - -127140.0 - - - 0.2444 - V - - - - - 0.00003474 - - - -0.04391 - V - - - - - - - V - 37.78 - - - 1.0 - - - 0.311 - - V - 79.23 - - - - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate of the j gate. - - - - - - - beta_j - - - - 0.1212 - - - - -0.01052 - V - - - - 1.0 - - - -0.1378 - - V - 40.14 - - - - - - - - V - -40.0 - - - - - 0.3 - - - - -0.0000002535 - V - - - - 1.0 - - - -0.1 - - V - 32.0 - - - - - - - - - - - - - - - - The kinetics of the j gate. - - - - - - - - time - j - - - - alpha_j - - 1.0 - j - - - - beta_j - j - - - - - - - - - - - - - The JWR model creates a new mathematical model to describe the - L-type calcium channel that is based on the experimentally observed - mode-switching behaviour of the channel. Inactivation occurs as - calcium ion binding induces the channel to switch (from mode normal) - to a mode in which transitions to open states are extremely slow - (mode Ca). The channel has one voltage inactivation gate, y. As well - as Ca, the channel is assumed permeable to K ions also. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the calcium current component of the total channel - current, given as the maximal current multiplied by the - voltage-dependent inactivation gate and the open probability of the - channel based on the mode-switching model. - - - - - - - i_Ca_L_Ca - - i_Ca_L_Ca_max - y - - O - O_Ca - - - - - - - - - - Calculation of the potassium current component of the total channel - current. - - - - - - - i_Ca_L_K - - p_k - y - - O - O_Ca - - - - V - - F - 2.0 - - - - R - T - - - - - - Ki - - - - V - F - - - R - T - - - - - Ko - - - - - - V - F - - - R - T - - - - 1.0 - - - - - - - - - - - The potassium permeability of the channel, which depends on the - calcium current component. - - - - - - - p_k - - P_K - - 1.0 - - i_Ca_L_Ca_max - i_Ca_L_Ca_half - - - - - - - - - - - The maximal calcium current through the channel. - - - - - - - i_Ca_L_Ca_max - - P_Ca - 4.0 - - - V - - F - 2.0 - - - - R - T - - - - - - 0.001 - - - 2.0 - V - - F - - R - T - - - - - - - 0.341 - Cao - - - - - - 2.0 - V - - F - - R - T - - - - - 1.0 - - - - - - - - - - - Rate constants for state changes in mode normal. - - - - - - - alpha - - 0.4 - - - - V - 12.0 - - 10.0 - - - - - - - - beta - - 0.05 - - - - V - 12.0 - - -13.0 - - - - - - - - - - - Rate constants for state changes in mode Ca (corresponding to - alpha-prime and beta-prime in the JRW paper). - - - - - - - alpha_a - - alpha - a - - - - - - beta_b - - beta - b - - - - - - - - - Rate constant for switching between mode normal and mode Ca. - - - - - - - gamma - - 0.1875 - Ca_SS - - - - - - - - - The kinetics of the state transitions in mode normal. - In the normal mode, the calcium channel is able to make the - transition to the open, conducting state (O) from the closed state - (C) at a normal rate. - - - - - - - - time - C0 - - - - - beta - C1 - - - omega - C_Ca0 - - - - - - 4.0 - alpha - - gamma - - C0 - - - - - - - - time - C1 - - - - - 4.0 - alpha - C0 - - - 2.0 - beta - C2 - - - - omega - b - - C_Ca1 - - - - - beta - - 3.0 - alpha - - - gamma - a - - - C1 - - - - - - - - time - C2 - - - - - 3.0 - alpha - C1 - - - 3.0 - beta - C3 - - - - omega - - b - 2.0 - - - C_Ca2 - - - - - - beta - 2.0 - - - 2.0 - alpha - - - gamma - - a - 2.0 - - - - C2 - - - - - - - - time - C3 - - - - - 2.0 - alpha - C2 - - - 4.0 - beta - C4 - - - - omega - - b - 3.0 - - - C_Ca3 - - - - - - beta - 3.0 - - alpha - - gamma - - a - 3.0 - - - - C3 - - - - - - - - time - C4 - - - - - alpha - C3 - - - g - O - - - - omega - - b - 4.0 - - - C_Ca4 - - - - - - beta - 4.0 - - f - - gamma - - a - 4.0 - - - - C4 - - - - - - - - time - O - - - - f - C4 - - - g - O - - - - - - - - - - The kinetics of the state transitions in mode Ca. - Calcium binding to the Ca channel induces a conformational change - from normal mode to mode Ca. This effectively inhibits the - conduction of calcium ions because in mode Ca, the calcium channel - makes the transition to the open, conducting state (O) extremely - slowly. - - - - - - - - time - C_Ca0 - - - - - beta_b - C_Ca1 - - - gamma - C_Ca0 - - - - - - 4.0 - alpha_a - - omega - - C_Ca0 - - - - - - - - time - C_Ca1 - - - - - 4.0 - alpha_a - C_Ca0 - - - 2.0 - beta_b - C_Ca2 - - - gamma - a - C1 - - - - - beta_b - - 3.0 - alpha_a - - - omega - b - - - C_Ca1 - - - - - - - - time - C_Ca2 - - - - - 3.0 - alpha_a - C_Ca1 - - - 3.0 - beta_b - C_Ca3 - - - gamma - - a - 2.0 - - C2 - - - - - - beta_b - 2.0 - - - 2.0 - alpha_a - - - omega - - b - 2.0 - - - - C_Ca2 - - - - - - - - time - C_Ca3 - - - - - 2.0 - alpha_a - C_Ca2 - - - 4.0 - beta_b - C_Ca4 - - - gamma - - a - 3.0 - - C3 - - - - - - beta_b - 3.0 - - alpha_a - - omega - - b - 3.0 - - - - C_Ca3 - - - - - - - - time - C_Ca4 - - - - - alpha_a - C_Ca3 - - - g_ - O_Ca - - - gamma - - a - 4.0 - - C4 - - - - - - beta_b - 4.0 - - f_ - - omega - - b - 4.0 - - - - C_Ca4 - - - - - - - - time - O_Ca - - - - f_ - C_Ca4 - - - g_ - O_Ca - - - - - - - - - - - - - The voltage-dependent inactivation gate for the L-type calcium - channel - the y gate. - - - - - - - - - - - - - - - - - - - - - The kinetics of the y gate. - - - - - - - - time - y - - - - y_infinity - y - - tau_y - - - - - - y_infinity - - - 1.0 - - 1.0 - - - - V - 55.0 - - 7.5 - - - - - - 0.1 - - 1.0 - - - - - V - - 21.0 - - 6.0 - - - - - - - - - - tau_y - - 20.0 - - 600.0 - - 1.0 - - - - V - 30.0 - - 9.5 - - - - - - - - - - - - - - - - The time-dependent potassium current has an X^2 dependence on it's - activation gate, and an Xi inactivation gate. This channel is also - assumed permeable to sodium ions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the maximal channel conductance, dependent on - extracellular potassium concentration. - - - - - - - g_K - - g_K_max - - - Ko - 5.4 - - - - - - - - - - - The reversal potential of the channel. - - - - - - - E_K - - - - R - T - - F - - - - - Ko - - P_NaK - Nao - - - - Ki - - P_NaK - Nai - - - - - - - - - - - - - Calculation of the time-dependent potassium current. - - - - - - - i_K - - g_K - Xi - - X - 2.0 - - - V - E_K - - - - - - - - - - - - - The voltage- and time-dependent activation gate for the - time-dependent potassium current - the X gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the X gate. - - - - - - - alpha_X - - 0.0000719 - - - V - 30.0 - - - 1.0 - - - -0.148 - - V - 30.0 - - - - - - - - - - - - - - The closing rate of the X gate. - - - - - - - beta_X - - 0.000131 - - - V - 30.0 - - - -1.0 - - - 0.0687 - - V - 30.0 - - - - - - - - - - - - - - The kinetics of the X gate. - - - - - - - - time - X - - - - alpha_X - - 1.0 - X - - - - beta_X - X - - - - - - - - - - - - - The time-independent inactivation gate for the time-dependent - potassium channel. - - - - - - - - - - - - - - - - - Xi is the inward rectification parameter and is given by the - following equation. - - - - - - - Xi - - 1.0 - - 1.0 - - - - V - 56.26 - - 32.1 - - - - - - - - - - - - - - - - The time-independent potassium current. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the maximal channel conductance, dependent on - extracellular potassium concentration. - - - - - - - g_K1 - - g_K1_max - - - Ko - 5.4 - - - - - - - - - - - The following equation calculates the reversal potential of the - time-independent potassium current. - - - - - - - E_K1 - - - - R - T - - F - - - - Ko - Ki - - - - - - - - - - - Calculate the current. - - - - - - - i_K1 - - g_K1 - K1_infinity - - V - E_K1 - - - - - - - - - - - - - - The time constants for the K1 gate are small enough that the gating - variable can be approximated with it's steady-state value. - - - - - - - - - - - - - - - - - - - - - The opening rate of the K1 gate. - - - - - - - alpha_K1 - - 1.02 - - 1.0 - - - 0.2385 - - - V - E_K1 - - 59.215 - - - - - - - - - - - - - The closing rate of the K1 gate. - - - - - - - beta_K1 - - - - 0.49124 - - - 0.08032 - - - V - 5.476 - - E_K1 - - - - - - - 0.06175 - - V - - E_K1 - 594.31 - - - - - - - 1.0 - - - -0.5143 - - - V - E_K1 - - 4.753 - - - - - - - - - - - - - The steady-state approximation for the K1 gating kinetics. - - - - - - - K1_infinity - - alpha_K1 - - alpha_K1 - beta_K1 - - - - - - - - - - - - - - The plateau potassium current component contains the equations which - describe the contribution of a time independent [K]o-insensitive - channel at plateau potentials. - - - - - - - - - - - - - - - - - - - - - - - The channel's reversal potential. - - - - - - - E_Kp - E_K1 - - - - - - - - The activation variable. - - - - - - - Kp - - 1.0 - - 1.0 - - - - 7.488 - V - - 5.98 - - - - - - - - - - - - Calculation of the plateau potassium current. - - - - - - - i_Kp - - g_Kp - Kp - - V - E_Kp - - - - - - - - - - - - - - The Na/Ca exchanger component describes how a protein molecule in - the cell surface membrane transports Na ions into the cytosol and - exports Ca ions into the extracellular volume, in a ratio of 3:1 - respectively. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the Na/Ca exchanger current. - - - - - - - i_NaCa - - k_NaCa - - 1.0 - - - K_mNa - 3.0 - - - Nao - 3.0 - - - - - 1.0 - - K_mCa - Cao - - - - 1.0 - - 1.0 - - k_sat - - - - eta - 1.0 - - V - - F - - R - T - - - - - - - - - - - - eta - V - - F - - R - T - - - - - - Nai - 3.0 - - Cao - - - - - - eta - 1.0 - - V - - F - - R - T - - - - - - Nao - 3.0 - - Cai - - - - - - - - - - - - - - - The sarcolemmal calcium pump is an additional mechanism for removing - Ca ions from the myoplasm to help maintain a low intracellular - calcium concentration when at rest. - - - - - - - - - - - - - - - - - - - - - The calcium pump current. - - - - - - - i_p_Ca - - I_pCa - - Cai - - K_mpCa - Cai - - - - - - - - - - - - - - The sodium background current is a time-independent diffusion of - Na ions down their electrochemical gradient, through the cell - surface membrane into the cytosol. - - - - - - - - - - - - - - - - - - - - - - The reversal potential for the background sodium channel. - - - - - - - E_NaN - E_Na - - - - - - - - Calculation of the background sodium current. - - - - - - - i_Na_b - - g_Nab - - V - E_NaN - - - - - - - - - - - - - The calcium background current describes a time-independent - diffusion of Ca ions down their electrochemical gradient through the - cell surface membrane into the cytosol. However, calcium is not - allowed to accumulate to high intracellular concentrations. This - influx is balanced by the Ca ion extrusion through the Na-Ca - exchanger and the sarcolemmal Ca pump. - - - - - - - - - - - - - - - - - - - - - - - - - - The reversal potential for the background calcium current. - - - - - - - E_CaN - - - - R - T - - - 2.0 - F - - - - - Cao - Cai - - - - - - - - - - - Calculation of the background calcium current. - - - - - - - i_Ca_b - - g_Cab - - V - E_CaN - - - - - - - - - - - - - The sodium potassium pump is an active protein in the cell membrane - which couples the free energy released by the hydrolysis of ATP to - the movement of Na and K ions against their electrochemical - gradients through the cell membrane. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the Na/K pump current. - - - - - - - f_NaK - - 1.0 - - - 1.0 - - 0.1245 - - - - -0.1 - V - F - - - R - T - - - - - - - 0.0365 - sigma - - - - - V - - F - - - R - T - - - - - - - - - - - sigma - - - 1.0 - 7.0 - - - - - Nao - 67.3 - - - 1.0 - - - - - - - i_NaK - - I_NaK - f_NaK - - 1.0 - - 1.0 - - - K_mNai - Nai - - 1.5 - - - - - Ko - - Ko - K_mKo - - - - - - - - - \ - - - - - The nonspecific calcium activated current describes a channel which - is activated by calcium ions, but is permeable to only sodium and - potassium ions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The reversal potential of the channel. - - - - - - - EnsCa - - - - R - T - - F - - - - - Ko - Nao - - - Ki - Nai - - - - - - - - - - - - The potential offset for the channel. - - - - - - - VnsCa - - V - EnsCa - - - - - - - - - The sodium component of the channel's current. - - - - - - - i_ns_Na - - I_ns_Na - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The potassium component of the channel's current. - - - - - - - i_ns_K - - I_ns_K - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The total nonspecific calcium activated current. - - - - - - - i_ns_Ca - - i_ns_Na - i_ns_K - - - - - - - - - The maximal sodium component current. - - - - - - - I_ns_Na - - P_ns_Ca - - 1.0 - 2.0 - - - - VnsCa - - F - 2.0 - - - - R - T - - - - - - 0.75 - Nai - - - - VnsCa - F - - - R - T - - - - - - 0.75 - Nao - - - - - - - VnsCa - F - - - R - T - - - - 1.0 - - - - - - - - - - - The maximal potassium component current. - - - - - - - I_ns_K - - P_ns_Ca - - 1.0 - 2.0 - - - - VnsCa - - F - 2.0 - - - - R - T - - - - - - 0.75 - Ki - - - - VnsCa - F - - - R - T - - - - - - 0.75 - Ko - - - - - - - VnsCa - F - - - R - T - - - - 1.0 - - - - - - - - - - - - - - - In the JRW model, subcellular calcium regulatory mechanisms are - described in detail. There are six calcium fluxes to consider; - J_rel, J_leak, J_up, J_tr, J_xfer and J_trpn. In addition, three - membrane current fluxes are also necessary for the formulation of - calcium regulation; i_p_Ca, i_Ca_L_Ca and i_NaCa. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculate some volume fractions as proportions of the total - myoplasmic volume. - - - - - - - V_SS - - 5.828e-5 - V_myo - - - - - - V_NSR - - 0.081 - V_myo - - - - - - V_JSR - - 0.00464 - V_myo - - - - - - - - - The calcium release flux from the JSR into the restricted subspace - is governed by the fraction of RyR channels in an open state. - - - - - - - J_rel - - v1 - RyR_open - - Ca_JSR - Ca_SS - - - - - - - - - - The "open" RyR's are those P_O1 and P_O2 states. - - - - - - - RyR_open - - P_O1 - P_O2 - - - - - - - - - The kinetic equations governing the transitions between the four - states used to model the RyR's. - - - - - - - - time - P_C1 - - - - - k_a_plus - - - Ca_SS - nCa - - P_C1 - - - k_a_minus - P_O1 - - - - - - - - time - P_O1 - - - - - k_a_plus - - Ca_SS - nCa - - P_C1 - - - - k_a_minus - P_O1 - - - k_b_plus - - Ca_SS - mCa - - P_O1 - - - k_c_plus - P_O1 - - - - - k_b_minus - P_O2 - - - k_c_minus - P_C2 - - - - - - - - time - P_O2 - - - - k_b_plus - - Ca_SS - mCa - - P_O1 - - - k_b_minus - P_O2 - - - - - - - - time - P_C2 - - - - k_c_plus - P_O1 - - - k_c_minus - P_C2 - - - - - - - - - - Calculate the leakage flux from the NSR into the myoplasm. - - - - - - - J_leak - - v2 - - Ca_NSR - Cai - - - - - - - - - - Calculate the uptake flux into the NSR from the myoplasm. - - - - - - - J_up - - v3 - - - Cai - 2.0 - - - - K_mup - 2.0 - - - Cai - 2.0 - - - - - - - - - - - - Calculate the translocation flux between the uptake (NSR) and - release (JSR) stores. - - - - - - - J_tr - - - Ca_NSR - Ca_JSR - - tau_tr - - - - - - - - - Calculate the calcium flux from the diffusion of calcium out of the - restricted subspace into the myoplasm. - - - - - - - J_xfer - - - Ca_SS - Cai - - tau_xfer - - - - - - - - - The kinetics of calcium binding to the myoplasm buffer troponin - - both high and low affinity binding sites. - - - - - - - J_htrpn - - - k_htrpn_plus - Cai - - HTRPN_tot - HTRPNCa - - - - k_htrpn_minus - HTRPNCa - - - - - - - J_ltrpn - - - k_ltrpn_plus - Cai - - LTRPN_tot - LTRPNCa - - - - k_ltrpn_minus - LTRPNCa - - - - - - - J_trpn - - J_htrpn - J_ltrpn - - - - - - - - - Keep track of the concentration of calcium ions bound to high and - low affinity troponin binding sites. - - - - - - - - time - HTRPNCa - - J_htrpn - - - - - - time - LTRPNCa - - J_ltrpn - - - - - - - - Calcium is buffered by calmodulin (CMDN) in the subspace and - myoplasm, and by calsequestrin (CSQN) in the JSR. These are fast - buffers and their effect is modelled using the rapid buffering - approximation. - - - - - - - Bi - - 1.0 - - 1.0 - - - CMDN_tot - K_mCMDN - - - - K_mCMDN - Cai - - 2.0 - - - - - - - - - B_SS - - 1.0 - - 1.0 - - - CMDN_tot - K_mCMDN - - - - K_mCMDN - Ca_SS - - 2.0 - - - - - - - - - B_JSR - - 1.0 - - 1.0 - - - CSQN_tot - K_mCSQN - - - - K_mCSQN - Ca_JSR - - 2.0 - - - - - - - - - - - - The kinetics of the calcium ion concentration changes in the various - compartments of the model. - - - - - - - - time - Cai - - - Bi - - - J_leak - J_xfer - - - J_up - J_trpn - - - - i_Ca_b - - 2.0 - i_NaCa - - - i_p_Ca - - - Am - - 2.0 - V_myo - F - - - - - - - - - - - - time - Ca_SS - - - B_SS - - - - J_rel - - V_JSR - V_SS - - - - J_xfer - - V_myo - V_SS - - - - - i_Ca_L_Ca - - Am - - 2.0 - V_SS - F - - - - - - - - - - - time - Ca_JSR - - - B_JSR - - J_tr - J_rel - - - - - - - - time - Ca_NSR - - - - - J_up - J_leak - - - V_myo - V_NSR - - - - J_tr - - V_JSR - V_NSR - - - - - - - - - - - - - - The descriptions of the rate of change of [Na]i and [K]i are the - same as the LR-II model. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The rate of change of intracellular sodium ion concentration. - - - - - - - - time - Nai - - - - - i_Na - i_Na_b - i_ns_Na - - i_NaCa - 3.0 - - - i_NaK - 3.0 - - - - - Am - - V_myo - F - - - - - - - - - - - The rate of change of intracellular potassium ion concentration. - - - - - - - - time - Ki - - - - - i_Ca_L_K - i_K - i_K1 - i_Kp - i_ns_K - - - i_NaK - 2.0 - - - - - - Am - - V_myo - F - - - - - - - - - - - The rate of change of extracellular potassium ion concentration. - - - - - - - - time - Ko - - - - i_Ca_L_K - i_K - i_K1 - i_Kp - i_ns_K - - - i_NaK - 2.0 - - - - - Am - - V_myo - F - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Bioelectrics/MonodomainCUDA/n98.xml b/Bioelectrics/MonodomainCUDA/n98.xml deleted file mode 100644 index 2945739a..00000000 --- a/Bioelectrics/MonodomainCUDA/n98.xml +++ /dev/null @@ -1,5799 +0,0 @@ - - - - - - - - - - - - - - - - Lloyd - Catherine - May - - - c.lloyd@auckland.ac.nz - - - - The University of Auckland - The Bioengineering Research Group - - - - - - 2001-12-18 - - - - - - Added more metadata. - - - - Lloyd - Catherine - May - - - - 2002-07-22 - - - - - Corrected units. - - - - Lloyd - Catherine - May - - - - 2002-03-01 - - - - - Corrected several equations. - - - - Lloyd - Catherine - May - - - - 2002-02-26 - - - - - Corrected the i_K1 and i_K_ACh calculations. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Updated metadata to conform to the 16/1/02 CellML Metadata 1.0 - Specification. - - - - Cuellar - Autumn - A. - - - - 2002-01-21 - - - - - Altered some of the connections. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Added some initial values from Penny Noble's documentation. Removed - the blocked h_gate component from the fast sodium current as it - belongs to a separate model which considers the effect of drugs. - - - - Lloyd - Catherine - May - - - - 2002-05-06 - - - - - Fixed up the CellML/MathML to enable the model to be solved in CMISS. The - model is no longer a direct translation of the Noble 1998 article, but - I believe it accurately represents the intent of the model. - - - - Nickerson - David - P - - - - 2003-04-05 - - - - - - Bioengineering Institute, The University of Auckland. - - - - - - - - The Noble 1998 Improved Guinea-Pig Ventricular Cell Model - - - - - - This is the CellML description of Noble's 1998 improved guinea-pig - ventricular cell model. It incorporates a diadic space, rapid and - slow potassium currents and length- and tension-dependent processes. - - - - Catherine Lloyd - - - - Guinea-Pig - - Ventricular Myocyte - - - - 9487284 - - - - - - - Noble - Denis - - - - - - - Varghese - Anthony - - - - - - - Kohl - Peter - - - - - - - Noble - Penny - - - - - - - Improved guinea-pig ventricular cell model incorporating a diadic - space, IKr and IKs, and length- and tension-dependent processes - - - 1998 - - - Canadian Journal of Cardiology - - 14 - 123 - 134 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This component is used to declare variables that are used by - all or most of the other components, in this case just `time'. - - - - - - - - - - - - - This component is the `root' node of our model. - It defines the action potential variable `V'. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A dummy equation used to get the total stimulus current into CMISS. - - - - - - - IStimC - IStim - - - - - - - - The ODE governing the membrane potential -- given by the summation of the - ionic currents and an applied stimulus. - - - - - - - - time - V - - - - IStim - - i_K1 - i_to - i_K - i_K_ATP - i_b_K - i_NaK - i_Na - i_b_Na - i_p_Na - i_NaCa - i_NaCa_ds - i_Ca_L_Ca - i_Ca_L_Ca_ds - i_Ca_L_K - i_Ca_L_K_ds - i_Ca_L_Na - i_Ca_L_Na_ds - i_b_Ca - i_Na_stretch - i_K_stretch - i_Ca_stretch - i_Ns_stretch - i_An_stretch - i_K_ACh - - - Cm - - - - - - - - - - - A component that conveniently keeps the reversal potential calculations - together. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the sodium reversal potential from the current intra- and - extracellular concentration of sodium ions. - - - - - - - E_Na - - - - R - T - - F - - - - Na_o - Na_i - - - - - - - - - - Calculation of the potassium reversal potential from the current intra- and - extracellular concentration of potassium ions. - - - - - - - E_K - - - - R - T - - F - - - - K_o - K_i - - - - - - - - - - Calculation of the potassium reversal potential for the slow component of - the delayed rectifier. - - - - - - - E_Ks - - - - R - T - - F - - - - - K_o - - P_kna - Na_o - - - - K_i - - P_kna - Na_i - - - - - - - - - - - - Calculation of the calcium reversal potential. - - - - - - - E_Ca - - 0.5 - - - R - T - - F - - - - Ca_o - Ca_i - - - - - - - - - - Calculation of the reversal potential for the fast sodium channel. - - - - - - - E_mh - - - - R - T - - F - - - - - Na_o - - P_nak - K_o - - - - Na_i - - P_nak - K_i - - - - - - - - - - - - - - - Description of the time independent inward potassium current. - - - - - - - - - - - - - - - - - - - - - - - Calculation of the time independent potassium current. - - - - - - - i_K1 - - g_K1 - - K_o - - K_o - K_mk1 - - - - - V - E_K - - - 1.0 - - - - 1.25 - - V - - E_K - 10.0 - - - - - - R - T - - F - - - - - - - - - - - - - - - - A component to group the potassium currents. - - - - - - - - - - - - - - - Simple summation of the individual potassium currents into a - single current. - - - - - - - i_K - - i_Kr - i_Ks - i_KNa - - - - - - - - - - - The rapid component of the delayed rectifier current. - - - - - - - - - - - - - - - - - - - - - - Calculation of the rapid component of the delayed rectifier current. - - - - - - - i_Kr - - - - g_Kr1 - Xr1 - - - g_Kr2 - Xr2 - - - - 1.0 - - 1.0 - - - - V - 9.0 - - 22.4 - - - - - - V - E_K - - - - - - - - - - - - The fast activation gate for the rapid component of the delayed - rectifier. - - - - - - - - - - - - - - The gating kinetics for the fast gate of the rapid component - of the delayed rectifier. - - - - - - - - time - Xr1 - - - - - 0.05 - - 1.0 - - - - - V - 5.0 - - - 9.0 - - - - - - 1.0 - Xr1 - - - - 0.00005 - - - - - V - 20.0 - - 15.0 - - - - Xr1 - - - - - - - - - - - - The slow gate of the rapid component of the delayed rectifier. - - - - - - - - - - - - - - Gating kinetics for the slow gate of the rapid component of - the delayed rectifier. - - - - - - - - time - Xr2 - - - - - 0.05 - - 1.0 - - - - - V - 5.0 - - - 9.0 - - - - - - 1.0 - Xr2 - - - - 0.0004 - - - - - - V - 30.0 - - 30.0 - - 3.0 - - - - Xr2 - - - - - - - - - - - - The slow component of the delayed rectifier current. - - - - - - - - - - - - - - - - - - - - Calculation of the slow component current of the delayed rectifier. - - - - - - - i_Ks - - - g_Ks - - Xs - 2.0 - - - - V - E_Ks - - - - - - - - - - - - The gate for the slow component of the delayed rectifier current. - - - - - - - - - - - - - - The gating kinetics for the slow component of the delayed - rectifier current. - - - - - - - - time - Xs - - - - - 0.014 - - 1.0 - - - - - V - 40.0 - - - 9.0 - - - - - - 1.0 - Xs - - - - Xs - 0.001 - - - - V - - 45.0 - - - - - - - - - - - - - - Background potassium current. - - - - - - - - - - - - - - - - - - Calculation of the background potassium current. - - - - - - - i_b_K - - g_bk - - V - E_K - - - - - - - - - - - - An ATP dependent potassium current. Included here for completeness, but - this current is only used when modelling ischaemia - and this version - of the model has not been tested for this. - - - - - - - - - - - - - - - - - - - Calculation of the ATP dependent potassium current. - - - - - - - i_K_ATP - - - g_K_ATP - - V - 80.0 - - - - 1.0 - - - ATP - K_ATP - - 2.0 - - - - - - - - - - - - - A sodium activated potassium current. Again, included for completeness - but generally not used and untested. - - - - - - - - - - - - - - - - - - - - Calculation of the sodium activated potassium current. - - - - - - - i_KNa - - g_K_Na - - Na_i - - Na_i - K_kna - - - - V - E_K - - - - - - - - - - - - The fast sodium current - the driving force of the upstroke of the - cardiac action potential. - - - - - - - - - - - - - - - - - - - - - Calculation of the fast sodium current. - - - - - - - i_Na - - g_Na - - m - 3.0 - - h - - V - E_mh - - - - - - - - - - - - The activation gate for the fast sodium current. - - - - - - - - - - - - - - - - - The gating kinetics for the activation gate of the fast sodium current. - - - - - - - - time - m - - - - alpha - - 1.0 - m - - - - beta - m - - - - - - - - - Calculation of the opening rate of the activation gate for the fast - sodium current. - - - - - - - alpha - - - 2.0 - - - - V - 41.0 - - - 0.1e-4 - - - - - - 0.2 - - V - 41.0 - - - - 1.0 - - - -0.1 - - V - 41.0 - - - - - - - - - - - - - - Calculation of the closing rate of the activation gate for the fast - sodium current. - - - - - - - beta - - 8.0 - - - -0.055556 - - V - 66.0 - - - - - - - - - - - - - - The inactivation gate for the fast sodium current. - - - - - - - - - - - - - - The gating kinetics for the inactivation gate of the fast sodium - current. - - - - - - - - time - h - - - - - 0.02 - - - -0.125 - - V - 75.0 - - - - - - 1.0 - h - - - - h - - 2.0 - - 1.0 - - 320.0 - - - -0.1 - - V - 75.0 - - - - - - - - - - - - - - - - - - The persistent sodium current. - - - - - - - - - - - - - - - - - - Calculation of the persistent sodium current. - - - - - - - i_p_Na - - g_pna - - 1.0 - - 1.0 - - - - - V - 52.0 - - 8.0 - - - - - - - V - E_Na - - - - - - - - - - - - The background sodium current. - - - - - - - - - - - - - - - - - - - Calculation of the sodium background current. - - - - - - - i_b_Na - - g_bna - - V - E_Na - - - - - - - - - - - - - This component describes an inward ionic current which is the sum - of calcium, sodium and potassium ions through the membrane channel. - The channel has one activation gate (d) and two inactivation gates - (f and f2 (or f2ds in the diadic space)). A fraction of these channels - (ICaLfract) open into the diadic subspace, with the remainder being - evenly distributed throughout the membrane area. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The calcium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_Ca - - - 1.0 - ICaLfract - - 4.0 - P_ca - d - f - f2 - - - - V - 50.0 - - - - R - T - - F - - - - 1.0 - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - - Ca_i - - - 50.0 - - - R - T - - - 2.0 - F - - - - - - - Ca_o - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The potassium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_K - - - 1.0 - ICaLfract - - P_caK - P_ca - d - f - f2 - - - K_i - - - 50.0 - - - R - T - - F - - - - - - K_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The sodium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_Na - - - 1.0 - ICaLfract - - P_caNa - P_ca - d - f - f2 - - - Na_i - - - 50.0 - - - R - T - - F - - - - - - Na_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The calcium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_Ca_ds - - ICaLfract - 4.0 - P_ca - d - f - f2ds - - - - V - 50.0 - - - - R - T - - F - - - - 1.0 - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - - Ca_ds - - - 50.0 - - - R - T - - - 2.0 - F - - - - - - - Ca_o - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The potassium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_K_ds - - ICaLfract - P_caK - P_ca - d - f - f2ds - - - K_i - - - 50.0 - - - R - T - - F - - - - - - K_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The sodium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_Na_ds - - ICaLfract - P_caNa - P_ca - d - f - f2ds - - - Na_i - - - 50.0 - - - R - T - - F - - - - - - Na_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - - - - The activation gate of the L-type calcium channel. - - - - - - - - - - - - - - - - - The gating kinetics for the activation gate. - - - - - - - - time - d - - - - alpha - - 1.0 - d - - - - beta - d - - - - - - - - - The opening rate for the activation gate. - - - - - - - alpha - - - 0.36 - - - - V - 19.0 - - - 1.0e-3 - - - - - - 0.09 - - V - 19.0 - - - - 1.0 - - - - - V - 19.0 - - - 4.0 - - - - - - - - - - - - - The closing rate for the activation gate. - - - - - - - beta - - - 0.36 - - - - V - 19.0 - - - 1.0e-3 - - - - - - -0.036 - - V - 19.0 - - - - 1.0 - - - - V - 19.0 - - 10.0 - - - - - - - - - - - - - - - - The first inactivation gate for the L-type calcium channel. - - - - - - - - - - - - - - - - - - - The gating kinetics for the first inactivation gate. - - - - - - - - time - f - - - - alpha - - 1.0 - f - - - - beta - f - - - - - - - - - The opening rate for the inactivation gate. - - - - - - - alpha - - - 0.0075 - - - - V - 34.0 - - - 1.0e-3 - - - - - -0.001875 - - - V - 34.0 - - - 1.0 - - - - V - 34.0 - - 4.0 - - - - - - - - - - - - - - The closing rate for the inactivation gate. - - - - - - - beta - - 0.0036 - - 1.0 - - - - - V - 34.0 - - 4.0 - - - - - - - - - - - - - - - The second inactivation gate for L-type calcium channels in the - membrane outside the diadic subspace. - - - - - - - - - - - - - - - - - - - The gating kinetics for the inactivation gate. - - - - - - - - time - f2 - - - CaInact - - 1.0 - - - Ca_i - - K_cachoff - Ca_i - - - f2 - - - - - - - - - - - - - The second inactivation gate for L-type calcium channels in the - membrane when open into the diadic subspace. - - - - - - - - - - - - - - - - - - The gating kinetics for the inactivation gate. - - - - - - - - time - f2ds - - - CaInactDS - - 1.0 - - - Ca_ds - - K_dsoff - Ca_ds - - - f2ds - - - - - - - - - - - - - The background calcium current. - - - - - - - - - - - - - - - - - - Calculation of the background calcium current. - - - - - - - i_b_Ca - - g_bca - - V - E_Ca - - - - - - - - - - - - The doubly gated transient outward current. - - - - - - - - - - - - - - - - - - - - - - - Evaluation of the transient outward current. - - - - - - - i_to - - g_to - - g_tos - - s - - 1.0 - g_tos - - - - r - - V - E_K - - - - - - - - - - - - The first gate of the transient outward current. - - - - - - - - - - - - - - The gating kinetics. - - - - - - - - time - s - - - - 0.000033 - - - - V - - 17.0 - - - - 1.0 - s - - - - - 0.033 - - 1.0 - - - - - V - 10.0 - - - 8.0 - - - - - s - - - - - - - - - - - - The second of the two gates for the transient outward current. - - - - - - - - - - - - - - - The gating kinetics for the r gate. - - - - - - - - time - r - - - 0.333 - - r_ss - r - - - - - - - - - Calculation of the steady-state component of the gating kinetics - for the r gate. - - - - - - - r_ss - - 1.0 - - 1.0 - - - -0.2 - - V - 4.0 - - - - - - - - - - - - - - - Acetylcholine (ACh) dependent potassium current. Once more, - this current has been included for completeness with respect - to the original publication but is usually left out of simulations. - It is useful for simulating specific cellular conditions, but - this formulation has not been tested. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Evaluation of the ACh dependent potassium current. - - - - - - - i_K_ACh - - g_KACh - - K_o - - K_o - K_KACh - - - x_ACh1 - x_ACh2 - - - ACh - 1.4969 - - - - ACh - 1.4969 - - - K_ACh - 1.4969 - - - - - - V - E_K - - - 1.0 - - - - 0.4 - - V - - E_K - 140.0 - - - - - - R - T - - F - - - - - - - - - - - - - - - - The first of two gates for the ACh dependent potassium current. - - - - - - - - - - - - - - - Gating kinetics for the first gate. - - - - - - - - time - x_ACh1 - - - - alpha_ACh - - 1.0 - x_ACh1 - - - - - 0.00582 - - 1.0 - - - - - V - 50.0 - - 15.0 - - - - - - x_ACh1 - - - - - - - - - - - - The second of the two gates for the ACh dependent potassium current. - - - - - - - - - - - - - - - Gating kinetics for the second gate. - - - - - - - - time - x_ACh2 - - - - alpha_ACh - - 1.0 - x_ACh2 - - - - - 0.12 - - 1.0 - - - - - V - 50.0 - - 15.0 - - - - - - x_ACh2 - - - - - - - - - - - - The sodium potassium pump. - - - - - - - - - - - - - - - - - - - - Calculation of the sodium potassium pump current. - - - - - - - i_NaK - - i_NaK_max - - K_o - - K_o - K_mk - - - - Na_i - - Na_i - K_mNa - - - - - - - - - - - - - The sodium calcium exchanger. A fraction of the Na-Ca exchangers - (INaCaFract) are assumed to emmpty into the diadic subspace, while - the remainder of the channels open into the bulk cytosol. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the sodium calcium exchanger current for the channels - exposed to the bulk myoplasm. - - - - - - - i_NaCa - - - 1.0 - INaCaFract - - K_NaCa - - - - - - gamma - - V - - - R - T - - F - - - - - - Na_i - 3.0 - - Ca_o - - - - - - gamma - 1.0 - - - V - - - R - T - - F - - - - - - Na_o - 3.0 - - Ca_i - - - - 1.0 - - d_NaCa - - - Ca_i - - Na_o - 3.0 - - - - Ca_o - - Na_i - 3.0 - - - - - - - - 1.0 - - 1.0 - - Ca_i - 0.0069 - - - - - - - - - - - Calculation of the sodium calcium exchanger current for the channels - opening into the diadic subspace. - - - - - - - i_NaCa_ds - - INaCaFract - K_NaCa - - - - - - gamma - - V - - - R - T - - F - - - - - - Na_i - 3.0 - - Ca_o - - - - - - gamma - 1.0 - - - V - - - R - T - - F - - - - - - Na_o - 3.0 - - Ca_ds - - - - 1.0 - - d_NaCa - - - Ca_ds - - Na_o - 3.0 - - - - Ca_o - - Na_i - 3.0 - - - - - - - - 1.0 - - 1.0 - - Ca_ds - 0.0069 - - - - - - - - - - - - - - The sarcoplasmic reticulum calcium pump which transports calcium - from the bulk myoplasm into the network SR. - - - - - - - - - - - - - - - - - - - - Calculation of the calcium uptake flux. - - - - - - - i_up - - - - 0.0004 - Ca_i - - - 0.00003 - Ca_up - - - K_cyca - K_xcs - - K_srca - - - - - Ca_i - - Ca_up - - - K_cyca - K_xcs - - K_srca - - - - K_cyca - K_xcs - - K_cyca - - - - - - - - - - - - Diffusion down the concentration gradient to transfer calcium from - the uptake stores in the network SR to the release stores in the - junctional SR. - - - - - - - - - - - - - - - - Calculation of the transfer flux between the uptake and release - calcium stores. - - - - - - - i_tr - - 0.05 - - Ca_up - Ca_rel - - - - - - - - - - - - This component describes the addition of - length dependence to the Noble models. However, in this implementation - of the model, it is unused - sarcomere length (SL) is a constant 0, - resulting in the removal of length dependence from the model. - - - - - - - - - - - - - - - - - Calculation of the scaling factor for the stretch activated currents - based on the change in length from the reference state. - - - - - - - f_stretch - - 1.0 - - 1.0 - - - -2.0 - gamma_SAC_SL - - SL - SLRef - - - - - - - - - - - - - - - The length dependent leakage of calcium from the junctional - SR into the cytolsol. - - - - - - - - - - - - - - - - i_leak - - - - gamma_SR_SL - SL - - - alpha_SRleak - Ca_rel - - - - - - - - - - - Description of the diffusion of calcium out of the diadic - subspace into the bulk cytosol. - - - - - - - - - - - - - - - - Calculation of the flux of calcium out of the diadic subspace. - - - - - - - i_decay - - alpha_ca_ds_decay - Ca_ds - - - - - - - - - - - The calcium induced calcium release from the junctional SR into - the bulk myoplasm. Assumed that activation of calcium release sites - by the diadic subspace calcium triggers calcium release in the whole - cytosol. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The fraction of release sites in the open state. - - - - - - - OpenReleaseChannelFract - - - ActivatorFract - - ActivatorFract - 0.25 - - - 2.0 - - - - - - - - Calculation of the calcium release flux from the JSR into the cytosol. - - - - - - - i_rel - - alpha_rel - OpenReleaseChannelFract - Ca_rel - - - - - - - - Regulatory binding sites. - - - - - - - RegulatoryBindingSite - - - - Ca_i - - Ca_i - K_mca - - - - - 1.0 - - Ca_i - - Ca_i - K_mca - - - - - Ca_ds - - Ca_ds - K_mca_ds - - - - - 2.0 - - - - - - - - Fraction of release channels in the precursor state. - - - - - - - PrecursorFract - - 1.0 - - ActivatorFract - ProductFract - - - - - - - alpha_act - - 0.5 - RegulatoryBindingSite - - - - - - alpha_inact - - 0.06 - - 0.5 - RegulatoryBindingSite - - - - - - - SR_speed_factor - - - 5.0 - - V - -50.0 - - - - 1.0 - - - - - - - - - time - - ActivatorFract - - - SR_speed_factor - - - alpha_act - PrecursorFract - - - alpha_inact - ActivatorFract - - - - - - - - - - time - - ProductFract - - - SR_speed_factor - - - alpha_inact - ActivatorFract - - - 0.001 - ProductFract - - - - - - - - - - - - - A stretch activated calcium current. Unused and untested in this - implementation, but included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ca_stretch - - g_Ca_stretch - f_stretch - - V - E_Ca - - - - - - - - - - - - Stretch activated potassium current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_K_stretch - - g_K_stretch - f_stretch - - V - E_K - - - - - - - - - - - - A stretch activated sodium current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Na_stretch - - g_Na_stretch - f_stretch - - V - E_Na - - - - - - - - - - - - A non-specific stretch activated current. Not used and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ns_stretch - - g_Ns_stretch - f_stretch - - V - E_Ns_stretch - - - - - - - - - - - - A anion specific stretch ativated current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_An_stretch - - g_An_stretch - f_stretch - - V - E_An_stretch - - - - - - - - - - - - A convenient grouping of all the ionic concentration differential - equations. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The rate of change of intracellular sodium concentration. - - - - - - - - time - Na_i - - - - - Am - - V_i - F - - - - - i_Na - i_p_Na - - i_b_Na - - Na_o - 140.0 - - - - i_NaK - 3.0 - - - i_NaCa - 3.0 - - - i_NaCa_ds - 3.0 - - i_Ca_L_Na - i_Ca_L_Na_ds - i_Na_stretch - - - - - - - - - The rate of change of intracellular potassium concentration. - - - - - - - - time - K_i - - - - - Am - - V_i - F - - - - - - i_K1 - i_to - i_b_K - i_K - i_K_stretch - i_Ca_L_K - i_Ca_L_K_ds - i_K_ACh - i_K_ATP - - - i_NaK - 2.0 - - - - - - - - - - The rate of change of intracellular calcium concentration. - - - - - - - - time - Ca_i - - - - - - - Am - - 2.0 - V_i - F - - - - - - i_Ca_L_Ca - i_b_Ca - i_Ca_stretch - - - i_NaCa - 2.0 - - - - - i_rel - - V_rel - V_i - - - - i_leak - - V_rel - V_i - - - - i_decay - - V_ds - V_i - - - - - i_up - dy_Ca_calmod - dy_Ca_troponin - - - - - - - - - The rate of change of calcium concentration in the diadic subspace. - - - - - - - - time - Ca_ds - - - - - - Am - - 2.0 - V_ds - F - - - - - i_Ca_L_Ca_ds - - i_NaCa_ds - 2.0 - - - - i_decay - - - - - - - - The rate of change of calcium concentration in the network SR - uptake store. - - - - - - - - time - Ca_up - - - - - V_i - V_up - - i_up - - i_tr - - - - - - - - The rate of change of calcium concentration in the junctional SR - release store. - - - - - - - - time - Ca_rel - - - - - V_up - V_rel - - i_tr - - - i_rel - i_leak - - - - - - - - - The rate of change of calcium bound to calmodulin. - - - - - - - dy_Ca_calmod - - - 100.0 - Ca_i - - CALM - Ca_calmod - - - - 0.05 - Ca_calmod - - - - - - - - time - Ca_calmod - - dy_Ca_calmod - - - - - - - The rate of change of calcium bound to troponin. - - - - - - - dy_Ca_troponin - - - alpha_trop - Ca_i - - TROP - Ca_troponin - - - - beta_trop - Ca_troponin - - - - - - - - time - Ca_troponin - - dy_Ca_troponin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Bioelectrics/Monodomain_Shiqiang/input/FHN.xml b/Bioelectrics/Monodomain_Shiqiang/input/FHN.xml deleted file mode 100644 index c01c9d20..00000000 --- a/Bioelectrics/Monodomain_Shiqiang/input/FHN.xml +++ /dev/null @@ -1,355 +0,0 @@ - - - - -
- - The FitzHugh-Nagumo Simplified Cardiac Myocyte Model - - Catherine - Lloyd - - Bioengineering Institute, University of Auckland - - - -
- Model Status - - This version of the model has been curated by Penny Noble using - COR and is also known to read in to JSim and PCEnv. There is also a PCEnv session file associated with this model. - -
- -Model Structure - - -Often it is not necessary to model the ionic currents of a cell with the accuracy and complexity inherent in the biophysically based models. With a view to investigating phenomena on a larger spatial and temporal scale, several ionic current models have been developed that do not seek to model subcellular processes but only to provide an action potential at a minimal computational cost. - - - -The FitzHugh-Nagumo model (1961) is based on the cubic excitation model (see The Polynomial Model, 1975), but it also includes a recovery variable so both depolarisation and repolarisation can be modelled. In 1994, Rogers and McCulloch modified the original model to generate a more realistic action potential. The velocity of the upstroke was increased and the large hyperpolarisation at the end of the recovery phase was removed. The model parameters were also updated. In 1996, this form of the already modified FitzHugh_Nagumo model was further updated by Aliev and Panfilov. They altered the equation which modelled the change of the recovery variable to provide a more realistic restitution period and to allow for reentrant phenomena. - - - -The complete original paper references are cited below: - - - -Impulses and physiological states in theoretical models of nerve membrane, FitzHugh, R.A., 1961, - Biophys. J. - , 1, 445-466. - - - -An active pulse transmission line simulating nerve axon, Nagumo, J., Animoto, S., Yoshizawa, S., 1962, Proc. Inst. Radio Engineers, 50, 2061-2070. - - - -A collocation-Galerkin finite element model of cardiac action potential propagation, Rogers, J.M., McCulloch, A.D., 1994a, - IEEE Trans. Biomed. Eng. - , 41, 743-757. - - - -A simple two-variable model of cardiac excitation, Aliev, R.R. and Panfilov, A.V., 1996, - Chaos, Solitons and Fractals - , 7, 293-301. PubMed ID: 8796189 - - - -The raw CellML description of the simplified cardiac myocyte models can be downloaded in various formats as described in . For an example of a more complete documentation for an electrophysiological model, see The Hodgkin-Huxley Squid Axon Model, 1952. - - - -
- - - - - - - - - - - - - - - - - - - - - - - t - - v - - - - 1 - - - - - - - v - - - v - alpha - - - - 1 - v - - - w - - I - - - - - - - - - t - - w - - - - 1 - epsilon - - - v - - - gamma - w - - - - - - - - - - - - - - - - - - - - - J - Nagumo - - - - - - - - - - - - - - S - Yoshizawa - - - 1962-10-01 00:00 - - - - - - - - Peter - Villiger - J - - - - An active pulse transmission line simulating nerve axon - 50 - 2061 - - - 2070 - - - J - Nagumo - - - Penny - Noble - J - - - - - - - - - - - - - - - - - - Penny - Noble - - - - 1000 - 10000 - - - - - - - Department of Physiology, Anatomy & Genetics, University of Oxford - - - - - - - Biophysical Journal - - - S - Arimoto - - - - - - - - Impulses and Physiological States in Theoretical Models of Nerve Membrane - 1 - 445 - - - 466 - - - 2005-06-14T00:00:00+00:00 - - - - - - - - keyword - - - simplified model - neuron - electrophysiology - cardiac - Myocyte - - - - - - - - - added metadata - - - - - Units checked, curated. - - - - - - - - - - - 2007-11-29T12:16:16+13:00 - - - - - - Oxford University - The Bioengineering Institute - - - Biophysical Journal - - - - - - Richard - Fitzhugh - A - - - - - - - - - - - penny.noble@physiol.ox.ac.uk - - - 1961-01-01 - - - - - - - 2006-03-31 - - - \ No newline at end of file diff --git a/Bioelectrics/Monodomain_Shiqiang/input/LRd.xml b/Bioelectrics/Monodomain_Shiqiang/input/LRd.xml deleted file mode 100644 index 1fd24b84..00000000 --- a/Bioelectrics/Monodomain_Shiqiang/input/LRd.xml +++ /dev/null @@ -1,4320 +0,0 @@ - - - - - - - - - - - - - Lloyd - Catherine - May - - - c.lloyd@auckland.ac.nz - - - - The University of Auckland - The Bioengineering Institute - - - - - - 2002-03-28 - - - - - - Fixed maths. - - - - Lloyd - Catherine - May - - - - 2003-07-30 - - - - - Fixed maths: alpha_J_calculation in fast_sodium_current_j_gate, - beta_K1_calculation in time_independent_potassium_current_K1_gate, and i_NaK_calculation in sodium_potassium_pump. - - - - Lloyd - Catherine - May - - - - 2003-06-05 - - - - - - The University of Auckland, The Bioengineering Institute - - - - - - - - The Luo-Rudy II Model of Mammalian Ventricular Cardiac Action - Potentials, 1994 - - - - - - This is the CellML description of Luo and Rudy's mathematical model of - the mammalian cardiac ventricular action potential. It is a - significant development on their original 1991 model. While this - version of the model qualitatively compares well to the LR II paper - for the action potential, the intracellular calcium dynamics have not - been included correctly - namely there is no calcium-induced - calcium-release (CICR) process in this version of the model. The - original version of the model simulates CICR via a mechanism whereby - CICR is induced if and only if the calcium accumulated in the cell in - the 2 ms following (dV/dt)max exceeds a given threshold. This sort of - process is a bit tricky to include in the CellML (or at least in a way - that will work with the CellML abilitites of CMISS) so has been left - out for now. - - - - Catherine Lloyd - - - - - Mammalia - - Ventricular Myocyte - - - - 7514509 - - - - bdf - newton - dense - - - - - - - 0.01 - - - 1.0 - - - 0 - - - 700 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The main component for the model, contains all ionic currents and - defines the transmembrane potential. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - We need to use dV/dt in the calulation of calcium-induced - calcium-release, so we make it accessible here. - - - - - - - dV_dt - - - I_st - - i_Na - i_Ca_L - i_K - i_K1 - i_Kp - i_NaCa - i_p_Ca - i_Na_b - i_Ca_b - i_NaK - i_ns_Ca - - - Cm - - - - - - - - - Assign the rate of change of potential for the differential - equation. - - - - - - - - time - V - - dV_dt - - - - - - - - - - - The fast sodium current is primarily responsible for the upstroke of - the action potential. - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the fast sodium current. - - - - - - - i_Na - - g_Na - - m - 3.0 - - h - j - - V - E_Na - - - - - - - - - - Calculation of reversal potential for the fast sodium channel. - - - - - - - E_Na - - - - R - T - - F - - - - Nao - Nai - - - - - - - - - - - - - The voltage-dependent activation gate for the fast sodium channel - - the m gate. - - - - - - - - - - - - - - - - - - The opening rate for the m gate. - - - - - - - alpha_m - - - 0.32 - - V - 47.13 - - - - 1.0 - - - -0.1 - - V - 47.13 - - - - - - - - - - - - - The closing rate for the m gate. - - - - - - - beta_m - - 0.08 - - - - V - - 11.0 - - - - - - - - - - - The kinetics of the m gate. - - - - - - - - time - m - - - - alpha_m - - 1.0 - m - - - - beta_m - m - - - - - - - - - - - - The voltage-dependent inactivation gate for the fast sodium channel - - the h gate. - - - - - - - - - - - - - - - - - - The opening rate for the h gate. - - - - - - - alpha_h - - - - 0.135 - - - - 80.0 - V - - -6.8 - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate for the h gate. - - - - - - - beta_h - - - - - 3.56 - - - 0.079 - V - - - - - 310000.0 - - - 0.35 - V - - - - - - V - -40.0 - - - - - 1.0 - - 0.13 - - 1.0 - - - - V - 10.66 - - -11.1 - - - - - - - - - - - - - - - The kinetics of the h gate. - - - - - - - - time - h - - - - alpha_h - - 1.0 - h - - - - beta_h - h - - - - - - - - - - - - The voltage-dependent slow inactivation gate for the fast sodium - channel - the j gate. - - - - - - - - - - - - - - - - - - The opening rate for the j gate. - - - - - - - alpha_j - - - - - - -127140.0 - - - 0.2444 - V - - - - - 0.00003474 - - - -0.04391 - V - - - - - - - V - 37.78 - - - 1.0 - - - 0.311 - - V - 79.23 - - - - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate for the j gate. - - - - - - - beta_j - - - - - 0.1212 - - - -0.01052 - V - - - - - 1.0 - - - -0.1378 - - V - 40.14 - - - - - - - V - -40.0 - - - - - - 0.3 - - - -0.0000002535 - V - - - - - 1.0 - - - -0.1 - - V - 32.0 - - - - - - - - - - - - - - - The kinetics of for the j gate. - - - - - - - - time - j - - - - alpha_j - - 1.0 - j - - - - beta_j - j - - - - - - - - - - - - The L-type calcium channel. Primarily a calcium specific channel, - but with small potassium and sodium components, activated at plateau - potentials. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The calcium component of the total L-type channel current. - - - - - - - i_CaCa - - d - f - f_Ca - I_CaCa - - - - - - - - - The sodium component of the total L-type channel current. - - - - - - - i_CaNa - - d - f - f_Ca - I_CaNa - - - - - - - - - The potassium component of the total L-type channel current. - - - - - - - i_CaK - - d - f - f_Ca - I_CaK - - - - - - - - - The maximum calcium component of the total L-type channel current. - - - - - - - I_CaCa - - P_Ca - - 2.0 - 2.0 - - - - V - - F - 2.0 - - - - R - T - - - - - - gamma_Cai - Cai - - - - 2.0 - V - F - - - R - T - - - - - - gamma_Cao - Cao - - - - - - - 2.0 - V - F - - - R - T - - - - 1.0 - - - - - - - - - - - The maximum sodium component of the total L-type channel current. - - - - - - - I_CaNa - - P_Na - - 1.0 - 2.0 - - - - V - - F - 2.0 - - - - R - T - - - - - - gamma_Nai - Nai - - - - 1.0 - V - F - - - R - T - - - - - - gamma_Nao - Nao - - - - - - - 1.0 - V - F - - - R - T - - - - 1.0 - - - - - - - - - - - The maximum potassium component of the total L-type channel current. - - - - - - - I_CaK - - P_K - - 1.0 - 2.0 - - - - V - - F - 2.0 - - - - R - T - - - - - - gamma_Ki - Ki - - - - 1.0 - V - F - - - R - T - - - - - - gamma_Ko - Ko - - - - - - - 1.0 - V - F - - - R - T - - - - 1.0 - - - - - - - - - - - The total current of the L-type channel current. - - - - - - - i_Ca_L - - i_CaCa - i_CaK - i_CaNa - - - - - - - - - - - The voltage-dependent activation gate for the L-type calcium - channel - the d gate. - - - - - - - - - - - - - - - - - - - - The opening rate of the d gate. - - - - - - - alpha_d - - d_infinity - tau_d - - - - - - - d_infinity - - 1.0 - - 1.0 - - - - - V - 10.0 - - 6.24 - - - - - - - - - - - tau_d - - d_infinity - - - 1.0 - - - - - V - 10.0 - - 6.24 - - - - - - 0.035 - - V - 10.0 - - - - - - - - - - - - The closing rate of the d gate. - - - - - - - beta_d - - - 1.0 - d_infinity - - tau_d - - - - - - - - - The kinetics of the d gate. - - - - - - - - time - d - - - - alpha_d - - 1.0 - d - - - - beta_d - d - - - - - - - - - - - - The voltage-dependent inactivation gate for the L-type calcium - channel - the f gate. - - - - - - - - - - - - - - - - - - - - The opening rate of the f gate. - - - - - - - alpha_f - - f_infinity - tau_f - - - - - - - f_infinity - - - 1.0 - - 1.0 - - - - V - 35.06 - - 8.6 - - - - - - 0.6 - - 1.0 - - - - 50.0 - V - - 20.0 - - - - - - - - - - - tau_f - - 1.0 - - - 0.0197 - - - - - 0.0337 - - V - 10.0 - - - 2.0 - - - - - 0.02 - - - - - - - - - - The closing rate of the f gate. - - - - - - - beta_f - - - 1.0 - f_infinity - - tau_f - - - - - - - - - The kinetics of the f gate. - - - - - - - - time - f - - - - alpha_f - - 1.0 - f - - - - beta_f - f - - - - - - - - - - - - The calcium-dependent inactivation gate for the L-type calcium - channel - the fCa gate. - - - - - - - - - - - - - - - - - - The kinetics of the fCa gate. - - - - - - - f_Ca - - 1.0 - - 1.0 - - - Cai - Km_Ca - - 2.0 - - - - - - - - - - - - - The time-dependent potassium reploarisation current. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The conductance for the channel. - - - - - - - g_K - - g_K_max - - - Ko - 5.4 - - - - - - - - - - - The reversal potential of the channel. - - - - - - - E_K - - - - R - T - - F - - - - - Ko - - PR_NaK - Nao - - - - Ki - - PR_NaK - Nai - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_K - - g_K - - X - 2.0 - - Xi - - V - E_K - - - - - - - - - - - - The time-dependent activation gate for the time-dependent potassium - current - the X gate. - - - - - - - - - - - - - - - - - - The opening rate for the X gate. - - - - - - - alpha_X - - - 0.0000719 - - V - 30.0 - - - - 1.0 - - - -0.148 - - V - 30.0 - - - - - - - - - - - - - The closing rate for the X gate. - - - - - - - beta_X - - - 0.000131 - - V - 30.0 - - - - -1.0 - - - 0.0687 - - V - 30.0 - - - - - - - - - - - - - The kinetics of the X gate. - - - - - - - - time - X - - - - alpha_X - - 1.0 - X - - - - beta_X - X - - - - - - - - - - - - The time-independent inactivation gate for the time-dependent - potassium current - the Xi gate. - - - - - - - - - - - - - - - The kinetics of the Xi gate. - - - - - - - Xi - - 1.0 - - 1.0 - - - - V - 56.26 - - 32.1 - - - - - - - - - - - - - - The time-independent potassium repolarisation current. - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the channel conductance. - - - - - - - g_K1 - - g_K1_max - - - Ko - 5.4 - - - - - - - - - - - Calculation of the channel reversal potential. - - - - - - - E_K1 - - - - R - T - - F - - - - Ko - Ki - - - - - - - - - - - Calculation of the channel current. - - - - - - - i_K1 - - g_K1 - K1_infinity - - V - E_K1 - - - - - - - - - - - - The gating variable for the time-independent potassium current - the - K1 gate. - - - - - - - - - - - - - - - - - - The opening rate for the K1 gate. - - - - - - - alpha_K1 - - 1.02 - - 1.0 - - - 0.2385 - - - V - E_K1 - - 59.215 - - - - - - - - - - - - - The closing rate for the K1 gate. - - - - - - - beta_K1 - - - - 0.49124 - - - 0.08032 - - - V - 5.476 - - E_K1 - - - - - - - 0.06175 - - V - - E_K1 - 594.31 - - - - - - - 1.0 - - - -0.5143 - - - V - E_K1 - - 4.753 - - - - - - - - - - - - - The steady-state kinetics of the K1 gate. - - - - - - - K1_infinity - - alpha_K1 - - alpha_K1 - beta_K1 - - - - - - - - - - - - The potassium current active at plateau potentials. - - - - - - - - - - - - - - - - - - - - The reversal potential for the channel. - - - - - - - E_Kp - E_K1 - - - - - - - - The gating kinetics for the channel. - - - - - - - Kp - - 1.0 - - 1.0 - - - - 7.488 - V - - 5.98 - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Kp - - g_Kp - Kp - - V - E_Kp - - - - - - - - - - - - A calcium pump for removal of calcium from the cytosol to the - extracellular space. - - - - - - - - - - - - - - - - - - The calcium pump current. - - - - - - - i_p_Ca - - I_pCa - - Cai - - K_mpCa - Cai - - - - - - - - - - - - - The background sodium current. - - - - - - - - - - - - - - - - - - - The reversal potential for the channel. - - - - - - - E_NaN - E_Na - - - - - - - - Calculation of the current. - - - - - - - i_Na_b - - g_Nab - - V - E_NaN - - - - - - - - - - - - The background calcium current. - - - - - - - - - - - - - - - - - - - - - - - The reversal potential for the channel. - - - - - - - E_CaN - - - - R - T - - - 2.0 - F - - - - - Cao - Cai - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ca_b - - g_Cab - - V - E_CaN - - - - - - - - - - - - The sodium/potassium exchanger current which extrudes three sodium - ions from the cell in exchange for two potassium ions entering the - cell. - - - - - - - - - - - - - - - - - - - - - - - - - f_NaK - - 1.0 - - - 1.0 - - 0.1245 - - - -0.1 - - - V - F - - - R - T - - - - - - - - 0.0365 - sigma - - - - - V - F - - - R - T - - - - - - - - - - - - - sigma - - - 1.0 - 7.0 - - - - - Nao - 67.3 - - - 1.0 - - - - - - - - - - Calculation of the exchanger current. - - - - - - - i_NaK - - I_NaK - f_NaK - - 1.0 - - 1.0 - - - K_mNai - Nai - - 1.5 - - - - - Ko - - Ko - K_mKo - - - - - - - - - - - - - A non-specific calcium activated channel - assumed impermeable to - calcium ions but permeable to sodium and potassium ions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The channel reversal potential. - - - - - - - EnsCa - - - - R - T - - F - - - - - Ko - Nao - - - Ki - Nai - - - - - - - - - - Vns - - V - EnsCa - - - - - - - - - The sodium component of the channel's current. - - - - - - - i_ns_Na - - I_ns_Na - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The potassium component of the channel's current. - - - - - - - i_ns_K - - I_ns_K - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The total current through the channel. - - - - - - - i_ns_Ca - - i_ns_Na - i_ns_K - - - - - - - - - The maximum sodium component of the channel's current. - - - - - - - I_ns_Na - - P_ns_Ca - - 1.0 - 2.0 - - - - Vns - - F - 2.0 - - - - R - T - - - - - - gamma_Nai - Nai - - - - 1.0 - Vns - F - - - R - T - - - - - - gamma_Nao - Nao - - - - - - - 1.0 - Vns - F - - - R - T - - - - 1.0 - - - - - - - - - - - The maximum potassium component of the channel's current. - - - - - - - I_ns_K - - P_ns_Ca - - 1.0 - 2.0 - - - - Vns - - F - 2.0 - - - - R - T - - - - - - gamma_Ki - Ki - - - - 1.0 - Vns - F - - - R - T - - - - - - gamma_Ko - Ko - - - - - - - 1.0 - Vns - F - - - R - T - - - - 1.0 - - - - - - - - - - - - - The sodium-calcium exchanger current, exchanges three sodium ions - for one calcium ion. - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the exchanger current. - - - - - - - i_NaCa - - K_NaCa - - 1.0 - - - K_mNa - 3.0 - - - Nao - 3.0 - - - - - 1.0 - - K_mCa - Cao - - - - 1.0 - - 1.0 - - K_sat - - - - eta - 1.0 - - V - - F - - R - T - - - - - - - - - - - - eta - V - - F - - R - T - - - - - - Nai - 3.0 - - Cao - - - - - - eta - 1.0 - - V - - F - - R - T - - - - - - Nao - 3.0 - - Cai - - - - - - - - - - - - - The various calcium fluxes into and from the sarcoplasmic reticulum. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The release flux from the junctional sarcoplasmic reticulum into the - cytosol. - - - - - - - i_rel - - G_rel - - Ca_JSR - Cai - - - - - - - - - - Calculation of the release channel conductance. This is incorrect as - there is no CICR induced via the accumulation of calcium in the - cytosol in the period following max(dV/dt) - - - - - - - G_rel - - G_rel_peak - - - delta_Ca_i2 - delta_Ca_ith - - - - K_mrel - delta_Ca_i2 - - delta_Ca_ith - - - - 1.0 - - - - t_CICR - tau_on - - - - - - - - t_CICR - tau_off - - - - - - - - - - G_rel_peak - - - 0.0 - - delta_Ca_i2 - delta_Ca_ith - - - - G_rel_max - - - - - - - - - - The uptake flux into the sarcoplasmic reticulum from the cytosol. - - - - - - - i_up - - I_up - - Cai - - Cai - K_mup - - - - - - - - - - - Calcium leak flux from the network sarcoplasmic reticulum into the - cytosol. - - - - - - - i_leak - - K_leak - Ca_NSR - - - - - - - K_leak - - I_up - Ca_NSR_max - - - - - - - - - Translocation flux from the network to the junctional sarcoplasmic - reticulum. - - - - - - - i_tr - - - Ca_NSR - Ca_JSR - - tau_tr - - - - - - - - - - - Component grouping together the differential equations for the - various ionic concentrations that the model tracks. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The change in intracellular sodium concentration. - - - - - - - - time - Nai - - - - - i_Na - i_CaNa - i_Na_b - i_ns_Na - - i_NaCa - 3.0 - - - i_NaK - 3.0 - - - - - Am - - V_myo - F - - - - - - - - - - - The change in intracellular calcium concentration. - - - - - - - - time - Cai - - - - - - - i_CaCa - i_p_Ca - i_Ca_b - - i_NaCa - - - - Am - - 2.0 - V_myo - F - - - - - i_rel - - V_JSR - V_myo - - - - - i_leak - i_up - - - V_NSR - V_myo - - - - - - - - - - - The change in intracellular potassium concentration. - - - - - - - - time - Ki - - - - - i_CaK - i_K - i_K1 - i_Kp - i_ns_K - - - i_NaK - 2.0 - - - - - - Am - - V_myo - F - - - - - - - - - - - The change in calcium concentration in the junctional sarcoplasmic - reticulum. - - - - - - - - time - Ca_JSR - - - - i_rel - - i_tr - - V_NSR - V_JSR - - - - - - - - - - - - The change in calcium concentration in the network sarcoplasmic - reticulum. - - - - - - - - time - Ca_NSR - - - - - i_leak - i_tr - - i_up - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Bioelectrics/Monodomain_Shiqiang/input/jrw-1998.xml b/Bioelectrics/Monodomain_Shiqiang/input/jrw-1998.xml deleted file mode 100644 index 6a407ee4..00000000 --- a/Bioelectrics/Monodomain_Shiqiang/input/jrw-1998.xml +++ /dev/null @@ -1,5332 +0,0 @@ - - - - - - - - - - - - - Lloyd - Catherine - May - - - c.lloyd@auckland.ac.nz - - - - The University of Auckland - The Bioengineering Research Group - - - - - - 2001-09-24 - - - - - - Corrected equations. - - - - Lloyd - Catherine - May - - - - 2003-07-30 - - - - - Corrected equations: alpha_j_calculation and beta_j_calculation in - fast_sodium_current_j_gate, alpha_X_calculation and beta_X_calculation in time_dependent_potassium_current_X_gate, and f_NaK_calculation and - i_NaK_calculation in Ca_release_current_from_JSR. - - - - Lloyd - Catherine - May - - - - 2003-06-04 - - - - - Added some initial values from Penny Noble's documentation. - - - - Lloyd - Catherine - May - - - - 2002-05-06 - - - - - Corrected several equations, variable units and their initial values. - - - - Lloyd - Catherine - May - - - - 2002-02-28 - - - - - Corrected several equations. - - - - Lloyd - Catherine - May - - - - 2002-02-25 - - - - - Altered some of the connections. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Changed tau_y_calculation after checking mathml using the validator. - - - - Lloyd - Catherine - May - - - - 2001-12-07 - - - - - Removed document type definition as this is declared as optional - according to the W3C recommendation. - - - - Lloyd - Catherine - May - - - - 2001-10-19 - - - - - - - The University of Auckland, Bioengineering Research Group - - - - - - - - The Jafri-Rice-Winslow Model for Calcium Regulation in the Ventricular - Myocyte, 1997 - - - - - - This is the CellML description of Jafri, Rice and Winslow's - mathematical model for calcium regulation in the ventricular myocyte. - It is based on an accurate model of the membrane currents and adds a - more sophisticated model of calcium handling. The JRW model is based - on the LR-II model for ventricular action potentials, with several - modifications. - - - - Catherine Lloyd - - - - - Mammalia - - Ventricular Myocyte - - - - 9512016 - - - - - - - Jafri - M - Saleet - - - - - - - Rice - John - Jeremy - - - - - - - Winslow - Raimond - L - - - - - - - Cardiac Ca2+ Dynamics: The Roles of Ryanodine Receptor Adaptation - and Sarcoplasmic Reticulum Load - - - 1998-03 - - - Biophysical Journal - - 74 - 1149 - 1168 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The main component of the model which defines the action potential. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The kinetics of the transmembrane potential, defined as the sum of - all the sarcolemmal currents and an applied stimulus current. - - - - - - - - time - V - - - - I_stim - - i_Na - i_Ca_L_Ca - i_Ca_L_K - i_K - i_NaCa - i_K1 - i_Kp - i_p_Ca - i_Na_b - i_Ca_b - i_NaK - i_ns_Ca - - - Cm - - - - - - - - This is a dummy equation that we simply use to make grabbing the - value in CMISS much easier. - - - - - - - - IStimC - I_stim - - - - - - - - - - The fast sodium current component contains the differential - equations governing the influx of sodium ions through the cell - surface membrane into the cell. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the fast sodium current using the three - Hodkin-Huxley type voltage-dependent gating variables m, h, and j. - - - - - - - i_Na - - g_Na - - m - 3.0 - - h - j - - V - E_Na - - - - - - - - - - The sodium reversal potential. - - - - - - - E_Na - - - - R - T - - F - - - - Nao - Nai - - - - - - - - - - - - - - The voltage-dependent activation gate for the fast sodium current - - the m gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the m gate. - - - - - - - alpha_m - - - 0.32 - - V - 47.13 - - - - 1.0 - - - -0.1 - - V - 47.13 - - - - - - - - - - - - - The closing rate of the m gate. - - - - - - - beta_m - - 0.08 - - - - V - - 11.0 - - - - - - - - - - - The kinetics of the m gate. - - - - - - - - time - m - - - - alpha_m - - 1.0 - m - - - - beta_m - m - - - - - - - - - - - - - The voltage-dependent inactivation gate for the fast sodium current - - the h gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the h gate. - - - - - - - alpha_h - - - - 0.135 - - - - 80.0 - V - - -6.8 - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate of the h gate. - - - - - - - beta_h - - - - - 3.56 - - - 0.079 - V - - - - - 310000.0 - - - 0.35 - V - - - - - - V - -40.0 - - - - - 1.0 - - 0.13 - - 1.0 - - - - V - 10.66 - - -11.1 - - - - - - - - - - - - - - - The kinetics of the h gate. - - - - - - - - time - h - - - - alpha_h - - 1.0 - h - - - - beta_h - h - - - - - - - - - - - - - The voltage-dependent slow inactivation gate for the fast sodium - current - the j gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the j gate. - - - - - - - alpha_j - - - - - - -127140.0 - - - 0.2444 - V - - - - - 0.00003474 - - - -0.04391 - V - - - - - - - V - 37.78 - - - 1.0 - - - 0.311 - - V - 79.23 - - - - - - - - V - -40.0 - - - - 0.0 - - - - - - - - - - The closing rate of the j gate. - - - - - - - beta_j - - - - 0.1212 - - - - -0.01052 - V - - - - 1.0 - - - -0.1378 - - V - 40.14 - - - - - - - - V - -40.0 - - - - - 0.3 - - - - -0.0000002535 - V - - - - 1.0 - - - -0.1 - - V - 32.0 - - - - - - - - - - - - - - - - The kinetics of the j gate. - - - - - - - - time - j - - - - alpha_j - - 1.0 - j - - - - beta_j - j - - - - - - - - - - - - - The JWR model creates a new mathematical model to describe the - L-type calcium channel that is based on the experimentally observed - mode-switching behaviour of the channel. Inactivation occurs as - calcium ion binding induces the channel to switch (from mode normal) - to a mode in which transitions to open states are extremely slow - (mode Ca). The channel has one voltage inactivation gate, y. As well - as Ca, the channel is assumed permeable to K ions also. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the calcium current component of the total channel - current, given as the maximal current multiplied by the - voltage-dependent inactivation gate and the open probability of the - channel based on the mode-switching model. - - - - - - - i_Ca_L_Ca - - i_Ca_L_Ca_max - y - - O - O_Ca - - - - - - - - - - Calculation of the potassium current component of the total channel - current. - - - - - - - i_Ca_L_K - - p_k - y - - O - O_Ca - - - - V - - F - 2.0 - - - - R - T - - - - - - Ki - - - - V - F - - - R - T - - - - - Ko - - - - - - V - F - - - R - T - - - - 1.0 - - - - - - - - - - - The potassium permeability of the channel, which depends on the - calcium current component. - - - - - - - p_k - - P_K - - 1.0 - - i_Ca_L_Ca_max - i_Ca_L_Ca_half - - - - - - - - - - - The maximal calcium current through the channel. - - - - - - - i_Ca_L_Ca_max - - P_Ca - 4.0 - - - V - - F - 2.0 - - - - R - T - - - - - - 0.001 - - - 2.0 - V - - F - - R - T - - - - - - - 0.341 - Cao - - - - - - 2.0 - V - - F - - R - T - - - - - 1.0 - - - - - - - - - - - Rate constants for state changes in mode normal. - - - - - - - alpha - - 0.4 - - - - V - 12.0 - - 10.0 - - - - - - - - beta - - 0.05 - - - - V - 12.0 - - -13.0 - - - - - - - - - - - Rate constants for state changes in mode Ca (corresponding to - alpha-prime and beta-prime in the JRW paper). - - - - - - - alpha_a - - alpha - a - - - - - - beta_b - - beta - b - - - - - - - - - Rate constant for switching between mode normal and mode Ca. - - - - - - - gamma - - 0.1875 - Ca_SS - - - - - - - - - The kinetics of the state transitions in mode normal. - In the normal mode, the calcium channel is able to make the - transition to the open, conducting state (O) from the closed state - (C) at a normal rate. - - - - - - - - time - C0 - - - - - beta - C1 - - - omega - C_Ca0 - - - - - - 4.0 - alpha - - gamma - - C0 - - - - - - - - time - C1 - - - - - 4.0 - alpha - C0 - - - 2.0 - beta - C2 - - - - omega - b - - C_Ca1 - - - - - beta - - 3.0 - alpha - - - gamma - a - - - C1 - - - - - - - - time - C2 - - - - - 3.0 - alpha - C1 - - - 3.0 - beta - C3 - - - - omega - - b - 2.0 - - - C_Ca2 - - - - - - beta - 2.0 - - - 2.0 - alpha - - - gamma - - a - 2.0 - - - - C2 - - - - - - - - time - C3 - - - - - 2.0 - alpha - C2 - - - 4.0 - beta - C4 - - - - omega - - b - 3.0 - - - C_Ca3 - - - - - - beta - 3.0 - - alpha - - gamma - - a - 3.0 - - - - C3 - - - - - - - - time - C4 - - - - - alpha - C3 - - - g - O - - - - omega - - b - 4.0 - - - C_Ca4 - - - - - - beta - 4.0 - - f - - gamma - - a - 4.0 - - - - C4 - - - - - - - - time - O - - - - f - C4 - - - g - O - - - - - - - - - - The kinetics of the state transitions in mode Ca. - Calcium binding to the Ca channel induces a conformational change - from normal mode to mode Ca. This effectively inhibits the - conduction of calcium ions because in mode Ca, the calcium channel - makes the transition to the open, conducting state (O) extremely - slowly. - - - - - - - - time - C_Ca0 - - - - - beta_b - C_Ca1 - - - gamma - C_Ca0 - - - - - - 4.0 - alpha_a - - omega - - C_Ca0 - - - - - - - - time - C_Ca1 - - - - - 4.0 - alpha_a - C_Ca0 - - - 2.0 - beta_b - C_Ca2 - - - gamma - a - C1 - - - - - beta_b - - 3.0 - alpha_a - - - omega - b - - - C_Ca1 - - - - - - - - time - C_Ca2 - - - - - 3.0 - alpha_a - C_Ca1 - - - 3.0 - beta_b - C_Ca3 - - - gamma - - a - 2.0 - - C2 - - - - - - beta_b - 2.0 - - - 2.0 - alpha_a - - - omega - - b - 2.0 - - - - C_Ca2 - - - - - - - - time - C_Ca3 - - - - - 2.0 - alpha_a - C_Ca2 - - - 4.0 - beta_b - C_Ca4 - - - gamma - - a - 3.0 - - C3 - - - - - - beta_b - 3.0 - - alpha_a - - omega - - b - 3.0 - - - - C_Ca3 - - - - - - - - time - C_Ca4 - - - - - alpha_a - C_Ca3 - - - g_ - O_Ca - - - gamma - - a - 4.0 - - C4 - - - - - - beta_b - 4.0 - - f_ - - omega - - b - 4.0 - - - - C_Ca4 - - - - - - - - time - O_Ca - - - - f_ - C_Ca4 - - - g_ - O_Ca - - - - - - - - - - - - - The voltage-dependent inactivation gate for the L-type calcium - channel - the y gate. - - - - - - - - - - - - - - - - - - - - - The kinetics of the y gate. - - - - - - - - time - y - - - - y_infinity - y - - tau_y - - - - - - y_infinity - - - 1.0 - - 1.0 - - - - V - 55.0 - - 7.5 - - - - - - 0.1 - - 1.0 - - - - - V - - 21.0 - - 6.0 - - - - - - - - - - tau_y - - 20.0 - - 600.0 - - 1.0 - - - - V - 30.0 - - 9.5 - - - - - - - - - - - - - - - - The time-dependent potassium current has an X^2 dependence on it's - activation gate, and an Xi inactivation gate. This channel is also - assumed permeable to sodium ions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the maximal channel conductance, dependent on - extracellular potassium concentration. - - - - - - - g_K - - g_K_max - - - Ko - 5.4 - - - - - - - - - - - The reversal potential of the channel. - - - - - - - E_K - - - - R - T - - F - - - - - Ko - - P_NaK - Nao - - - - Ki - - P_NaK - Nai - - - - - - - - - - - - - Calculation of the time-dependent potassium current. - - - - - - - i_K - - g_K - Xi - - X - 2.0 - - - V - E_K - - - - - - - - - - - - - The voltage- and time-dependent activation gate for the - time-dependent potassium current - the X gate. - - - - - - - - - - - - - - - - - - - - - The opening rate of the X gate. - - - - - - - alpha_X - - 0.0000719 - - - V - 30.0 - - - 1.0 - - - -0.148 - - V - 30.0 - - - - - - - - - - - - - - The closing rate of the X gate. - - - - - - - beta_X - - 0.000131 - - - V - 30.0 - - - -1.0 - - - 0.0687 - - V - 30.0 - - - - - - - - - - - - - - The kinetics of the X gate. - - - - - - - - time - X - - - - alpha_X - - 1.0 - X - - - - beta_X - X - - - - - - - - - - - - - The time-independent inactivation gate for the time-dependent - potassium channel. - - - - - - - - - - - - - - - - - Xi is the inward rectification parameter and is given by the - following equation. - - - - - - - Xi - - 1.0 - - 1.0 - - - - V - 56.26 - - 32.1 - - - - - - - - - - - - - - - - The time-independent potassium current. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the maximal channel conductance, dependent on - extracellular potassium concentration. - - - - - - - g_K1 - - g_K1_max - - - Ko - 5.4 - - - - - - - - - - - The following equation calculates the reversal potential of the - time-independent potassium current. - - - - - - - E_K1 - - - - R - T - - F - - - - Ko - Ki - - - - - - - - - - - Calculate the current. - - - - - - - i_K1 - - g_K1 - K1_infinity - - V - E_K1 - - - - - - - - - - - - - - The time constants for the K1 gate are small enough that the gating - variable can be approximated with it's steady-state value. - - - - - - - - - - - - - - - - - - - - - The opening rate of the K1 gate. - - - - - - - alpha_K1 - - 1.02 - - 1.0 - - - 0.2385 - - - V - E_K1 - - 59.215 - - - - - - - - - - - - - The closing rate of the K1 gate. - - - - - - - beta_K1 - - - - 0.49124 - - - 0.08032 - - - V - 5.476 - - E_K1 - - - - - - - 0.06175 - - V - - E_K1 - 594.31 - - - - - - - 1.0 - - - -0.5143 - - - V - E_K1 - - 4.753 - - - - - - - - - - - - - The steady-state approximation for the K1 gating kinetics. - - - - - - - K1_infinity - - alpha_K1 - - alpha_K1 - beta_K1 - - - - - - - - - - - - - - The plateau potassium current component contains the equations which - describe the contribution of a time independent [K]o-insensitive - channel at plateau potentials. - - - - - - - - - - - - - - - - - - - - - - - The channel's reversal potential. - - - - - - - E_Kp - E_K1 - - - - - - - - The activation variable. - - - - - - - Kp - - 1.0 - - 1.0 - - - - 7.488 - V - - 5.98 - - - - - - - - - - - - Calculation of the plateau potassium current. - - - - - - - i_Kp - - g_Kp - Kp - - V - E_Kp - - - - - - - - - - - - - - The Na/Ca exchanger component describes how a protein molecule in - the cell surface membrane transports Na ions into the cytosol and - exports Ca ions into the extracellular volume, in a ratio of 3:1 - respectively. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the Na/Ca exchanger current. - - - - - - - i_NaCa - - k_NaCa - - 1.0 - - - K_mNa - 3.0 - - - Nao - 3.0 - - - - - 1.0 - - K_mCa - Cao - - - - 1.0 - - 1.0 - - k_sat - - - - eta - 1.0 - - V - - F - - R - T - - - - - - - - - - - - eta - V - - F - - R - T - - - - - - Nai - 3.0 - - Cao - - - - - - eta - 1.0 - - V - - F - - R - T - - - - - - Nao - 3.0 - - Cai - - - - - - - - - - - - - - - The sarcolemmal calcium pump is an additional mechanism for removing - Ca ions from the myoplasm to help maintain a low intracellular - calcium concentration when at rest. - - - - - - - - - - - - - - - - - - - - - The calcium pump current. - - - - - - - i_p_Ca - - I_pCa - - Cai - - K_mpCa - Cai - - - - - - - - - - - - - - The sodium background current is a time-independent diffusion of - Na ions down their electrochemical gradient, through the cell - surface membrane into the cytosol. - - - - - - - - - - - - - - - - - - - - - - The reversal potential for the background sodium channel. - - - - - - - E_NaN - E_Na - - - - - - - - Calculation of the background sodium current. - - - - - - - i_Na_b - - g_Nab - - V - E_NaN - - - - - - - - - - - - - The calcium background current describes a time-independent - diffusion of Ca ions down their electrochemical gradient through the - cell surface membrane into the cytosol. However, calcium is not - allowed to accumulate to high intracellular concentrations. This - influx is balanced by the Ca ion extrusion through the Na-Ca - exchanger and the sarcolemmal Ca pump. - - - - - - - - - - - - - - - - - - - - - - - - - - The reversal potential for the background calcium current. - - - - - - - E_CaN - - - - R - T - - - 2.0 - F - - - - - Cao - Cai - - - - - - - - - - - Calculation of the background calcium current. - - - - - - - i_Ca_b - - g_Cab - - V - E_CaN - - - - - - - - - - - - - The sodium potassium pump is an active protein in the cell membrane - which couples the free energy released by the hydrolysis of ATP to - the movement of Na and K ions against their electrochemical - gradients through the cell membrane. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the Na/K pump current. - - - - - - - f_NaK - - 1.0 - - - 1.0 - - 0.1245 - - - - -0.1 - V - F - - - R - T - - - - - - - 0.0365 - sigma - - - - - V - - F - - - R - T - - - - - - - - - - - sigma - - - 1.0 - 7.0 - - - - - Nao - 67.3 - - - 1.0 - - - - - - - i_NaK - - I_NaK - f_NaK - - 1.0 - - 1.0 - - - K_mNai - Nai - - 1.5 - - - - - Ko - - Ko - K_mKo - - - - - - - - - \ - - - - - The nonspecific calcium activated current describes a channel which - is activated by calcium ions, but is permeable to only sodium and - potassium ions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The reversal potential of the channel. - - - - - - - EnsCa - - - - R - T - - F - - - - - Ko - Nao - - - Ki - Nai - - - - - - - - - - - - The potential offset for the channel. - - - - - - - VnsCa - - V - EnsCa - - - - - - - - - The sodium component of the channel's current. - - - - - - - i_ns_Na - - I_ns_Na - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The potassium component of the channel's current. - - - - - - - i_ns_K - - I_ns_K - - 1.0 - - 1.0 - - - K_m_ns_Ca - Cai - - 3.0 - - - - - - - - - - - - The total nonspecific calcium activated current. - - - - - - - i_ns_Ca - - i_ns_Na - i_ns_K - - - - - - - - - The maximal sodium component current. - - - - - - - I_ns_Na - - P_ns_Ca - - 1.0 - 2.0 - - - - VnsCa - - F - 2.0 - - - - R - T - - - - - - 0.75 - Nai - - - - VnsCa - F - - - R - T - - - - - - 0.75 - Nao - - - - - - - VnsCa - F - - - R - T - - - - 1.0 - - - - - - - - - - - The maximal potassium component current. - - - - - - - I_ns_K - - P_ns_Ca - - 1.0 - 2.0 - - - - VnsCa - - F - 2.0 - - - - R - T - - - - - - 0.75 - Ki - - - - VnsCa - F - - - R - T - - - - - - 0.75 - Ko - - - - - - - VnsCa - F - - - R - T - - - - 1.0 - - - - - - - - - - - - - - - In the JRW model, subcellular calcium regulatory mechanisms are - described in detail. There are six calcium fluxes to consider; - J_rel, J_leak, J_up, J_tr, J_xfer and J_trpn. In addition, three - membrane current fluxes are also necessary for the formulation of - calcium regulation; i_p_Ca, i_Ca_L_Ca and i_NaCa. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculate some volume fractions as proportions of the total - myoplasmic volume. - - - - - - - V_SS - - 5.828e-5 - V_myo - - - - - - V_NSR - - 0.081 - V_myo - - - - - - V_JSR - - 0.00464 - V_myo - - - - - - - - - The calcium release flux from the JSR into the restricted subspace - is governed by the fraction of RyR channels in an open state. - - - - - - - J_rel - - v1 - RyR_open - - Ca_JSR - Ca_SS - - - - - - - - - - The "open" RyR's are those P_O1 and P_O2 states. - - - - - - - RyR_open - - P_O1 - P_O2 - - - - - - - - - The kinetic equations governing the transitions between the four - states used to model the RyR's. - - - - - - - - time - P_C1 - - - - - k_a_plus - - - Ca_SS - nCa - - P_C1 - - - k_a_minus - P_O1 - - - - - - - - time - P_O1 - - - - - k_a_plus - - Ca_SS - nCa - - P_C1 - - - - k_a_minus - P_O1 - - - k_b_plus - - Ca_SS - mCa - - P_O1 - - - k_c_plus - P_O1 - - - - - k_b_minus - P_O2 - - - k_c_minus - P_C2 - - - - - - - - time - P_O2 - - - - k_b_plus - - Ca_SS - mCa - - P_O1 - - - k_b_minus - P_O2 - - - - - - - - time - P_C2 - - - - k_c_plus - P_O1 - - - k_c_minus - P_C2 - - - - - - - - - - Calculate the leakage flux from the NSR into the myoplasm. - - - - - - - J_leak - - v2 - - Ca_NSR - Cai - - - - - - - - - - Calculate the uptake flux into the NSR from the myoplasm. - - - - - - - J_up - - v3 - - - Cai - 2.0 - - - - K_mup - 2.0 - - - Cai - 2.0 - - - - - - - - - - - - Calculate the translocation flux between the uptake (NSR) and - release (JSR) stores. - - - - - - - J_tr - - - Ca_NSR - Ca_JSR - - tau_tr - - - - - - - - - Calculate the calcium flux from the diffusion of calcium out of the - restricted subspace into the myoplasm. - - - - - - - J_xfer - - - Ca_SS - Cai - - tau_xfer - - - - - - - - - The kinetics of calcium binding to the myoplasm buffer troponin - - both high and low affinity binding sites. - - - - - - - J_htrpn - - - k_htrpn_plus - Cai - - HTRPN_tot - HTRPNCa - - - - k_htrpn_minus - HTRPNCa - - - - - - - J_ltrpn - - - k_ltrpn_plus - Cai - - LTRPN_tot - LTRPNCa - - - - k_ltrpn_minus - LTRPNCa - - - - - - - J_trpn - - J_htrpn - J_ltrpn - - - - - - - - - Keep track of the concentration of calcium ions bound to high and - low affinity troponin binding sites. - - - - - - - - time - HTRPNCa - - J_htrpn - - - - - - time - LTRPNCa - - J_ltrpn - - - - - - - - Calcium is buffered by calmodulin (CMDN) in the subspace and - myoplasm, and by calsequestrin (CSQN) in the JSR. These are fast - buffers and their effect is modelled using the rapid buffering - approximation. - - - - - - - Bi - - 1.0 - - 1.0 - - - CMDN_tot - K_mCMDN - - - - K_mCMDN - Cai - - 2.0 - - - - - - - - - B_SS - - 1.0 - - 1.0 - - - CMDN_tot - K_mCMDN - - - - K_mCMDN - Ca_SS - - 2.0 - - - - - - - - - B_JSR - - 1.0 - - 1.0 - - - CSQN_tot - K_mCSQN - - - - K_mCSQN - Ca_JSR - - 2.0 - - - - - - - - - - - - The kinetics of the calcium ion concentration changes in the various - compartments of the model. - - - - - - - - time - Cai - - - Bi - - - J_leak - J_xfer - - - J_up - J_trpn - - - - i_Ca_b - - 2.0 - i_NaCa - - - i_p_Ca - - - Am - - 2.0 - V_myo - F - - - - - - - - - - - - time - Ca_SS - - - B_SS - - - - J_rel - - V_JSR - V_SS - - - - J_xfer - - V_myo - V_SS - - - - - i_Ca_L_Ca - - Am - - 2.0 - V_SS - F - - - - - - - - - - - time - Ca_JSR - - - B_JSR - - J_tr - J_rel - - - - - - - - time - Ca_NSR - - - - - J_up - J_leak - - - V_myo - V_NSR - - - - J_tr - - V_JSR - V_NSR - - - - - - - - - - - - - - The descriptions of the rate of change of [Na]i and [K]i are the - same as the LR-II model. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The rate of change of intracellular sodium ion concentration. - - - - - - - - time - Nai - - - - - i_Na - i_Na_b - i_ns_Na - - i_NaCa - 3.0 - - - i_NaK - 3.0 - - - - - Am - - V_myo - F - - - - - - - - - - - The rate of change of intracellular potassium ion concentration. - - - - - - - - time - Ki - - - - - i_Ca_L_K - i_K - i_K1 - i_Kp - i_ns_K - - - i_NaK - 2.0 - - - - - - Am - - V_myo - F - - - - - - - - - - - The rate of change of extracellular potassium ion concentration. - - - - - - - - time - Ko - - - - i_Ca_L_K - i_K - i_K1 - i_Kp - i_ns_K - - - i_NaK - 2.0 - - - - - Am - - V_myo - F - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Bioelectrics/Monodomain_Shiqiang/input/lindblad_murphey_clark_giles_1996.xml b/Bioelectrics/Monodomain_Shiqiang/input/lindblad_murphey_clark_giles_1996.xml deleted file mode 100644 index 36ea698b..00000000 --- a/Bioelectrics/Monodomain_Shiqiang/input/lindblad_murphey_clark_giles_1996.xml +++ /dev/null @@ -1,3779 +0,0 @@ - - - - - -
- -
- Model Status - - This model runs in OpenCell and COR and reproduce the published results. The units have been checked and they are consistent. - -
- -Model Structure - - -ABSTRACT: We have developed a mathematical model of the rabbit atrial myocyte and have used it in an examination of the ionic basis of the atrial action potential. Available biophysical data have been incorporated into the model to quantify the specific ultrastructural morphology, intracellular ion buffering, and time- and voltage-dependent currents and transport mechanisms of the rabbit atrial cell. When possible, mathematical expressions describing ionic currents identified in rabbit atrium are based on whole cell voltage-clamp data from enzymatically isolated rabbit atrial myocytes. This membrane model is coupled to equations describing Na+, K+, and Ca2+ homeostasis, including the uptake and release of Ca2+ by the sarcoplasmic reticulum and Ca2+ buffering. The resulting formulation can accurately simulate the whole cell voltage-clamp data on which it is based and provides fits to a family of rabbit atrial cell action potentials obtained at 35 degrees C over a range of stimulus rates (0.2-3.0 Hz). The model is utilized to provide a qualitative prediction of the intracellular Ca2+ concentration transient during the action potential and to illustrate the interactions between membrane currents that underlie repolarization in the rabbit atrial myocyte. - - - - - - - schematic diagram of Linblad et al 1996 model - - - - -A schematic representation of the Linblad et al 1996 model. - - - -The original paper reference is cited below: - - - -A model of the action potential and underlying membrane currents in a rabbit atrial cell, D. S. Lindblad, C. R. Murphey, J. W. Clark and W. R. Giles, 1996, American Journal of Physiology, 271, H1666-H1696. PubMed ID: 8897964. - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - i_Stim - - - stim_amplitude - - - - - time - stim_start - - - - time - stim_end - - - - - - - - time - stim_start - - - - - - - - - - time - stim_start - - stim_period - - - stim_period - - - stim_duration - - - - - 0 - - - - - - - - - time - - V - - - - - - - - 1 - - Cm - - - - i_Kr - i_Ks - i_Na - i_Ca_L - i_Ca_T - i_to - i_K1 - i_B_Na - i_B_Ca - i_B_Cl - i_p - i_CaP - i_NaCa - i_Stim - - - - - - - - - - - - - - - - - - - - - - - E_Na - - - - - - - R - T - - F - - - - - - Na_c - Na_i - - - - - - - i_Na - - - - - - - - - P_Na - - - m - 3 - - - - - - 0.635 - h1 - - - - 0.365 - h2 - - - Na_c - V - - - F - 2 - - - - - R - T - - - - - - - - - - - - - V - E_Na - - F - - - - R - T - - - - 1 - - - - - - - - - - - V - F - - - - R - T - - - - 1 - - - - - - - - - - - - - - - - E0_m - - - V - 44.4 - - - - - alpha_m - - - - - - - 460 - - E0_m - - - - - - - - E0_m - - - 12.673 - - - - 1 - - - - - - beta_m - - - 18400 - - - - - E0_m - - - 12.673 - - - - - - - - - - - time - - m - - - - - - alpha_m - - - 1 - m - - - - - beta_m - m - - - - - - - - - - - - - - - - - alpha_h - - - 44.9 - - - - - - - V - 66.9 - - - - 5.57 - - - - - - - - beta_h - - - 1491 - - - 1 - - - 323.3 - - - - - - - V - 94.6 - - - - 12.9 - - - - - - - - - - h_infinity - - - alpha_h - - - alpha_h - beta_h - - - - - - tau_h1 - - - - - 0.03 - - - 1 - - - - - - - V - 40 - - 6 - - - - - 3.5e-4 - - - - - - - - time - - h1 - - - - - - h_infinity - h1 - - tau_h1 - - - - - - - - - - - - - - tau_h2 - - - - - 0.12 - - - 1 - - - - - - - V - 60 - - 2 - - - - - 0.00295 - - - - - - - - time - - h2 - - - - - - h_infinity - h2 - - tau_h2 - - - - - - - - - - - - - - - - - d_prime - - - 1 - - - 1 - - - - - - - V - 33 - - - - 12 - - - - - - - - - i_Ca_L - - - g_Ca_L - d_L - f_L - d_prime - - - V - E_Ca_app - - - - - - - - - - - - - - - - - - - E0_alpha_d_L - - - V - 35 - - - - - E0_beta_d_L - - - V - 5 - - - - - alpha_d_L - - - - - - - - - 16.72 - - E0_alpha_d_L - - - - - - - - E0_alpha_d_L - - - 2.5 - - - - 1 - - - - - - - - - 50 - - V - - - - - - - - V - - - 4.808 - - - - 1 - - - - - - - beta_d_L - - - - - 4.48 - E0_beta_d_L - - - - - - - - E0_beta_d_L - 2.5 - - - 1 - - - - - - d_L_infinity - - - 1 - - - 1 - - - - - - - V - 0.95 - - - - 6.6 - - - - - - - - - tau_d_L - - - 1 - - - alpha_d_L - beta_d_L - - - - - - - - - time - - d_L - - - - - - d_L_infinity - d_L - - tau_d_L - - - - - - - - - - - - - - - - - - E0_f_L - - - V - 28 - - - - - alpha_f_L - - - - - 8.49 - E0_f_L - - - - - - - - E0_f_L - 4 - - - 1 - - - - - - beta_f_L - - - 67.922 - - - 1 - - - - - E0_f_L - - - 4 - - - - - - - - - f_L_infinity - - - alpha_f_L - - - alpha_f_L - beta_f_L - - - - - - x_f - - - - - V - 37.427 - - 20.213 - - - - - tau_f_L - - - - - 0.211 - - - - - - - x_f - - x_f - - - - 0.015 - - - - - - - - time - - f_L - - - - - - f_L_infinity - f_L - - tau_f_L - - - - - - - - - - - - - - - - i_Ca_T - - - g_Ca_T - d_T - f_T - - - V - E_Ca_T - - - - - - - - - - - - - - - - - - E0_d_T - - - V - 23 - - - - - alpha_d_T - - - 674.173 - - - - - E0_d_T - 30 - - - - - - - beta_d_T - - - 674.173 - - - - - E0_d_T - - - 30 - - - - - - - - d_T_infinity - - - 1 - - - 1 - - - - - E0_d_T - - - 6.1 - - - - - - - - - tau_d_T - - - 1 - - - alpha_d_T - beta_d_T - - - - - - - - - time - - d_T - - - - - - d_T_infinity - d_T - - tau_d_T - - - - - - - - - - - - - - - - - E0_f_T - - - V - 75 - - - - - alpha_f_T - - - 9.637 - - - - - E0_f_T - - - 83.333 - - - - - - - - beta_f_T - - - 9.637 - - - - - E0_f_T - 15.385 - - - - - - - f_T_infinity - - - alpha_f_T - - - alpha_f_T - beta_f_T - - - - - - tau_f_T - - - 1 - - - alpha_f_T - beta_f_T - - - - - - - - - time - - f_T - - - - - - f_T_infinity - f_T - - tau_f_T - - - - - - - - - - - - - - - - - - - - - - - E_K - - - - - - - R - T - - F - - - - - - K_c - K_i - - - - - - - i_to - - - g_to - r - - - - - 0.59 - - - s1 - 3 - - - - - 0.41 - - - s2 - 3 - - - - - - - - 0.6 - - - s3 - 6 - - - 0.4 - - - - V - E_K - - - - - - - - - - - - - - - - - alpha_r - - - 386.6 - - - - - V - 12 - - - - - - - beta_r - - - 8.011 - - - - - V - - - 7.2 - - - - - - - - r_infinity - - - 1 - - - 1 - - - - - - - V - 15 - - - - 5.633 - - - - - - - - - tau_r - - - - - 1 - - - alpha_r - beta_r - - - 4e-4 - - - - - - - - time - - r - - - - - - r_infinity - r - - tau_r - - - - - - - - - - - - - - s1_infinity - - - 1 - - - 1 - - - - - - - V - 28.29 - - 7.06 - - - - - - - - tau_s1 - - - - - 0.5466 - - - 1 - - - - - - - V - 32.8 - - 0.1 - - - - - 0.0204 - - - - - - - - time - - s1 - - - - - - s1_infinity - s1 - - tau_s1 - - - - - - - - - - - - - - s2_infinity - - - 1 - - - 1 - - - - - - - V - 28.29 - - 7.06 - - - - - - - - tau_s2 - - - - - 5.75 - - - 1 - - - - - - - V - 32.8 - - 0.1 - - - - - - - 0.45 - - - 1 - - - - - - - V - 13.54 - - - - 13.97 - - - - - - - - - - - - - time - - s2 - - - - - - s2_infinity - s2 - - tau_s2 - - - - - - - - - - - - - - s3_infinity - - - - - - - 1 - - - 1 - - - - - - - V - 50.67 - - 27.38 - - - - - 0.666 - - 1.666 - - - - - tau_s3 - - - - - 7.5 - - - 1 - - - - - - - V - 23 - - 0.5 - - - - - 0.5 - - - - - - - - time - - s3 - - - - - - s3_infinity - s3 - - tau_s3 - - - - - - - - - - - - - - - - - - - i_Ks - - - g_Ks - z - - - V - E_K - - - - - - i_Kr - - - g_Kr - p_a - p_i - - - V - E_K - - - - - - - - - - - - - - - - - alpha_z - - - 1.66 - - - - - V - 69.452 - - - - - - - beta_z - - - 0.3 - - - - - V - - - 21.826 - - - - - - - - z_infinity - - - 1 - - - 1 - - - - - - - V - 0.9 - - - - 13.8 - - - - - - - - - tau_z - - - - - 1 - - - alpha_z - beta_z - - - 0.06 - - - - - - - - time - - z - - - - - - z_infinity - z - - tau_z - - - - - - - - - - - - - - - - alpha_p_a - - - 9 - - - - - V - 25.371 - - - - - - - beta_p_a - - - 1.3 - - - - - V - - - 13.026 - - - - - - - - p_a_infinity - - - 1 - - - 1 - - - - - - - V - 5.1 - - - - 7.4 - - - - - - - - - tau_p_a - - - 1 - - - alpha_p_a - beta_p_a - - - - - - - - - time - - p_a - - - - - - p_a_infinity - p_a - - tau_p_a - - - - - - - - - - - - - - - - alpha_p_i - - - 100 - - - - - V - - - 54.645 - - - - - - - - beta_p_i - - - 656 - - - - - V - 106.157 - - - - - - - p_i_infinity - - - 1 - - - 1 - - - - - - - V - 47.3921 - - 18.6603 - - - - - - - - tau_p_i - - - 1 - - - alpha_p_i - beta_p_i - - - - - - - - - time - - p_i - - - - - - p_i_infinity - p_i - - tau_p_i - - - - - - - - - - - - - - - - - - - - - i_K1 - - - - - g_K1 - - - V - E_K - - - - - - K_c - - - K_c - KmK1 - - - 3 - - 1 - - - - 1 - - - - - - - steepK1 - F - - - - - V - E_K - - shiftK1 - - - - - R - T - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - E_Ca - - - - - - - R - T - - - - 2 - F - - - - - - - Ca_c - Ca_i - - - - - - - E_Cl - - - - - - - R - T - - F - - - - - - Cl_i - Cl_c - - - - - - - E_B_Cl - - - E_Cl - - - 0.49 - - - E_Cl - 30.59 - - - - - - - i_B_Na - - - g_B_Na - - - V - E_Na - - - - - - i_B_Ca - - - g_B_Ca - - - V - E_Ca - - - - - - i_B_Cl - - - g_B_Cl - - - V - E_B_Cl - - - - 1 - - - - - - - V - - - E_Cl - 36.95 - - - 74.514 - - - - - - - - - - - - - - - - - - - - i_p - - - - - - - - - - - - - i_NaK_max - K_c - - - - K_c - k_NaK_K - - - - - Na_i - 1.5 - - - - - - - Na_i - 1.5 - - - - k_NaK_Na - 1.5 - - - - 1.6 - - - - 1.5 - - - - - - - V - 60 - - - - 40 - - - - - - - - - - - - - - - - - - i_CaP - - - - - i_CaP_max - Ca_i - - - - Ca_i - k_CaP - - - - - - - - - - - - - - - - - - - - - - - i_NaCa - - - - - k_NaCa - - - - - - - Na_i - 3 - - Ca_c - - - - - - - gamma - F - V - - - - R - T - - - - - - - - - Na_c - 3 - - Ca_i - - - - - - - - - gamma - 1 - - V - F - - - - R - T - - - - - - - - - 1 - - - d_NaCa - - - - - - - Na_c - 3 - - Ca_i - - - - - - Na_i - 3 - - Ca_c - - - - - 1 - - - Ca_i - 0.0069 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - time - - Na_i - - - - - - - - i_Na - i_B_Na - - - 3 - i_p - - - - 3 - i_NaCa - - - - - - Vol_i - F - - - - - - - - - time - - K_i - - - - - - - - - - i_to - i_K1 - i_Kr - i_Ks - - - - 2 - i_p - - - - - - Vol_i - F - - - - - - - - - time - - Ca_i - - - - - - - - - - - - - - - - i_Ca_L - i_Ca_T - i_B_Ca - i_CaP - - - - 2 - i_NaCa - - - i_up - - i_rel - - - - - 2 - Vol_Ca - F - - - - - - - 0.08 - dOTCdt - - - - 0.16 - dOTMgCdt - - - - 0.045 - dOCdt - - - - - - - - - - - - - - - - - - - - - dOCdt - - - - - 200000 - Ca_i - - - 1 - O_C - - - - - 476 - O_C - - - - - - - - - time - - O_C - - dOCdt - - - - dOTCdt - - - - - 78400 - Ca_i - - - 1 - O_TC - - - - - 392 - O_TC - - - - - - - - - time - - O_TC - - dOTCdt - - - - dOTMgCdt - - - - - 200000 - Ca_i - - - - - 1 - O_TMgC - - O_TMgMg - - - - - 6.6 - O_TMgC - - - - - - - - - time - - O_TMgC - - dOTMgCdt - - - - - - - time - - O_TMgMg - - - - - - 2000 - Mg_i - - - - - 1 - O_TMgC - - O_TMgMg - - - - - 666 - O_TMgMg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - time - - O_Calse - - - - - - 480 - Ca_rel - - - 1 - O_Calse - - - - - 400 - O_Calse - - - - - - - - - time - - Ca_rel - - - - - - - - i_tr - i_rel - - - - 2 - Vol_rel - F - - - - - 31 - - - - time - - O_Calse - - - - - - - - - - time - - Ca_up - - - - - - i_up - i_tr - - - - 2 - Vol_up - F - - - - - - - - - time - - F1 - - - - - - k_F3 - F3 - - - - r_act - F1 - - - - - - - - - time - - F2 - - - - - - r_act - F1 - - - - r_inact - F2 - - - - - - - - - time - - F3 - - - - - - F2 - r_inact - - - - k_F3 - F3 - - - - - - r_act - - - - - 203.8 - - - - - 0.08 - - - V - 40 - - - - - - - 203.8 - - - - - Ca_i - - - Ca_i - k_rel - - - 4 - - - - - - - r_inact - - - 33.96 - - - 339.6 - - - - - Ca_i - - - Ca_i - k_rel - - - 4 - - - - - - - i_up - - - - - I_up_max - - - - - Ca_i - k_cyca - - - - - - - - k_xcs - 2 - - Ca_up - - k_srca - - - - - - - - - - Ca_i - k_cyca - - k_cyca - - - - - - k_xcs - - - Ca_up - k_srca - - - k_srca - - - - - - - i_tr - - - - - - - Ca_up - Ca_rel - - 2 - F - Vol_rel - - tau_tr - - - - - i_rel - - - alpha_rel - - - - - F2 - - - F2 - 0.25 - - - 2 - - - - Ca_rel - Ca_i - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - unknown - - - American Journal of Physiology - - - C - Murphey - R - - - - penny.noble@dpag.ox.ac.uk - - - - - - W - Giles - R - - - - - - - - James Lawson - - - J - Clark - W - - - - - - - Department of Physiology, Anatomy & Genetics, University of Oxford - - - - - - - This model has been curated and unit checked and is known to run in PCEnv and COR and is able to reproduce the results published in the paper on which it is based. - - - 8897964 - - - - - - - - 1996-10-01 00:00 - - - Oxford University - Department of Physiology, Anatomy & Genetics - - - - - - - - - - 10 - 100000 - 0.0001 - - - Peter - Villiger - J - - - - - - - This is a CellML description of Lindblad et al.'s 1996 paper "A Model of the Action Potential and Underlying Membrane Currents in a Rabbit Atrial Cell" - - - - - - - keyword - - - electrophysiology - atrial myocyte - rabbit - - - - - - - - Penny - Noble - J - - - James Lawson - - - - added metadata - - - - D - Lindblad - S - - - - - - - - unknown - unknown - unknown - - - 2008-01-22T00:00:00+13:00 - - - unknown - unknown - - - - - - - - - - - 2007-03-22 - - - - A Model of the Action Potential and Underlying Membrane Currents in a Rabbit Atrial Cell - 271(4pt2) - H1666 - - - H1696 - - - - - - - 2006-03-31 - - - - - - - - \ No newline at end of file diff --git a/Bioelectrics/Monodomain_Shiqiang/input/maltsev_rate_modulation.xml b/Bioelectrics/Monodomain_Shiqiang/input/maltsev_rate_modulation.xml deleted file mode 100644 index 8804ac14..00000000 --- a/Bioelectrics/Monodomain_Shiqiang/input/maltsev_rate_modulation.xml +++ /dev/null @@ -1,4487 +0,0 @@ - - - -
- - Synergism of coupled subsarcolemmal Ca2+ clocks and sarcolemmal voltage clocks confers robust and flexible pacemaker function in a novel pacemaker cell model - - Catherine - Lloyd - - Auckland Bioengineering Institute, The University of Auckland - - - -
- Model Status - - This CellML model has been tested in OpenCell and COR and the units are balanced. The model runs to recreate the published results. This particular variant of the model uses the initial conditions from the paper (and is not intended to be a steady state model). - -
- - Model Structure - -ABSTRACT: Recent experimental studies have demonstrated that sinoatrial node cells (SANC) generate spontaneous, rhythmic, local subsarcolemmal Ca(2+) releases (Ca(2+) clock), which occur during late diastolic depolarization (DD) and interact with the classic sarcolemmal voltage oscillator (membrane clock) by activating Na(+)-Ca(2+) exchanger current (I(NCX)). This and other interactions between clocks, however, are not captured by existing essentially membrane-delimited cardiac pacemaker cell numerical models. Using wide-scale parametric analysis of classic formulations of membrane clock and Ca(2+) cycling, we have constructed and initially explored a prototype rabbit SANC model featuring both clocks. Our coupled oscillator system exhibits greater robustness and flexibility than membrane clock operating alone. Rhythmic spontaneous Ca(2+) releases of sarcoplasmic reticulum (SR)-based Ca(2+) clock ignite rhythmic action potentials via late DD I(NCX) over much broader ranges of membrane clock parameters [e.g., L-type Ca(2+) current (I(CaL)) and/or hyperpolarization-activated ("funny") current (I(f)) conductances]. The system Ca(2+) clock includes SR and sarcolemmal Ca(2+) fluxes, which optimize cell Ca(2+) balance to increase amplitudes of both SR Ca(2+) release and late DD I(NCX) as SR Ca(2+) pumping rate increases, resulting in a broad pacemaker rate modulation (1.8-4.6 Hz). In contrast, the rate modulation range via membrane clock parameters is substantially smaller when Ca(2+) clock is unchanged or lacking. When Ca(2+) clock is disabled, the system parametric space for fail-safe SANC operation considerably shrinks: without rhythmic late DD I(NCX) ignition signals membrane clock substantially slows, becomes dysrhythmic, or halts. In conclusion, the Ca(2+) clock is a new critical dimension in SANC function. A synergism of the coupled function of Ca(2+) and membrane clocks confers fail-safe SANC operation at greatly varying rates. - - -The original paper reference is cited below: - - -Synergism of coupled subsarcolemmal Ca2+ clocks and sarcolemmal voltage clocks confers robust and flexible pacemaker function in a novel pacemaker cell model, Victor A. Maltsev and Edward G. Lakatta, 2009, American Journal of Physiology, 286, H594-H615. PubMed ID: 19136600 - - - - - - reaction diagram - - - - - Schematic diagram of the interacting Ca2+ clock and membrane clock in a model of rabbit sinoatrial node cells. - - -
- - - - Vm - membrane potential - - - - - electric_potentials - electric potentials - - - - - i_CaL - L-type calcium current - - - - - i_CaT - T-type calcium current - - - - - i_Kr - rapidly activating delayed rectifier potassium current - - - - - i_Ks - slowly activating delayed rectifier potassium current - - - - - AP_sensitive_currents - 4-aminopyridine-sensitive currents - - - - - i_f - hyperpolarization-activated, "funny" current - - - - - i_st - sustained inward current - - - - - i_b_Na - sodium dependent background current - - - - - i_NaK - sodium-potassium pump current - - - - - i_b_Ca - calcium background current - - - - - i_NaCa - sodium-calcium exchanger current - - - - - j_SRCarel - calcium release flux from the sarcoplasmic reticulum via RyRs - - - - - intracellular_calcium_fluxes - intracellular calcium fluxes - - - - - calcium_buffering - calcium buffering - - - - - calcium_dynamics - dynamics of calcium concentrations in cell compartments - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - time - - Vm - - - - - - - - i_CaL - i_CaT - i_f - i_st - i_Kr - i_Ks - i_to - i_sus - i_NaK - i_NaCa - i_b_Ca - i_b_Na - i_K_Ach - - - Cm - - - - - - - - - - - - - - - - - - - - E_Na - - - - - - - R - T - - F - - - - - - Nao - Nai - - - - - - - E_K - - - - - - - R - T - - F - - - - - - Ko - Ki - - - - - - - E_Ks - - - - - - - R - T - - F - - - - - - - - Ko - - - 0.12 - Nao - - - - - Ki - - - 0.12 - Nai - - - - - - - - - - - - - - - - - - - - - - - i_CaL - - - Cm - g_CaL - - - Vm - E_CaL - - dL - fL - fCa - - - - - - - - - - - - - - - - - - - dL_infinity - - - 1 - - - 1 - - - - - - - - - Vm - 13.5 - - - 6 - - - - - - - - tau_dL - - - 1 - - - alpha_dL - beta_dL - - - - - - alpha_dL - - - - - - - - - 0.02839 - - - - adVm - 35 - - - - - - - - - - - - - adVm - 35 - - - 2.5 - - - 1 - - - - - - - 0.0849 - adVm - - - - - - - - - - adVm - - 4.8 - - - 1 - - - - - - - adVm - - - - - 35.00001 - - - - Vm - - - 35 - - - - - 0.00001 - - - Vm - 0 - - - - Vm - - - - - - beta_dL - - - - - 0.01143 - - - bdVm - 5 - - - - - - - - - - - bdVm - 5 - - 2.5 - - - 1 - - - - - - bdVm - - - 5.00001 - - - Vm - 5 - - - - Vm - - - - - - - - - time - - dL - - - - - - dL_infinity - dL - - tau_dL - - - - - - - - - - - - - - fL_infinity - - - 1 - - - 1 - - - - - - - Vm - 35 - - 7.3 - - - - - - - - tau_fL - - - 44.3 - - - 257.1 - - - - - - - - - - - Vm - 32.5 - - 13.9 - - 2 - - - - - - - - - - - - time - - fL - - - - - - fL_infinity - fL - - tau_fL - - - - - - - - - - - - - - - - - fCa_infinity - - - Km_fCa - - - Km_fCa - Ca_sub - - - - - - tau_fCa - - - fCa_infinity - alpha_fCa - - - - - - - - time - - fCa - - - - - - fCa_infinity - fCa - - tau_fCa - - - - - - - - - - - - - - - - - i_CaT - - - Cm - g_CaT - - - Vm - E_CaT - - dT - fT - - - - - - - - - - - - - - dT_infinity - - - 1 - - - 1 - - - - - - - - - Vm - 26.3 - - - 6 - - - - - - - - tau_dT - - - 1 - - - - - 1.068 - - - - - - - Vm - 26.3 - - 30 - - - - - - 1.068 - - - - - - - - - Vm - 26.3 - - - 30 - - - - - - - - - - - - time - - dT - - - - - - dT_infinity - dT - - tau_dT - - - - - - - - - - - - - - fT_infinity - - - 1 - - - 1 - - - - - - - Vm - 61.7 - - 5.6 - - - - - - - - tau_fT - - - 1 - - - - - 0.0153 - - - - - - - - - Vm - 61.7 - - - 83.3 - - - - - - 0.015 - - - - - - - Vm - 61.7 - - 15.38 - - - - - - - - - - - - time - - fT - - - - - - fT_infinity - fT - - tau_fT - - - - - - - - - - - - - - - - - - i_Kr - - - Cm - g_Kr - - - Vm - E_K - - - - - - 0.6 - paF - - - - 0.4 - paS - - - pi_ - - - - - - - - - - - - - - - - pa_infinity - - - 1 - - - 1 - - - - - - - - - Vm - 23.2 - - - 10.6 - - - - - - - - tau_paS - - - 0.84655354 - - - - - 0.0042 - - - - - Vm - 17 - - - - - - 0.00015 - - - - - - - Vm - - 21.6 - - - - - - - - - tau_paF - - - 0.84655354 - - - - - 0.0372 - - - - - Vm - 15.9 - - - - - - 0.00096 - - - - - - - Vm - - 22.5 - - - - - - - - - - - - time - - paS - - - - - - pa_infinity - paS - - tau_paS - - - - - - - - time - - paF - - - - - - pa_infinity - paF - - tau_paF - - - - - - - - - - - - - - pi_infinity - - - 1 - - - 1 - - - - - - - Vm - 28.6 - - 17.1 - - - - - - - - tau_pi - - - 1 - - - - - 0.1 - - - - - - - Vm - - 54.645 - - - - - - 0.656 - - - - - Vm - 106.157 - - - - - - - - - - - - time - - pi_ - - - - - - pi_infinity - pi_ - - tau_pi - - - - - - - - - - - - - - - - i_Ks - - - Cm - g_Ks - - - Vm - E_Ks - - - - n - 2 - - - - - - - - - - - - - - - - - n_infinity - - - alpha_n - - - alpha_n - beta_n - - - - - - tau_n - - - 1 - - - alpha_n - beta_n - - - - - - alpha_n - - - 0.014 - - - 1 - - - - - - - - - Vm - 40 - - - 9 - - - - - - - - beta_n - - - 0.001 - - - - - - - Vm - - 45 - - - - - - - - - - time - - n - - - - - - n_infinity - n - - tau_n - - - - - - - - - - - - - - - - - - - i_to - - - Cm - g_to - - - Vm - E_K - - q - r - - - - - i_sus - - - Cm - g_sus - - - Vm - E_K - - r - - - - - - - - - - - - - - q_infinity - - - 1 - - - 1 - - - - - - - Vm - 49 - - 13 - - - - - - - - tau_q - - - 6.06 - - - 39.102 - - - - - 0.57 - - - - - - - 0.08 - - - - Vm - 44 - - - - - - - 0.065 - - - - - 0.1 - - - Vm - 45.93 - - - - - - - - - - - - - - time - - q - - - - - - q_infinity - q - - tau_q - - - - - - - - - - - - - - r_infinity - - - 1 - - - 1 - - - - - - - - - Vm - 19.3 - - - 15 - - - - - - - - tau_r - - - 2.75352 - - - 14.40516 - - - - - 1.037 - - - - - 0.09 - - - Vm - 30.61 - - - - - - - 0.369 - - - - - - - 0.12 - - - - Vm - 23.84 - - - - - - - - - - - - - - time - - r - - - - - - r_infinity - r - - tau_r - - - - - - - - - - - - - - - - - - - i_f_Na - - - Cm - 0.3833 - g_if - - - Vm - E_Na - - - - y - 2 - - - - - - i_f_K - - - Cm - 0.6167 - g_if - - - Vm - E_K - - - - y - 2 - - - - - - i_f - - - i_f_Na - i_f_K - - - - - - - - - - - - - - - - y_infinity - - - 1 - - - 1 - - - - - - - Vm - VIf_half - - 13.5 - - - - - - - - tau_y - - - 0.7166529 - - - - - - - - - - - Vm - 386.9 - - - 45.302 - - - - - - - - - Vm - 73.08 - - 19.231 - - - - - - - - - - - time - - y - - - - - - y_infinity - y - - tau_y - - - - - - - - - - - - - - - - - - i_st - - - Cm - g_st - - - Vm - E_st - - qa - qi - - - - - - - - - - - - - - - - qa_infinity - - - 1 - - - 1 - - - - - - - - - Vm - 57 - - - 5 - - - - - - - - tau_qa - - - 1 - - - alpha_qa - beta_qa - - - - - - alpha_qa - - - 1 - - - - - 0.15 - - - - - - - Vm - - 11 - - - - - - 0.2 - - - - - - - Vm - - 700 - - - - - - - - - beta_qa - - - 1 - - - - - 16 - - - - - Vm - 8 - - - - - - 15 - - - - - Vm - 50 - - - - - - - - - - - - time - - qa - - - - - - qa_infinity - qa - - tau_qa - - - - - - - - - - - - - - - - qi_infinity - - - alpha_qi - - - alpha_qi - beta_qi - - - - - - tau_qi - - - 6.65 - - - alpha_qi - beta_qi - - - - - - alpha_qi - - - 1 - - - - - 3100 - - - - - Vm - 13 - - - - - - 700 - - - - - Vm - 70 - - - - - - - - - beta_qi - - - - - 1 - - - - - 95 - - - - - - - Vm - - 10 - - - - - - 50 - - - - - - - Vm - - 700 - - - - - - - - 0.000229 - - - 1 - - - - - - - Vm - - 5 - - - - - - - - - - - - time - - qi - - - - - - qi_infinity - qi - - tau_qi - - - - - - - - - - - - - - i_b_Na - - - Cm - g_b_Na - - - Vm - E_Na - - - - - - - - - - - - - - - - - - - - i_NaK - - - - - Cm - i_NaK_max - - - - - - 1 - - - - - Km_Kp - Ko - - 1.2 - - - - - 1 - - - - - Km_Nap - Nai - - 1.3 - - - - - 1 - - - - - - - - - - - Vm - E_Na - - 120 - - - 30 - - - - - - - - - - - - - - - - - - i_b_Ca - - - Cm - g_b_Ca - - - Vm - E_CaL - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - i_NaCa - - - - - Cm - kNaCa - - - - - x2 - k21 - - - - x1 - k12 - - - - - - x1 - x2 - x3 - x4 - - - - - - x1 - - - - - k41 - k34 - - - k23 - k21 - - - - - k21 - k32 - - - k43 - k41 - - - - - - - x2 - - - - - k32 - k43 - - - k14 - k12 - - - - - k41 - k12 - - - k34 - k32 - - - - - - - x3 - - - - - k14 - k43 - - - k23 - k21 - - - - - k12 - k23 - - - k43 - k41 - - - - - - - x4 - - - - - k23 - k34 - - - k14 - k12 - - - - - k14 - k21 - - - k34 - k32 - - - - - - - k43 - - - Nai - - - K3ni - Nai - - - - - - RTOnF - - - - - R - T - - F - - - - - k12 - - - - - - - Ca_sub - Kci - - - - - - - - - - Qci - - Vm - - RTOnF - - - - di - - - - - k14 - - - - - - - - - - - Nai - K1ni - - Nai - - K2ni - - - - 1 - - - Nai - K3ni - - - - - - - - - Qn - Vm - - - - 2 - RTOnF - - - - - di - - - - - k41 - - - - - - - - - Qn - - Vm - - - - 2 - RTOnF - - - - - - - di - - - 1 - - - - - Ca_sub - Kci - - - - 1 - - - - - - - - - Qci - - Vm - - RTOnF - - - - - Nai - Kcni - - - - - - - - Nai - K1ni - - - - 1 - - - - - Nai - K2ni - - - - 1 - - - Nai - K3ni - - - - - - - - - - k34 - - - Nao - - - K3no - Nao - - - - - - k21 - - - - - - - Cao - Kco - - - - - - - - Qco - Vm - - RTOnF - - - - do - - - - - k23 - - - - - - - - - - - Nao - K1no - - Nao - - K2no - - - - 1 - - - Nao - K3no - - - - - - - - - - - Qn - - Vm - - - - 2 - RTOnF - - - - - do - - - - - k32 - - - - - - - Qn - Vm - - - - 2 - RTOnF - - - - - - - do - - - 1 - - - - - Cao - Kco - - - - 1 - - - - - - - Qco - Vm - - RTOnF - - - - - - - - - Nao - K1no - - - - 1 - - - - - Nao - K2no - - - - 1 - - - Nao - K3no - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - j_SRCarel - - - ks - O - - - Ca_jsr - Ca_sub - - - - - - kCaSR - - - MaxSR - - - - - MaxSR - MinSR - - - - 1 - - - - - EC50_SR - Ca_jsr - - HSR - - - - - - - - koSRCa - - - koCa - kCaSR - - - - - kiSRCa - - - kiCa - kCaSR - - - - - - - - time - - R - - - - - - - - kim - RI - - - - kiSRCa - Ca_sub - R - - - - - - - koSRCa - - - Ca_sub - 2 - - R - - - - kom - O - - - - - - - - - - time - - O - - - - - - - - koSRCa - - - Ca_sub - 2 - - R - - - - kom - O - - - - - - - kiSRCa - Ca_sub - O - - - - kim - I - - - - - - - - - - time - - I - - - - - - - - kiSRCa - Ca_sub - O - - - - kim - I - - - - - - - kom - I - - - - koSRCa - - - Ca_sub - 2 - - RI - - - - - - - - - - time - - RI - - - - - - - - kom - I - - - - koSRCa - - - Ca_sub - 2 - - RI - - - - - - - kim - RI - - - - kiSRCa - Ca_sub - R - - - - - - - - - - - - - - - - - - - - - - j_Ca_dif - - - - - Ca_sub - Cai - - tau_dif_Ca - - - - - b_up - - - - - b_up_max - Ach - - - - K_up_half - Ach - - - - - - P_up - - - P_up_basal - - - 1 - b_up - - - - - - j_up - - - P_up - - - 1 - - - K_up - Cai - - - - - - - j_tr - - - - - Ca_nsr - Ca_jsr - - tau_tr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - time - - fTC - - delta_fTC - - - - delta_fTC - - - - - kf_TC - Cai - - - 1 - fTC - - - - - kb_TC - fTC - - - - - - - - - time - - fTMC - - delta_fTMC - - - - delta_fTMC - - - - - kf_TMC - Cai - - - 1 - - - fTMC - fTMM - - - - - - kb_TMC - fTMC - - - - - - - - - time - - fTMM - - delta_fTMM - - - - delta_fTMM - - - - - kf_TMM - Mgi - - - 1 - - - fTMC - fTMM - - - - - - kb_TMM - fTMM - - - - - - - - - time - - fCMi - - delta_fCMi - - - - delta_fCMi - - - - - kf_CM - Cai - - - 1 - fCMi - - - - - kb_CM - fCMi - - - - - - - - - time - - fCMs - - delta_fCMs - - - - delta_fCMs - - - - - kf_CM - Ca_sub - - - 1 - fCMs - - - - - kb_CM - fCMs - - - - - - - - - time - - fCQ - - delta_fCQ - - - - delta_fCQ - - - - - kf_CQ - Ca_jsr - - - 1 - fCQ - - - - - kb_CQ - fCQ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - time - - Cai - - - - - - - - - - j_Ca_dif - V_sub - - - - j_up - V_nsr - - - V_i - - - - - - CM_tot - delta_fCMi - - - - TC_tot - delta_fTC - - - - TMC_tot - delta_fTMC - - - - - - - - - - time - - Ca_sub - - - - - - - - j_SRCarel - V_jsr - - V_sub - - - - - - - - - - i_CaL - i_CaT - i_b_Ca - - - - 2 - i_NaCa - - - - - 2 - F - V_sub - - - j_Ca_dif - - - CM_tot - delta_fCMs - - - - - - - - - - time - - Ca_nsr - - - - j_up - - - - - j_tr - V_jsr - - V_nsr - - - - - - - - - time - - Ca_jsr - - - - j_tr - - - j_SRCarel - - - CQ_tot - delta_fCQ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - V_cell - - - 0.001 - - - - R_cell - 2 - - L_cell - - - - - V_sub - - - 0.001 - 2 - - L_sub - - - R_cell - - - L_sub - 2 - - - L_cell - - - - - V_jsr - - - V_jsr_part - V_cell - - - - - V_i - - - - - V_i_part - V_cell - - V_sub - - - - - V_nsr - - - V_nsr_part - V_cell - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - i_K_Ach - - - 0 - - - Ach - 0 - - - - - - a - g_K_Ach - - - Vm - E_K - - - - - - - - - - - - - - - - - - - alpha - - - 0.001 - 17 - - - - - 0.0133 - - - Vm - 40 - - - - - - - - beta - - - 0 - - - Ach - 0 - - - - - - - - 0.001 - 12.32 - - - - 1 - - - 0.0042 - Ach - - - - - - - - - a_infinity - - - beta - - - alpha - beta - - - - - - tau_a - - - 1 - - - alpha - beta - - - - - - - - - time - - a - - - - - - a_infinity - a - - tau_a - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - s - - - - - s_max - - - Ach - n_f - - - - - - - K_f_half - n_f - - - - Ach - n_f - - - - - - - VIf_half - - - VIf_half_basal - s - - - - - - - - - - - - - - - - - - - - - - - - b_cal - - - - - b_cal_max - Ach - - - - K_cal_half - Ach - - - - - - g_CaL - - - g_CaL_basal - - - 1 - b_cal - - - - - - - - - - - - - - - - - - Maltsev - V - A - - - - - - keyword - - - - - - - - - - - - - - - - - - - Non-steady state model translated from the published paper - - - - - - cardiac - electrophysiology - - - - - - - - - - - - Synergism of coupled subsarcolemmal Ca2+ clocks and sarcolemmal voltage clocks confers robust and flexible pacemaker function in a novel pacemaker cell model. - - - - - - - - - - - H561 - 296(3) - H562 - - - - - - - - - - - - - - - - - - - - - - - - Am J Physiol Heart Circ Physiol. - - - The University of Auckland - Auckland Bioengineering Institute - - - - - - 19136600 - - - 10000 - 10000 - 10 - - - Lloyd - Catherine - May - - - - - - - - - - - - - - 2009-03 - - - Lakatta - E - G - - - c.lloyd@auckland.ac.nz - - - - - - - - - - - - - - diff --git a/Bioelectrics/Monodomain_Shiqiang/input/n98.xml b/Bioelectrics/Monodomain_Shiqiang/input/n98.xml deleted file mode 100644 index 2945739a..00000000 --- a/Bioelectrics/Monodomain_Shiqiang/input/n98.xml +++ /dev/null @@ -1,5799 +0,0 @@ - - - - - - - - - - - - - - - - Lloyd - Catherine - May - - - c.lloyd@auckland.ac.nz - - - - The University of Auckland - The Bioengineering Research Group - - - - - - 2001-12-18 - - - - - - Added more metadata. - - - - Lloyd - Catherine - May - - - - 2002-07-22 - - - - - Corrected units. - - - - Lloyd - Catherine - May - - - - 2002-03-01 - - - - - Corrected several equations. - - - - Lloyd - Catherine - May - - - - 2002-02-26 - - - - - Corrected the i_K1 and i_K_ACh calculations. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Updated metadata to conform to the 16/1/02 CellML Metadata 1.0 - Specification. - - - - Cuellar - Autumn - A. - - - - 2002-01-21 - - - - - Altered some of the connections. - - - - Lloyd - Catherine - May - - - - 2002-01-04 - - - - - Added some initial values from Penny Noble's documentation. Removed - the blocked h_gate component from the fast sodium current as it - belongs to a separate model which considers the effect of drugs. - - - - Lloyd - Catherine - May - - - - 2002-05-06 - - - - - Fixed up the CellML/MathML to enable the model to be solved in CMISS. The - model is no longer a direct translation of the Noble 1998 article, but - I believe it accurately represents the intent of the model. - - - - Nickerson - David - P - - - - 2003-04-05 - - - - - - Bioengineering Institute, The University of Auckland. - - - - - - - - The Noble 1998 Improved Guinea-Pig Ventricular Cell Model - - - - - - This is the CellML description of Noble's 1998 improved guinea-pig - ventricular cell model. It incorporates a diadic space, rapid and - slow potassium currents and length- and tension-dependent processes. - - - - Catherine Lloyd - - - - Guinea-Pig - - Ventricular Myocyte - - - - 9487284 - - - - - - - Noble - Denis - - - - - - - Varghese - Anthony - - - - - - - Kohl - Peter - - - - - - - Noble - Penny - - - - - - - Improved guinea-pig ventricular cell model incorporating a diadic - space, IKr and IKs, and length- and tension-dependent processes - - - 1998 - - - Canadian Journal of Cardiology - - 14 - 123 - 134 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This component is used to declare variables that are used by - all or most of the other components, in this case just `time'. - - - - - - - - - - - - - This component is the `root' node of our model. - It defines the action potential variable `V'. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A dummy equation used to get the total stimulus current into CMISS. - - - - - - - IStimC - IStim - - - - - - - - The ODE governing the membrane potential -- given by the summation of the - ionic currents and an applied stimulus. - - - - - - - - time - V - - - - IStim - - i_K1 - i_to - i_K - i_K_ATP - i_b_K - i_NaK - i_Na - i_b_Na - i_p_Na - i_NaCa - i_NaCa_ds - i_Ca_L_Ca - i_Ca_L_Ca_ds - i_Ca_L_K - i_Ca_L_K_ds - i_Ca_L_Na - i_Ca_L_Na_ds - i_b_Ca - i_Na_stretch - i_K_stretch - i_Ca_stretch - i_Ns_stretch - i_An_stretch - i_K_ACh - - - Cm - - - - - - - - - - - A component that conveniently keeps the reversal potential calculations - together. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the sodium reversal potential from the current intra- and - extracellular concentration of sodium ions. - - - - - - - E_Na - - - - R - T - - F - - - - Na_o - Na_i - - - - - - - - - - Calculation of the potassium reversal potential from the current intra- and - extracellular concentration of potassium ions. - - - - - - - E_K - - - - R - T - - F - - - - K_o - K_i - - - - - - - - - - Calculation of the potassium reversal potential for the slow component of - the delayed rectifier. - - - - - - - E_Ks - - - - R - T - - F - - - - - K_o - - P_kna - Na_o - - - - K_i - - P_kna - Na_i - - - - - - - - - - - - Calculation of the calcium reversal potential. - - - - - - - E_Ca - - 0.5 - - - R - T - - F - - - - Ca_o - Ca_i - - - - - - - - - - Calculation of the reversal potential for the fast sodium channel. - - - - - - - E_mh - - - - R - T - - F - - - - - Na_o - - P_nak - K_o - - - - Na_i - - P_nak - K_i - - - - - - - - - - - - - - - Description of the time independent inward potassium current. - - - - - - - - - - - - - - - - - - - - - - - Calculation of the time independent potassium current. - - - - - - - i_K1 - - g_K1 - - K_o - - K_o - K_mk1 - - - - - V - E_K - - - 1.0 - - - - 1.25 - - V - - E_K - 10.0 - - - - - - R - T - - F - - - - - - - - - - - - - - - - A component to group the potassium currents. - - - - - - - - - - - - - - - Simple summation of the individual potassium currents into a - single current. - - - - - - - i_K - - i_Kr - i_Ks - i_KNa - - - - - - - - - - - The rapid component of the delayed rectifier current. - - - - - - - - - - - - - - - - - - - - - - Calculation of the rapid component of the delayed rectifier current. - - - - - - - i_Kr - - - - g_Kr1 - Xr1 - - - g_Kr2 - Xr2 - - - - 1.0 - - 1.0 - - - - V - 9.0 - - 22.4 - - - - - - V - E_K - - - - - - - - - - - - The fast activation gate for the rapid component of the delayed - rectifier. - - - - - - - - - - - - - - The gating kinetics for the fast gate of the rapid component - of the delayed rectifier. - - - - - - - - time - Xr1 - - - - - 0.05 - - 1.0 - - - - - V - 5.0 - - - 9.0 - - - - - - 1.0 - Xr1 - - - - 0.00005 - - - - - V - 20.0 - - 15.0 - - - - Xr1 - - - - - - - - - - - - The slow gate of the rapid component of the delayed rectifier. - - - - - - - - - - - - - - Gating kinetics for the slow gate of the rapid component of - the delayed rectifier. - - - - - - - - time - Xr2 - - - - - 0.05 - - 1.0 - - - - - V - 5.0 - - - 9.0 - - - - - - 1.0 - Xr2 - - - - 0.0004 - - - - - - V - 30.0 - - 30.0 - - 3.0 - - - - Xr2 - - - - - - - - - - - - The slow component of the delayed rectifier current. - - - - - - - - - - - - - - - - - - - - Calculation of the slow component current of the delayed rectifier. - - - - - - - i_Ks - - - g_Ks - - Xs - 2.0 - - - - V - E_Ks - - - - - - - - - - - - The gate for the slow component of the delayed rectifier current. - - - - - - - - - - - - - - The gating kinetics for the slow component of the delayed - rectifier current. - - - - - - - - time - Xs - - - - - 0.014 - - 1.0 - - - - - V - 40.0 - - - 9.0 - - - - - - 1.0 - Xs - - - - Xs - 0.001 - - - - V - - 45.0 - - - - - - - - - - - - - - Background potassium current. - - - - - - - - - - - - - - - - - - Calculation of the background potassium current. - - - - - - - i_b_K - - g_bk - - V - E_K - - - - - - - - - - - - An ATP dependent potassium current. Included here for completeness, but - this current is only used when modelling ischaemia - and this version - of the model has not been tested for this. - - - - - - - - - - - - - - - - - - - Calculation of the ATP dependent potassium current. - - - - - - - i_K_ATP - - - g_K_ATP - - V - 80.0 - - - - 1.0 - - - ATP - K_ATP - - 2.0 - - - - - - - - - - - - - A sodium activated potassium current. Again, included for completeness - but generally not used and untested. - - - - - - - - - - - - - - - - - - - - Calculation of the sodium activated potassium current. - - - - - - - i_KNa - - g_K_Na - - Na_i - - Na_i - K_kna - - - - V - E_K - - - - - - - - - - - - The fast sodium current - the driving force of the upstroke of the - cardiac action potential. - - - - - - - - - - - - - - - - - - - - - Calculation of the fast sodium current. - - - - - - - i_Na - - g_Na - - m - 3.0 - - h - - V - E_mh - - - - - - - - - - - - The activation gate for the fast sodium current. - - - - - - - - - - - - - - - - - The gating kinetics for the activation gate of the fast sodium current. - - - - - - - - time - m - - - - alpha - - 1.0 - m - - - - beta - m - - - - - - - - - Calculation of the opening rate of the activation gate for the fast - sodium current. - - - - - - - alpha - - - 2.0 - - - - V - 41.0 - - - 0.1e-4 - - - - - - 0.2 - - V - 41.0 - - - - 1.0 - - - -0.1 - - V - 41.0 - - - - - - - - - - - - - - Calculation of the closing rate of the activation gate for the fast - sodium current. - - - - - - - beta - - 8.0 - - - -0.055556 - - V - 66.0 - - - - - - - - - - - - - - The inactivation gate for the fast sodium current. - - - - - - - - - - - - - - The gating kinetics for the inactivation gate of the fast sodium - current. - - - - - - - - time - h - - - - - 0.02 - - - -0.125 - - V - 75.0 - - - - - - 1.0 - h - - - - h - - 2.0 - - 1.0 - - 320.0 - - - -0.1 - - V - 75.0 - - - - - - - - - - - - - - - - - - The persistent sodium current. - - - - - - - - - - - - - - - - - - Calculation of the persistent sodium current. - - - - - - - i_p_Na - - g_pna - - 1.0 - - 1.0 - - - - - V - 52.0 - - 8.0 - - - - - - - V - E_Na - - - - - - - - - - - - The background sodium current. - - - - - - - - - - - - - - - - - - - Calculation of the sodium background current. - - - - - - - i_b_Na - - g_bna - - V - E_Na - - - - - - - - - - - - - This component describes an inward ionic current which is the sum - of calcium, sodium and potassium ions through the membrane channel. - The channel has one activation gate (d) and two inactivation gates - (f and f2 (or f2ds in the diadic space)). A fraction of these channels - (ICaLfract) open into the diadic subspace, with the remainder being - evenly distributed throughout the membrane area. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The calcium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_Ca - - - 1.0 - ICaLfract - - 4.0 - P_ca - d - f - f2 - - - - V - 50.0 - - - - R - T - - F - - - - 1.0 - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - - Ca_i - - - 50.0 - - - R - T - - - 2.0 - F - - - - - - - Ca_o - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The potassium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_K - - - 1.0 - ICaLfract - - P_caK - P_ca - d - f - f2 - - - K_i - - - 50.0 - - - R - T - - F - - - - - - K_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The sodium ion component of the total current through the channel into - the bulk myoplasm. - - - - - - - i_Ca_L_Na - - - 1.0 - ICaLfract - - P_caNa - P_ca - d - f - f2 - - - Na_i - - - 50.0 - - - R - T - - F - - - - - - Na_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The calcium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_Ca_ds - - ICaLfract - 4.0 - P_ca - d - f - f2ds - - - - V - 50.0 - - - - R - T - - F - - - - 1.0 - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - - Ca_ds - - - 50.0 - - - R - T - - - 2.0 - F - - - - - - - Ca_o - - - - - V - 50.0 - - - - - R - T - - - 2.0 - F - - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The potassium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_K_ds - - ICaLfract - P_caK - P_ca - d - f - f2ds - - - K_i - - - 50.0 - - - R - T - - F - - - - - - K_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - The sodium ion component of the total current through the channel into - the diadic subspace. - - - - - - - i_Ca_L_Na_ds - - ICaLfract - P_caNa - P_ca - d - f - f2ds - - - Na_i - - - 50.0 - - - R - T - - F - - - - - - Na_o - - - - - V - 50.0 - - - - - R - T - - F - - - - - - - 1.0 - - ACh - - ACh - K_AChICaL - - - - - - - - - - - - - - The activation gate of the L-type calcium channel. - - - - - - - - - - - - - - - - - The gating kinetics for the activation gate. - - - - - - - - time - d - - - - alpha - - 1.0 - d - - - - beta - d - - - - - - - - - The opening rate for the activation gate. - - - - - - - alpha - - - 0.36 - - - - V - 19.0 - - - 1.0e-3 - - - - - - 0.09 - - V - 19.0 - - - - 1.0 - - - - - V - 19.0 - - - 4.0 - - - - - - - - - - - - - The closing rate for the activation gate. - - - - - - - beta - - - 0.36 - - - - V - 19.0 - - - 1.0e-3 - - - - - - -0.036 - - V - 19.0 - - - - 1.0 - - - - V - 19.0 - - 10.0 - - - - - - - - - - - - - - - - The first inactivation gate for the L-type calcium channel. - - - - - - - - - - - - - - - - - - - The gating kinetics for the first inactivation gate. - - - - - - - - time - f - - - - alpha - - 1.0 - f - - - - beta - f - - - - - - - - - The opening rate for the inactivation gate. - - - - - - - alpha - - - 0.0075 - - - - V - 34.0 - - - 1.0e-3 - - - - - -0.001875 - - - V - 34.0 - - - 1.0 - - - - V - 34.0 - - 4.0 - - - - - - - - - - - - - - The closing rate for the inactivation gate. - - - - - - - beta - - 0.0036 - - 1.0 - - - - - V - 34.0 - - 4.0 - - - - - - - - - - - - - - - The second inactivation gate for L-type calcium channels in the - membrane outside the diadic subspace. - - - - - - - - - - - - - - - - - - - The gating kinetics for the inactivation gate. - - - - - - - - time - f2 - - - CaInact - - 1.0 - - - Ca_i - - K_cachoff - Ca_i - - - f2 - - - - - - - - - - - - - The second inactivation gate for L-type calcium channels in the - membrane when open into the diadic subspace. - - - - - - - - - - - - - - - - - - The gating kinetics for the inactivation gate. - - - - - - - - time - f2ds - - - CaInactDS - - 1.0 - - - Ca_ds - - K_dsoff - Ca_ds - - - f2ds - - - - - - - - - - - - - The background calcium current. - - - - - - - - - - - - - - - - - - Calculation of the background calcium current. - - - - - - - i_b_Ca - - g_bca - - V - E_Ca - - - - - - - - - - - - The doubly gated transient outward current. - - - - - - - - - - - - - - - - - - - - - - - Evaluation of the transient outward current. - - - - - - - i_to - - g_to - - g_tos - - s - - 1.0 - g_tos - - - - r - - V - E_K - - - - - - - - - - - - The first gate of the transient outward current. - - - - - - - - - - - - - - The gating kinetics. - - - - - - - - time - s - - - - 0.000033 - - - - V - - 17.0 - - - - 1.0 - s - - - - - 0.033 - - 1.0 - - - - - V - 10.0 - - - 8.0 - - - - - s - - - - - - - - - - - - The second of the two gates for the transient outward current. - - - - - - - - - - - - - - - The gating kinetics for the r gate. - - - - - - - - time - r - - - 0.333 - - r_ss - r - - - - - - - - - Calculation of the steady-state component of the gating kinetics - for the r gate. - - - - - - - r_ss - - 1.0 - - 1.0 - - - -0.2 - - V - 4.0 - - - - - - - - - - - - - - - Acetylcholine (ACh) dependent potassium current. Once more, - this current has been included for completeness with respect - to the original publication but is usually left out of simulations. - It is useful for simulating specific cellular conditions, but - this formulation has not been tested. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Evaluation of the ACh dependent potassium current. - - - - - - - i_K_ACh - - g_KACh - - K_o - - K_o - K_KACh - - - x_ACh1 - x_ACh2 - - - ACh - 1.4969 - - - - ACh - 1.4969 - - - K_ACh - 1.4969 - - - - - - V - E_K - - - 1.0 - - - - 0.4 - - V - - E_K - 140.0 - - - - - - R - T - - F - - - - - - - - - - - - - - - - The first of two gates for the ACh dependent potassium current. - - - - - - - - - - - - - - - Gating kinetics for the first gate. - - - - - - - - time - x_ACh1 - - - - alpha_ACh - - 1.0 - x_ACh1 - - - - - 0.00582 - - 1.0 - - - - - V - 50.0 - - 15.0 - - - - - - x_ACh1 - - - - - - - - - - - - The second of the two gates for the ACh dependent potassium current. - - - - - - - - - - - - - - - Gating kinetics for the second gate. - - - - - - - - time - x_ACh2 - - - - alpha_ACh - - 1.0 - x_ACh2 - - - - - 0.12 - - 1.0 - - - - - V - 50.0 - - 15.0 - - - - - - x_ACh2 - - - - - - - - - - - - The sodium potassium pump. - - - - - - - - - - - - - - - - - - - - Calculation of the sodium potassium pump current. - - - - - - - i_NaK - - i_NaK_max - - K_o - - K_o - K_mk - - - - Na_i - - Na_i - K_mNa - - - - - - - - - - - - - The sodium calcium exchanger. A fraction of the Na-Ca exchangers - (INaCaFract) are assumed to emmpty into the diadic subspace, while - the remainder of the channels open into the bulk cytosol. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calculation of the sodium calcium exchanger current for the channels - exposed to the bulk myoplasm. - - - - - - - i_NaCa - - - 1.0 - INaCaFract - - K_NaCa - - - - - - gamma - - V - - - R - T - - F - - - - - - Na_i - 3.0 - - Ca_o - - - - - - gamma - 1.0 - - - V - - - R - T - - F - - - - - - Na_o - 3.0 - - Ca_i - - - - 1.0 - - d_NaCa - - - Ca_i - - Na_o - 3.0 - - - - Ca_o - - Na_i - 3.0 - - - - - - - - 1.0 - - 1.0 - - Ca_i - 0.0069 - - - - - - - - - - - Calculation of the sodium calcium exchanger current for the channels - opening into the diadic subspace. - - - - - - - i_NaCa_ds - - INaCaFract - K_NaCa - - - - - - gamma - - V - - - R - T - - F - - - - - - Na_i - 3.0 - - Ca_o - - - - - - gamma - 1.0 - - - V - - - R - T - - F - - - - - - Na_o - 3.0 - - Ca_ds - - - - 1.0 - - d_NaCa - - - Ca_ds - - Na_o - 3.0 - - - - Ca_o - - Na_i - 3.0 - - - - - - - - 1.0 - - 1.0 - - Ca_ds - 0.0069 - - - - - - - - - - - - - - The sarcoplasmic reticulum calcium pump which transports calcium - from the bulk myoplasm into the network SR. - - - - - - - - - - - - - - - - - - - - Calculation of the calcium uptake flux. - - - - - - - i_up - - - - 0.0004 - Ca_i - - - 0.00003 - Ca_up - - - K_cyca - K_xcs - - K_srca - - - - - Ca_i - - Ca_up - - - K_cyca - K_xcs - - K_srca - - - - K_cyca - K_xcs - - K_cyca - - - - - - - - - - - - Diffusion down the concentration gradient to transfer calcium from - the uptake stores in the network SR to the release stores in the - junctional SR. - - - - - - - - - - - - - - - - Calculation of the transfer flux between the uptake and release - calcium stores. - - - - - - - i_tr - - 0.05 - - Ca_up - Ca_rel - - - - - - - - - - - - This component describes the addition of - length dependence to the Noble models. However, in this implementation - of the model, it is unused - sarcomere length (SL) is a constant 0, - resulting in the removal of length dependence from the model. - - - - - - - - - - - - - - - - - Calculation of the scaling factor for the stretch activated currents - based on the change in length from the reference state. - - - - - - - f_stretch - - 1.0 - - 1.0 - - - -2.0 - gamma_SAC_SL - - SL - SLRef - - - - - - - - - - - - - - - The length dependent leakage of calcium from the junctional - SR into the cytolsol. - - - - - - - - - - - - - - - - i_leak - - - - gamma_SR_SL - SL - - - alpha_SRleak - Ca_rel - - - - - - - - - - - Description of the diffusion of calcium out of the diadic - subspace into the bulk cytosol. - - - - - - - - - - - - - - - - Calculation of the flux of calcium out of the diadic subspace. - - - - - - - i_decay - - alpha_ca_ds_decay - Ca_ds - - - - - - - - - - - The calcium induced calcium release from the junctional SR into - the bulk myoplasm. Assumed that activation of calcium release sites - by the diadic subspace calcium triggers calcium release in the whole - cytosol. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The fraction of release sites in the open state. - - - - - - - OpenReleaseChannelFract - - - ActivatorFract - - ActivatorFract - 0.25 - - - 2.0 - - - - - - - - Calculation of the calcium release flux from the JSR into the cytosol. - - - - - - - i_rel - - alpha_rel - OpenReleaseChannelFract - Ca_rel - - - - - - - - Regulatory binding sites. - - - - - - - RegulatoryBindingSite - - - - Ca_i - - Ca_i - K_mca - - - - - 1.0 - - Ca_i - - Ca_i - K_mca - - - - - Ca_ds - - Ca_ds - K_mca_ds - - - - - 2.0 - - - - - - - - Fraction of release channels in the precursor state. - - - - - - - PrecursorFract - - 1.0 - - ActivatorFract - ProductFract - - - - - - - alpha_act - - 0.5 - RegulatoryBindingSite - - - - - - alpha_inact - - 0.06 - - 0.5 - RegulatoryBindingSite - - - - - - - SR_speed_factor - - - 5.0 - - V - -50.0 - - - - 1.0 - - - - - - - - - time - - ActivatorFract - - - SR_speed_factor - - - alpha_act - PrecursorFract - - - alpha_inact - ActivatorFract - - - - - - - - - - time - - ProductFract - - - SR_speed_factor - - - alpha_inact - ActivatorFract - - - 0.001 - ProductFract - - - - - - - - - - - - - A stretch activated calcium current. Unused and untested in this - implementation, but included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ca_stretch - - g_Ca_stretch - f_stretch - - V - E_Ca - - - - - - - - - - - - Stretch activated potassium current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_K_stretch - - g_K_stretch - f_stretch - - V - E_K - - - - - - - - - - - - A stretch activated sodium current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Na_stretch - - g_Na_stretch - f_stretch - - V - E_Na - - - - - - - - - - - - A non-specific stretch activated current. Not used and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_Ns_stretch - - g_Ns_stretch - f_stretch - - V - E_Ns_stretch - - - - - - - - - - - - A anion specific stretch ativated current - unused and untested, but - included for completeness. - - - - - - - - - - - - - - - - - - - Calculation of the current. - - - - - - - i_An_stretch - - g_An_stretch - f_stretch - - V - E_An_stretch - - - - - - - - - - - - A convenient grouping of all the ionic concentration differential - equations. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The rate of change of intracellular sodium concentration. - - - - - - - - time - Na_i - - - - - Am - - V_i - F - - - - - i_Na - i_p_Na - - i_b_Na - - Na_o - 140.0 - - - - i_NaK - 3.0 - - - i_NaCa - 3.0 - - - i_NaCa_ds - 3.0 - - i_Ca_L_Na - i_Ca_L_Na_ds - i_Na_stretch - - - - - - - - - The rate of change of intracellular potassium concentration. - - - - - - - - time - K_i - - - - - Am - - V_i - F - - - - - - i_K1 - i_to - i_b_K - i_K - i_K_stretch - i_Ca_L_K - i_Ca_L_K_ds - i_K_ACh - i_K_ATP - - - i_NaK - 2.0 - - - - - - - - - - The rate of change of intracellular calcium concentration. - - - - - - - - time - Ca_i - - - - - - - Am - - 2.0 - V_i - F - - - - - - i_Ca_L_Ca - i_b_Ca - i_Ca_stretch - - - i_NaCa - 2.0 - - - - - i_rel - - V_rel - V_i - - - - i_leak - - V_rel - V_i - - - - i_decay - - V_ds - V_i - - - - - i_up - dy_Ca_calmod - dy_Ca_troponin - - - - - - - - - The rate of change of calcium concentration in the diadic subspace. - - - - - - - - time - Ca_ds - - - - - - Am - - 2.0 - V_ds - F - - - - - i_Ca_L_Ca_ds - - i_NaCa_ds - 2.0 - - - - i_decay - - - - - - - - The rate of change of calcium concentration in the network SR - uptake store. - - - - - - - - time - Ca_up - - - - - V_i - V_up - - i_up - - i_tr - - - - - - - - The rate of change of calcium concentration in the junctional SR - release store. - - - - - - - - time - Ca_rel - - - - - V_up - V_rel - - i_tr - - - i_rel - i_leak - - - - - - - - - The rate of change of calcium bound to calmodulin. - - - - - - - dy_Ca_calmod - - - 100.0 - Ca_i - - CALM - Ca_calmod - - - - 0.05 - Ca_calmod - - - - - - - - time - Ca_calmod - - dy_Ca_calmod - - - - - - - The rate of change of calcium bound to troponin. - - - - - - - dy_Ca_troponin - - - alpha_trop - Ca_i - - TROP - Ca_troponin - - - - beta_trop - Ca_troponin - - - - - - - - time - Ca_troponin - - dy_Ca_troponin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/Bioelectrics/MonodomainCUDA/Atlas_Mesh.vtk b/Bioelectrics/input/Atlas_Mesh.vtk similarity index 100% rename from Bioelectrics/MonodomainCUDA/Atlas_Mesh.vtk rename to Bioelectrics/input/Atlas_Mesh.vtk diff --git a/Bioelectrics/MonodomainCUDA/LRd2.xml b/Bioelectrics/input/LRd2.xml similarity index 100% rename from Bioelectrics/MonodomainCUDA/LRd2.xml rename to Bioelectrics/input/LRd2.xml diff --git a/ClassicalField/Laplace/CMakeLists.txt b/ClassicalField/Laplace/CMakeLists.txt index 5ea48276..9d3da492 100644 --- a/ClassicalField/Laplace/CMakeLists.txt +++ b/ClassicalField/Laplace/CMakeLists.txt @@ -31,8 +31,8 @@ find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG) if (CMAKE_Fortran_COMPILER) add_subdirectory(Embedded1DLaplace) add_subdirectory(Embedded2DLaplace) - add_subdirectory(Laplace/C) - add_subdirectory(Laplace/Fortran) +# add_subdirectory(Laplace/C) + add_subdirectory(Laplace) add_subdirectory(GeneralisedLaplace/Fortran) add_subdirectory(LaplaceEllipsoid) add_subdirectory(NumberLaplace) diff --git a/ClassicalField/Laplace/Laplace/CMakeLists.txt b/ClassicalField/Laplace/Laplace/CMakeLists.txt new file mode 100644 index 00000000..9ffac615 --- /dev/null +++ b/ClassicalField/Laplace/Laplace/CMakeLists.txt @@ -0,0 +1,19 @@ +# Turn on Fortran preprocessing (#include directives) +if (MSVC) + set(PROC_OPT "/fpp") +else() + set(PROC_OPT "-cpp") +endif() + +# Build the Fortran example +add_executable(laplace_fortran Fortran/src/FortranExample.f90) +target_compile_options(laplace_fortran PRIVATE ${PROC_OPT}) +target_link_libraries(laplace_fortran PRIVATE opencmiss) + +# Build the C example +add_executable(laplace_c C/src/CExample.c) +target_link_libraries(laplace_c PRIVATE opencmiss) + +#add_test(NAME Laplace_Fortran COMMAND laplace_fortran) +#add_opencmiss_environment(Laplace_Fortran) + diff --git a/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt b/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt deleted file mode 100644 index d447c38b..00000000 --- a/ClassicalField/Laplace/Laplace/Fortran/CMakeLists.txt +++ /dev/null @@ -1,50 +0,0 @@ -# Add example executable -add_executable(laplace_fortran src/FortranExample.f90) - -# Turn on Fortran preprocessing (#include directives) -if (MSVC) - set(PROC_OPT "/fpp") -else() - set(PROC_OPT "-cpp") -endif() -target_compile_options(laplace_fortran PRIVATE ${PROC_OPT}) - -# Link to opencmiss -# ----------------- -# -# This simply uses the opencmiss target created by OC_INIT() above. -# -# Alternatively, you can also directly invoke 'find_package(Iron )' to explicitly -# require that version. But then you have to deal with setting up the correct MPI include directives and library paths. -# -# If required, add any other required link libraries (cellml, petsc ..) here, too. -# For example, if you needed PetSC functionality, issue -# -# find_package(PETSC REQUIRED) -# target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc) -# -# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name. -target_link_libraries(laplace_fortran PRIVATE opencmiss) - -# Add a simple test that runs the executable -add_test(NAME Laplace_Fortran COMMAND laplace_fortran) -add_opencmiss_environment(Laplace_Fortran) - -################### -# Developer notice! -# -# If you write Fortran code and use MPI, you need to use the following MPI directives: -# -# #ifndef NOMPIMOD -# USE MPI -# #endif -# [...] -# IMPLICIT NONE -# [...] -# #ifdef NOMPIMOD -# #include "mpif.h" -# #endif -# -# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make -# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly. -# From aff959410ffeb4dce4f04913bccea5f674ed32d5 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Mon, 31 Oct 2016 13:44:30 +1300 Subject: [PATCH 26/28] added corrected Guccione Cube example --- FiniteElasticity/GuccioneCube/README.md | 2 + FiniteElasticity/GuccioneCube/guccione.cellml | 290 +++++++++ FiniteElasticity/GuccioneCube/plot.py | 47 ++ FiniteElasticity/GuccioneCube/run.py | 30 + FiniteElasticity/GuccioneCube/simulation.py | 590 ++++++++++++++++++ .../GuccioneCube/view-unit-cube.com | 41 ++ 6 files changed, 1000 insertions(+) create mode 100644 FiniteElasticity/GuccioneCube/README.md create mode 100644 FiniteElasticity/GuccioneCube/guccione.cellml create mode 100644 FiniteElasticity/GuccioneCube/plot.py create mode 100644 FiniteElasticity/GuccioneCube/run.py create mode 100644 FiniteElasticity/GuccioneCube/simulation.py create mode 100644 FiniteElasticity/GuccioneCube/view-unit-cube.com diff --git a/FiniteElasticity/GuccioneCube/README.md b/FiniteElasticity/GuccioneCube/README.md new file mode 100644 index 00000000..e6040337 --- /dev/null +++ b/FiniteElasticity/GuccioneCube/README.md @@ -0,0 +1,2 @@ +# guccione-cube +A unit cube of material with the Guccione material law in CellML being stretched in OpenCMISS. diff --git a/FiniteElasticity/GuccioneCube/guccione.cellml b/FiniteElasticity/GuccioneCube/guccione.cellml new file mode 100644 index 00000000..425f1174 --- /dev/null +++ b/FiniteElasticity/GuccioneCube/guccione.cellml @@ -0,0 +1,290 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Q + + + + + 2 + c2 + + + E11 + E22 + E33 + + + + + c3 + + + E11 + 2 + + + + + c4 + + + + + E33 + 2 + + + + E22 + 2 + + + + + + E23 + 2 + + 2 + + + + + + 2 + c5 + + + + + E13 + 2 + + + + E12 + 2 + + + + + + + + Tdev11 + + + c1 + + + Q + + + + c2 + + + c3 + E11 + + + + + + + Tdev22 + + + c1 + + + Q + + + + c2 + + + c4 + E22 + + + + + + + Tdev33 + + + c1 + + + Q + + + + c2 + + + c4 + E33 + + + + + + + Tdev12 + + + c1 + + + Q + + c5 + E12 + + + + + Tdev13 + + + c1 + + + Q + + c5 + E13 + + + + + Tdev23 + + + c1 + + + Q + + c4 + E23 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Rajgopal + Vijayaraghavan + + + The University of Auckland + Auckland Bioengineering Institute + + + + 2003-12-28 + + + + + + keyword + + + constitutive material law + mechanical constitutive laws + + + + + + + diff --git a/FiniteElasticity/GuccioneCube/plot.py b/FiniteElasticity/GuccioneCube/plot.py new file mode 100644 index 00000000..f503916c --- /dev/null +++ b/FiniteElasticity/GuccioneCube/plot.py @@ -0,0 +1,47 @@ +# here we get the current path of this script so that we can specify things relative to +# this script, rather than the execution folder. And the modules path... +import sys, os +from os.path import dirname, join +ScriptPath = dirname(__file__) +RunScript = os.path.abspath(os.path.join(ScriptPath, "run.py")) +Root = os.getcwd() + +import matplotlib +matplotlib.use('Qt4Agg') +matplotlib.rcParams['backend.qt4']='PySide' +import matplotlib.pyplot as plt +import json +from subprocess import run, DEVNULL +from pprint import pprint + +colours = ['b', 'g', 'r', 'c', 'm', 'y', 'k'] +colourIndex = 0 + +parameterSets = [ + ["1.0", "5.0", "10.0", "5.0"], #defaults + ["0.25", "5.0", "10.0", "5.0"], + ["0.5", "5.0", "10.0", "5.0"], + ["0.75", "5.0", "10.0", "5.0"], + ["1.25", "5.0", "10.0", "5.0"], + ["1.5", "5.0", "10.0", "5.0"], + ["1.75", "5.0", "10.0", "5.0"], + ["2.0", "5.0", "10.0", "5.0"] + ] + +for i, parameters in enumerate(parameterSets, 0): + resultsFileName = os.path.abspath(os.path.join(Root, "results-{:03d}.json".format(i+1))) + run(["python", RunScript] + parameters + [resultsFileName], stdout=DEVNULL) + with open(resultsFileName) as resultsFile: + results = json.load(resultsFile) + labelText = str(results["materialParameters"]) + plt.plot(results["fibre"]["strain"], results["fibre"]["stress"], colours[colourIndex] + "-", label=labelText) + plt.plot(results["cross"]["strain"], results["cross"]["stress"], colours[colourIndex] + "1--") + colourIndex = colourIndex + 1 + if colourIndex >= len(colours): + colourIndex = 0 + +plt.ylim(ymax=50) +plt.ylabel('axial force') +plt.xlabel('axial strain') +plt.legend(loc=0) +plt.show() diff --git a/FiniteElasticity/GuccioneCube/run.py b/FiniteElasticity/GuccioneCube/run.py new file mode 100644 index 00000000..f6ae7765 --- /dev/null +++ b/FiniteElasticity/GuccioneCube/run.py @@ -0,0 +1,30 @@ + +from pprint import pprint +from simulation import simulate +import json +import sys + +materialParameters = [1.0, 5.0, 10.0, 5.0] +resultsFileName = "results.json" +if len(sys.argv) >= 5: + materialParameters = [float(sys.argv[1]), float(sys.argv[2]), float(sys.argv[3]), float(sys.argv[4])] + +if len(sys.argv) == 6: + resultsFileName = sys.argv[5] + +resultsFibre = simulate(0.0, materialParameters) + +# by re-orienting the fibre direction in the unit cube we can simulate a cross fibre extension +resultsCross = simulate(90.0, materialParameters) + +results = {} +results["materialParameters"] = materialParameters +results["fibre"] = resultsFibre +results["cross"] = resultsCross + +pprint(resultsFibre) +pprint(resultsCross) +pprint(results) + +with open(resultsFileName, 'w') as rjson: + json.dump(results, rjson) diff --git a/FiniteElasticity/GuccioneCube/simulation.py b/FiniteElasticity/GuccioneCube/simulation.py new file mode 100644 index 00000000..feafe88e --- /dev/null +++ b/FiniteElasticity/GuccioneCube/simulation.py @@ -0,0 +1,590 @@ +#!/usr/bin/env python + +# Based on the OpenCMISS-Iron uniaxial extension example, trying to replicate example 524 from classic-cm, using +# Guccione in CellML. + +#> Main script +# Add Python bindings directory to PATH +import sys, os +from numpy import pi + +# Intialise OpenCMISS +from opencmiss.iron import iron + +def usage(progName): + print("Usage: " + progName + " ") + print("\tAngle should be given in degrees.") + print("\tReplicating the examples 524-527 (0, 30, 60, 90 degree fibre angles) from cm-classic.") + +def simulate(fibreAngleIn, materialParameters): + ''' + Main function to run a finite elasticity simulation using OpenCMISS with a unit cube and the Guccione material law (in CellML). + fibreAngle is a scalar angle in degrees + materialParameters is a list of the four Guccione material parameters. + ''' + # Set problem parameters - Unit cube + height = 1.0 + width = 1.0 + length = 1.0 + +# if len(sys.argv) != 2: +# usage(sys.argv[0]) +# exit(-1) + + fa = fibreAngleIn + print("fa = " + str(fa)) + + # Fibre angles in radians: + fibreAngle = fa * pi / 180.0 + # (transversly isotropic, so assume 0 cross-fibre angle?) + sheetAngle = 90.0 * pi / 180.0 + fibreAngles = [fibreAngle, 0.0, sheetAngle] + + # Guccione constitutive relation: + constitutiveRelation = iron.EquationsSetSubtypes.CONSTITUTIVE_LAW_IN_CELLML_EVALUATE + constitutiveParameters = [0.88, 18.5, 3.58, 3.26] + constitutiveParameters = materialParameters + initialHydrostaticPressure = 0.0 + + UsePressureBasis = False + NumberOfGaussXi = 2 + + coordinateSystemUserNumber = 1 + regionUserNumber = 1 + basisUserNumber = 1 + pressureBasisUserNumber = 2 + generatedMeshUserNumber = 1 + meshUserNumber = 1 + decompositionUserNumber = 1 + geometricFieldUserNumber = 1 + fibreFieldUserNumber = 2 + materialFieldUserNumber = 3 + dependentFieldUserNumber = 4 + equationsSetFieldUserNumber = 5 + deformedFieldUserNumber = 6 + equationsSetUserNumber = 1 + problemUserNumber = 1 + + CellMLUserNumber = 1 + CellMLModelsFieldUserNumber = 7 + CellMLParametersFieldUserNumber = 8 + CellMLIntermediateFieldUserNumber = 9 + + # Set all diganostic levels on for testing + #iron.DiagnosticsSetOn(iron.DiagnosticTypes.ALL,[1,2,3,4,5],"Diagnostics",["DOMAIN_MAPPINGS_LOCAL_FROM_GLOBAL_CALCULATE"]) + + numberGlobalXElements = 1 + numberGlobalYElements = 1 + numberGlobalZElements = 1 + totalNumberOfNodes=8 + totalNumberOfElements=1 + InterpolationType = 1 + if(UsePressureBasis): + numberOfMeshComponents = 2 + else: + numberOfMeshComponents = 1 + if(numberGlobalZElements==0): + numberOfXi = 2 + else: + numberOfXi = 3 + + # Get the number of computational nodes and this computational node number + numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet() + computationalNodeNumber = iron.ComputationalNodeNumberGet() + + # Create a 3D rectangular cartesian coordinate system + coordinateSystem = iron.CoordinateSystem() + coordinateSystem.CreateStart(coordinateSystemUserNumber) + coordinateSystem.DimensionSet(3) + coordinateSystem.CreateFinish() + + # Create a region and assign the coordinate system to the region + region = iron.Region() + region.CreateStart(regionUserNumber,iron.WorldRegion) + region.LabelSet("Region") + region.coordinateSystem = coordinateSystem + region.CreateFinish() + + # Define basis + basis = iron.Basis() + basis.CreateStart(basisUserNumber) + if InterpolationType in (1,2,3,4): + basis.type = iron.BasisTypes.LAGRANGE_HERMITE_TP + elif InterpolationType in (7,8,9): + basis.type = iron.BasisTypes.SIMPLEX + basis.numberOfXi = numberOfXi + basis.interpolationXi = [iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE]*numberOfXi + if(NumberOfGaussXi>0): + basis.quadratureNumberOfGaussXi = [NumberOfGaussXi]*numberOfXi + basis.CreateFinish() + + if(UsePressureBasis): + # Define pressure basis + pressureBasis = iron.Basis() + pressureBasis.CreateStart(pressureBasisUserNumber) + if InterpolationType in (1,2,3,4): + pressureBasis.type = iron.BasisTypes.LAGRANGE_HERMITE_TP + elif InterpolationType in (7,8,9): + pressureBasis.type = iron.BasisTypes.SIMPLEX + pressureBasis.numberOfXi = numberOfXi + pressureBasis.interpolationXi = [iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE]*numberOfXi + if(NumberOfGaussXi>0): + pressureBasis.quadratureNumberOfGaussXi = [NumberOfGaussXi]*numberOfXi + pressureBasis.CreateFinish() + + # Start the creation of a manually generated mesh in the region + mesh = iron.Mesh() + mesh.CreateStart(meshUserNumber,region,numberOfXi) + mesh.NumberOfComponentsSet(numberOfMeshComponents) + mesh.NumberOfElementsSet(totalNumberOfElements) + + #Define nodes for the mesh + nodes = iron.Nodes() + nodes.CreateStart(region,totalNumberOfNodes) + nodes.CreateFinish() + + elements = iron.MeshElements() + meshComponentNumber=1 + elements.CreateStart(mesh,meshComponentNumber,basis) + elements.NodesSet(1,[1,2,3,4,5,6,7,8]) + elements.CreateFinish() + + mesh.CreateFinish() + + # Create a decomposition for the mesh + decomposition = iron.Decomposition() + decomposition.CreateStart(decompositionUserNumber,mesh) + decomposition.type = iron.DecompositionTypes.CALCULATED + decomposition.numberOfDomains = numberOfComputationalNodes + decomposition.CreateFinish() + + # Create a field for the geometry + geometricField = iron.Field() + geometricField.CreateStart(geometricFieldUserNumber,region) + geometricField.MeshDecompositionSet(decomposition) + geometricField.TypeSet(iron.FieldTypes.GEOMETRIC) + geometricField.VariableLabelSet(iron.FieldVariableTypes.U,"Geometry") + geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,1,1) + geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,2,1) + geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,3,1) + if InterpolationType == 4: + geometricField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN + geometricField.CreateFinish() + + # Update the geometric field parameters manually + geometricField.ParameterSetUpdateStart(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES) + # node 1 + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,1,1,0.0) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,1,2,0.0) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,1,3,0.0) + # node 2 + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,2,1,height) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,2,2,0.0) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,2,3,0.0) + # node 3 + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,3,1,0.0) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,3,2,width) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,3,3,0.0) + # node 4 + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,4,1,height) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,4,2,width) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,4,3,0.0) + # node 5 + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,5,1,0.0) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,5,2,0.0) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,5,3,length) + # node 6 + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,6,1,height) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,6,2,0.0) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,6,3,length) + # node 7 + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,7,1,0.0) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,7,2,width) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,7,3,length) + # node 8 + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,8,1,height) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,8,2,width) + geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1,1,8,3,length) + geometricField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES) + + # Create a fibre field and attach it to the geometric field + fibreField = iron.Field() + fibreField.CreateStart(fibreFieldUserNumber,region) + fibreField.TypeSet(iron.FieldTypes.FIBRE) + fibreField.MeshDecompositionSet(decomposition) + fibreField.GeometricFieldSet(geometricField) + fibreField.VariableLabelSet(iron.FieldVariableTypes.U,"Fibre") + if InterpolationType == 4: + fibreField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN + fibreField.CreateFinish() + + iron.Field.ComponentValuesInitialiseDP(fibreField, iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, + 1, fibreAngle) + iron.Field.ComponentValuesInitialiseDP(fibreField, iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, + 2, 0.0) + iron.Field.ComponentValuesInitialiseDP(fibreField, iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, + 3, sheetAngle) + + # # Create the material field + # materialField = iron.Field() + # materialField.CreateStart(materialFieldUserNumber,region) + # materialField.TypeSet(iron.FieldTypes.MATERIAL) + # materialField.MeshDecompositionSet(decomposition) + # materialField.GeometricFieldSet(geometricField) + # materialField.NumberOfVariablesSet(1) + # materialField.NumberOfComponentsSet(iron.FieldVariableTypes.U,len(constitutiveParameters)) + # materialField.VariableLabelSet(iron.FieldVariableTypes.U,"Material") + # materialField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,1,1) + # materialField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,2,1) + # if InterpolationType == 4: + # materialField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN + # materialField.CreateFinish() + + # Set constant material parameters: + # for (component, value) in enumerate(constitutiveParameters, 1): + # materialField.ComponentValuesInitialise( + # iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, + # component, value) + + # Create the dependent field + dependentField = iron.Field() + dependentField.CreateStart(dependentFieldUserNumber,region) + dependentField.VariableLabelSet(iron.FieldVariableTypes.U,"Dependent") + dependentField.TypeSet(iron.FieldTypes.GEOMETRIC_GENERAL) + dependentField.MeshDecompositionSet(decomposition) + dependentField.GeometricFieldSet(geometricField) + dependentField.DependentTypeSet(iron.FieldDependentTypes.DEPENDENT) + dependentField.NumberOfVariablesSet(4) + dependentField.VariableTypesSet([iron.FieldVariableTypes.U,iron.FieldVariableTypes.DELUDELN,iron.FieldVariableTypes.U1,iron.FieldVariableTypes.U2]) + dependentField.NumberOfComponentsSet(iron.FieldVariableTypes.U,4) + dependentField.NumberOfComponentsSet(iron.FieldVariableTypes.DELUDELN,4) + dependentField.NumberOfComponentsSet(iron.FieldVariableTypes.U1,6) + dependentField.NumberOfComponentsSet(iron.FieldVariableTypes.U2,6) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,1,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,2,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,3,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.DELUDELN,1,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.DELUDELN,2,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.DELUDELN,3,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1,1,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1,2,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1,3,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1,4,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1,5,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1,6,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2,1,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2,2,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2,3,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2,4,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2,5,1) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2,6,1) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U,4,iron.FieldInterpolationTypes.ELEMENT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.DELUDELN,4,iron.FieldInterpolationTypes.ELEMENT_BASED) + if(UsePressureBasis): + # Set the pressure to be nodally based and use the second mesh component + if InterpolationType == 4: + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U,4,iron.FieldInterpolationTypes.NODE_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.DELUDELN,4,iron.FieldInterpolationTypes.NODE_BASED) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,4,2) + dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.DELUDELN,4,2) + if InterpolationType == 4: + dependentField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN + + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U1,1,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U1,2,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U1,3,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U1,4,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U1,5,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U1,6,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U2,1,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U2,2,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U2,3,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U2,4,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U2,5,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + dependentField.ComponentInterpolationSet(iron.FieldVariableTypes.U2,6,iron.FieldInterpolationTypes.GAUSS_POINT_BASED) + + dependentField.VariableLabelSet(iron.FieldVariableTypes.U1,"strain") + dependentField.VariableLabelSet(iron.FieldVariableTypes.U2,"stress") + + dependentField.CreateFinish() + + # Initialise dependent field from undeformed geometry and displacement bcs and set hydrostatic pressure + iron.Field.ParametersToFieldParametersComponentCopy( + geometricField,iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1, + dependentField,iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,1) + iron.Field.ParametersToFieldParametersComponentCopy( + geometricField,iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,2, + dependentField,iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,2) + iron.Field.ParametersToFieldParametersComponentCopy( + geometricField,iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,3, + dependentField,iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,3) + iron.Field.ComponentValuesInitialiseDP( + dependentField,iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES,4,-8.0) + + # Create a deformed geometry field, as cmgui doesn't like displaying + # deformed fibres from the dependent field because it isn't a geometric field. + deformedField = iron.Field() + deformedField.CreateStart(deformedFieldUserNumber, region) + deformedField.MeshDecompositionSet(decomposition) + deformedField.TypeSet(iron.FieldTypes.GEOMETRIC) + deformedField.VariableLabelSet(iron.FieldVariableTypes.U, "DeformedGeometry") + for component in [1, 2, 3]: + deformedField.ComponentMeshComponentSet( + iron.FieldVariableTypes.U, component, 1) + if InterpolationType == 4: + deformedField.ScalingTypeSet(iron.FieldScalingTypes.ARITHMETIC_MEAN) + deformedField.CreateFinish() + + # Create the equations_set + equationsSetField = iron.Field() + equationsSet = iron.EquationsSet() + equationsSetSpecification = [iron.EquationsSetClasses.ELASTICITY, + iron.EquationsSetTypes.FINITE_ELASTICITY, + constitutiveRelation] + equationsSet.CreateStart(equationsSetUserNumber,region,fibreField, + equationsSetSpecification, equationsSetFieldUserNumber, equationsSetField) + equationsSet.CreateFinish() + + # Create the CellML environment + CellML = iron.CellML() + CellML.CreateStart(CellMLUserNumber, region) + + # here we get the current path of this script so that we can specify the CellML model document relative to + # this script, rather than the execution folder. + from os.path import dirname, join + script_path = dirname(__file__) + cellmlFile = join(script_path, "guccione.cellml") + # guccioneCellMLParameters = [0.88, 0.0, 18.5, 3.58, 3.26] # default values in CellML model + guccioneCellMLParameters = [1.0, 0.0, 5.0, 10.0, 5.0] + guccioneCellMLParameters = [materialParameters[0], 0.0, materialParameters[1], materialParameters[2], materialParameters[3]] + # the names of the variables in the CellML model for the parameters in the same order as the values above + guccioneCellMLParameterIds = ["interface/c1", "interface/c2", "interface/c3", "interface/c4", "interface/c5"] + # Import a Guccione material law from a file + GuccioneModel = CellML.ModelImport(cellmlFile) + # Now we have imported the model we are able to specify which variables from the model we want to set from openCMISS + CellML.VariableSetAsKnown(GuccioneModel, "equations/E11") + CellML.VariableSetAsKnown(GuccioneModel, "equations/E12") + CellML.VariableSetAsKnown(GuccioneModel, "equations/E13") + CellML.VariableSetAsKnown(GuccioneModel, "equations/E22") + CellML.VariableSetAsKnown(GuccioneModel, "equations/E23") + CellML.VariableSetAsKnown(GuccioneModel, "equations/E33") + for component, parameter in enumerate(guccioneCellMLParameterIds): + CellML.VariableSetAsKnown(GuccioneModel, parameter) + # and variables to get from the CellML + CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev11") + CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev12") + CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev13") + CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev22") + CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev23") + CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev33") + + CellML.CreateFinish() + + # Start the creation of CellML <--> OpenCMISS field maps + CellML.FieldMapsCreateStart() + #Now we can set up the field variable component <--> CellML model variable mappings. + #Map the strain components + CellML.CreateFieldToCellMLMap(dependentField,iron.FieldVariableTypes.U1,1, + iron.FieldParameterSetTypes.VALUES,GuccioneModel,"equations/E11", + iron.FieldParameterSetTypes.VALUES) + CellML.CreateFieldToCellMLMap(dependentField,iron.FieldVariableTypes.U1,2, iron.FieldParameterSetTypes.VALUES,GuccioneModel,"equations/E12", iron.FieldParameterSetTypes.VALUES) + CellML.CreateFieldToCellMLMap(dependentField,iron.FieldVariableTypes.U1,3, iron.FieldParameterSetTypes.VALUES,GuccioneModel,"equations/E13", iron.FieldParameterSetTypes.VALUES) + CellML.CreateFieldToCellMLMap(dependentField,iron.FieldVariableTypes.U1,4, iron.FieldParameterSetTypes.VALUES,GuccioneModel,"equations/E22", iron.FieldParameterSetTypes.VALUES) + CellML.CreateFieldToCellMLMap(dependentField,iron.FieldVariableTypes.U1,5, iron.FieldParameterSetTypes.VALUES,GuccioneModel,"equations/E23", iron.FieldParameterSetTypes.VALUES) + CellML.CreateFieldToCellMLMap(dependentField,iron.FieldVariableTypes.U1,6, iron.FieldParameterSetTypes.VALUES,GuccioneModel,"equations/E33", iron.FieldParameterSetTypes.VALUES) + #DOC-END map strain components + + #DOC-START map stress components + #Map the stress components + CellML.CreateCellMLToFieldMap(GuccioneModel,"equations/Tdev11", iron.FieldParameterSetTypes.VALUES,dependentField,iron.FieldVariableTypes.U2,1,iron.FieldParameterSetTypes.VALUES) + CellML.CreateCellMLToFieldMap(GuccioneModel,"equations/Tdev12", iron.FieldParameterSetTypes.VALUES,dependentField,iron.FieldVariableTypes.U2,2,iron.FieldParameterSetTypes.VALUES) + CellML.CreateCellMLToFieldMap(GuccioneModel,"equations/Tdev13", iron.FieldParameterSetTypes.VALUES,dependentField,iron.FieldVariableTypes.U2,3,iron.FieldParameterSetTypes.VALUES) + CellML.CreateCellMLToFieldMap(GuccioneModel,"equations/Tdev22", iron.FieldParameterSetTypes.VALUES,dependentField,iron.FieldVariableTypes.U2,4,iron.FieldParameterSetTypes.VALUES) + CellML.CreateCellMLToFieldMap(GuccioneModel,"equations/Tdev23", iron.FieldParameterSetTypes.VALUES,dependentField,iron.FieldVariableTypes.U2,5,iron.FieldParameterSetTypes.VALUES) + CellML.CreateCellMLToFieldMap(GuccioneModel,"equations/Tdev33", iron.FieldParameterSetTypes.VALUES,dependentField,iron.FieldVariableTypes.U2,6,iron.FieldParameterSetTypes.VALUES) + + #Finish the creation of CellML <--> OpenCMISS field maps + CellML.FieldMapsCreateFinish() + + #Create the CellML models field + CellMLModelsField = iron.Field() + CellML.ModelsFieldCreateStart(CellMLModelsFieldUserNumber,CellMLModelsField) + CellML.ModelsFieldCreateFinish() + + xidiv = 1.0/(NumberOfGaussXi+1) + for elem in [1]: + #Gauss point number counter + ctr = 0 + #Assign model for each quadraturePoint: + for xi in range(0,NumberOfGaussXi): + xi1 = (1.0+xi)*xidiv + for xj in range(0,NumberOfGaussXi): + xi2 = (1.0+xj)*xidiv + for xk in range(0,NumberOfGaussXi): + xi3 = (1.0+xk)*xidiv + ctr = ctr + 1 + CellMLModelsField.ParameterSetUpdateGaussPoint(iron.FieldVariableTypes.U, + iron.FieldParameterSetTypes.VALUES, + ctr, + 1, + 1, + GuccioneModel) + #Create the CellML parameters field --- the strain field + CellMLParametersField = iron.Field() + CellML.ParametersFieldCreateStart(CellMLParametersFieldUserNumber,CellMLParametersField) + CellML.ParametersFieldCreateFinish() + + # Create the CellML intermediate field --- the stress field + CellMLIntermediateField = iron.Field() + CellML.IntermediateFieldCreateStart(CellMLIntermediateFieldUserNumber,CellMLIntermediateField) + CellML.IntermediateFieldCreateFinish() + + for valueIndex, parameter in enumerate(guccioneCellMLParameterIds, 0): + component = CellML.FieldComponentGet(GuccioneModel, iron.CellMLFieldTypes.PARAMETERS, parameter) + print("Setting parameter: " + parameter + "; to value: " + str(guccioneCellMLParameters[valueIndex]) + "; field component: " + str(component)) + iron.Field.ComponentValuesInitialiseDP(CellMLParametersField, iron.FieldVariableTypes.U, + iron.FieldParameterSetTypes.VALUES, component, guccioneCellMLParameters[valueIndex]) + + + #equationsSet.MaterialsCreateStart(materialFieldUserNumber,materialField) + #equationsSet.MaterialsCreateFinish() + + equationsSet.DependentCreateStart(dependentFieldUserNumber,dependentField) + equationsSet.DependentCreateFinish() + + # Create equations + equations = iron.Equations() + equationsSet.EquationsCreateStart(equations) + equations.sparsityType = iron.EquationsSparsityTypes.SPARSE + equations.outputType = iron.EquationsOutputTypes.NONE + equationsSet.EquationsCreateFinish() + + def defineProblemSolver(): + # Define the problem + problem = iron.Problem() + problemSpecification = [iron.ProblemClasses.ELASTICITY, + iron.ProblemTypes.FINITE_ELASTICITY, + iron.ProblemSubtypes.FINITE_ELASTICITY_CELLML] + problem.CreateStart(problemUserNumber, problemSpecification) + problem.CreateFinish() + + # Create control loops + problem.ControlLoopCreateStart() + problem.ControlLoopCreateFinish() + + # Create problem solver + nonLinearSolver = iron.Solver() + linearSolver = iron.Solver() + problem.SolversCreateStart() + problem.SolverGet([iron.ControlLoopIdentifiers.NODE],1,nonLinearSolver) + nonLinearSolver.outputType = iron.SolverOutputTypes.PROGRESS + nonLinearSolver.NewtonJacobianCalculationTypeSet(iron.JacobianCalculationTypes.FD) + nonLinearSolver.NewtonLinearSolverGet(linearSolver) + linearSolver.linearType = iron.LinearSolverTypes.DIRECT + #linearSolver.libraryType = iron.SolverLibraries.LAPACK + problem.SolversCreateFinish() + + #Create the problem solver CellML equations + CellMLSolver = iron.Solver() + problem.CellMLEquationsCreateStart() + nonLinearSolver.NewtonCellMLSolverGet(CellMLSolver) + CellMLEquations = iron.CellMLEquations() + CellMLSolver.CellMLEquationsGet(CellMLEquations) + CellMLEquations.CellMLAdd(CellML) + problem.CellMLEquationsCreateFinish() + + # Create solver equations and add equations set to solver equations + solver = iron.Solver() + solverEquations = iron.SolverEquations() + problem.SolverEquationsCreateStart() + problem.SolverGet([iron.ControlLoopIdentifiers.NODE],1,solver) + solver.SolverEquationsGet(solverEquations) + solverEquations.sparsityType = iron.SolverEquationsSparsityTypes.SPARSE + equationsSetIndex = solverEquations.EquationsSetAdd(equationsSet) + problem.SolverEquationsCreateFinish() + + return [problem, solverEquations] + + def defineBoundaryConditions(solverEquations, increment): + # Prescribe boundary conditions (absolute nodal parameters) + boundaryConditions = iron.BoundaryConditions() + solverEquations.BoundaryConditionsCreateStart(boundaryConditions) + + #Set x=0 nodes to no x displacment in x. Set x=width nodes to 10% x displacement + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,1,1,iron.BoundaryConditionsTypes.FIXED,0.0) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,3,1,iron.BoundaryConditionsTypes.FIXED,0.0) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,5,1,iron.BoundaryConditionsTypes.FIXED,0.0) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,7,1,iron.BoundaryConditionsTypes.FIXED,0.0) + + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,2,1,iron.BoundaryConditionsTypes.FIXED,increment) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,4,1,iron.BoundaryConditionsTypes.FIXED,increment) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,6,1,iron.BoundaryConditionsTypes.FIXED,increment) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,8,1,iron.BoundaryConditionsTypes.FIXED,increment) + + # Set y=0 nodes to no y displacement + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,1,2,iron.BoundaryConditionsTypes.FIXED,0.0) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,2,2,iron.BoundaryConditionsTypes.FIXED,0.0) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,5,2,iron.BoundaryConditionsTypes.FIXED,0.0) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,6,2,iron.BoundaryConditionsTypes.FIXED,0.0) + + # Set z=0 nodes to no y displacement + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,1,3,iron.BoundaryConditionsTypes.FIXED,0.0) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,2,3,iron.BoundaryConditionsTypes.FIXED,0.0) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,3,3,iron.BoundaryConditionsTypes.FIXED,0.0) + boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,4,3,iron.BoundaryConditionsTypes.FIXED,0.0) + + solverEquations.BoundaryConditionsCreateFinish() + + # loop over load steps + + numberOfLoadSteps = 70 + displacementIncrement = 0.01 # 1% + displacementIncrementDimension = displacementIncrement*width # length units + resultRecord = {} + resultRecord["strain"] = [0.0] + resultRecord["stress"] = [0.0] + for counter in range(1, numberOfLoadSteps+1): + # define the problem, solver, control loops, etc. + [problem, solverEquations] = defineProblemSolver() + # define the boundary conditions + defineBoundaryConditions(solverEquations, displacementIncrementDimension) + # execute the experiment + problem.Solve() + # clean up + problem.Finalise() + solverEquations.Finalise() + + # export the results + filename = "results-{:03d}".format(counter) + + # Copy deformed geometry into deformed field + for component in [1, 2, 3]: + dependentField.ParametersToFieldParametersComponentCopy( + iron.FieldVariableTypes.U, + iron.FieldParameterSetTypes.VALUES, component, + deformedField, iron.FieldVariableTypes.U, + iron.FieldParameterSetTypes.VALUES, component) + + # Export results + fields = iron.Fields() + fields.CreateRegion(region) + fields.NodesExport(filename, "FORTRAN") + fields.ElementsExport(filename, "FORTRAN") + fields.Finalise() + + versionNumber = 1 + derivativeNumber = 1 + nodeNumber = 8 + componentNumber = 1 # x-dirn + reactionForceX = dependentField.ParameterSetGetNode(iron.FieldVariableTypes.DELUDELN, iron.FieldParameterSetTypes.VALUES, + versionNumber, derivativeNumber, nodeNumber, componentNumber) + print("Reaction force (x) at counter: " + str(counter) + ": " + str(reactionForceX)) + resultRecord["strain"].append(counter * displacementIncrement) + resultRecord["stress"].append(reactionForceX) + + coordinateSystem.Destroy() + region.Destroy() + basis.Destroy() + + return resultRecord \ No newline at end of file diff --git a/FiniteElasticity/GuccioneCube/view-unit-cube.com b/FiniteElasticity/GuccioneCube/view-unit-cube.com new file mode 100644 index 00000000..71a0e737 --- /dev/null +++ b/FiniteElasticity/GuccioneCube/view-unit-cube.com @@ -0,0 +1,41 @@ +if (defined $fibres) { + my $fn = "unit-cube.part0.exnode"; + my $i = 0; + foreach my $f ("524", "525", "526", "527") { + my $time = $i++; + print "time = $time; f = $f/$fn\n"; + gfx read node "$f/$fn" time $time; + } + gfx read elem "524/unit-cube.part0.exelem"; +} else { + gfx read node "unit-cube.part0.exnode"; + gfx read elem "unit-cube.part0.exelem"; +} + +gfx define faces; + +$f = "del U_del n"; +gfx define field reactions composite "$f.1" "$f.2" "$f.3"; + +gfx define tessellation eps minimum_divisions "1*2" refinement_factors "1" circle_divisions 12; + +gfx modify g_element "/" general clear; +gfx modify g_element "/" points domain_nodes coordinate Geometry tessellation default_points LOCAL glyph sphere size "0.01*0.01*0.01" offset 0,0,0 font default select_on material default selected_material default_selected render_shaded; +gfx modify g_element "/" points domain_nodes coordinate DeformedGeometry tessellation default_points LOCAL glyph sphere size "0.01*0.01*0.01" offset 0,0,0 font default select_on material gold selected_material default_selected render_shaded; +gfx modify g_element "/" lines domain_mesh1d coordinate Geometry tessellation default LOCAL circle_extrusion line_base_size 0.01 select_on material default selected_material default_selected render_shaded; +gfx modify g_element "/" lines domain_mesh1d coordinate DeformedGeometry tessellation default LOCAL circle_extrusion line_base_size 0.01 select_on material gold selected_material default_selected render_shaded; +gfx modify g_element "/" points domain_nodes coordinate DeformedGeometry tessellation default_points LOCAL glyph axes_xyz size "0.2*0.2*0.2" offset 0,0,0 font default select_on material gold selected_material default_selected render_shaded; +gfx modify g_element "/" points domain_nodes coordinate DeformedGeometry tessellation default_points LOCAL glyph arrow_solid size "0.2*0.2*0.2" offset 0,0,0 font default orientation reactions scale_factors "0*0*0" select_on material red selected_material default_selected render_shaded; +gfx modify g_element "/" points domain_mesh_highest_dimension coordinate DeformedGeometry tessellation eps LOCAL glyph cylinder_solid size "0.5*0.02*0.02" offset -0.3,0,0 font default orientation Fibre scale_factors "0*0*0" cell_centres select_on material default selected_material default_selected render_shaded; +gfx modify g_element "/" points domain_mesh_highest_dimension coordinate DeformedGeometry tessellation eps LOCAL glyph sheet size "0.5*0.2*0.2" offset -0.3,0,0 font default orientation Fibre scale_factors "0*0*0" cell_centres select_on material blue selected_material default_selected render_shaded; + + +gfx create window 1 double_buffer; +gfx modify window 1 image scene "/" filter default infinite_viewer_lighting two_sided_lighting; +gfx modify window 1 image add_light default; +gfx modify window 1 image add_light default_ambient; +gfx modify window 1 layout simple ortho_axes z -y eye_spacing 0.25 width 1408 height 898; +gfx modify window 1 set current_pane 1; +gfx modify window 1 background colour 0 0 0 texture none; +gfx modify window 1 view perspective eye_point 1.60026 -2.92777 0.628807 interest_point 0.5 0.5 0.5 up_vector -0.00543241 0.0358092 0.999344 view_angle 40 near_clipping_plane 0.245779 far_clipping_plane 7.23963 relative_viewport ndc_placement -1 1 2 2 viewport_coordinates 0 0 1 1; +gfx modify window 1 set transform_tool current_pane 1 std_view_angle 40 normal_lines no_antialias depth_of_field 0.0 fast_transparency blend_normal; From 7636f1876c443cf1f014408700511afc1ac75df8 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Tue, 1 Nov 2016 14:22:08 +1300 Subject: [PATCH 27/28] modified FiniteElasticity example to use multiple elements --- .../Monodomain/Fortran/src/FortranExample.f90 | 19 +- .../Monodomain/Python/Monodomain2DSquare.py | 4 +- .../Python/LargeUniAxialExtensionExample.py | 69 +- .../NavierStokes/LidDrivenCavity/LidDriven.py | 7 +- .../LidDrivenCavity.part0.exnode | 8426 ---------------- .../LidDrivenCavity.part0.exnode | 8871 ----------------- .../Makefile | 88 - 7 files changed, 59 insertions(+), 17425 deletions(-) delete mode 100644 FluidMechanics/NavierStokes/LidDrivenCavity/output/Re1000Elem10x10_GFEM/expected_results/LidDrivenCavity.part0.exnode delete mode 100644 FluidMechanics/NavierStokes/LidDrivenCavity/output/Re1000Elem10x10_RBS/expected_results/LidDrivenCavity.part0.exnode delete mode 100755 MultiPhysics/MultiCompTransport/MultiCompAdvectionDiffusion/MonolithicSchemeAdvectionDiffusion_FieldML/Makefile diff --git a/Bioelectrics/Monodomain/Fortran/src/FortranExample.f90 b/Bioelectrics/Monodomain/Fortran/src/FortranExample.f90 index 7c454a61..edffe5ed 100644 --- a/Bioelectrics/Monodomain/Fortran/src/FortranExample.f90 +++ b/Bioelectrics/Monodomain/Fortran/src/FortranExample.f90 @@ -66,7 +66,6 @@ PROGRAM MONODOMAINEXAMPLE #include "mpif.h" #endif - !Test program parameters REAL(CMISSRP), PARAMETER :: HEIGHT=1.0_CMISSRP @@ -107,8 +106,11 @@ PROGRAM MONODOMAINEXAMPLE INTEGER(CMISSIntg) :: gNacomponent,stimcomponent,node_idx REAL(CMISSRP) :: X,Y,DISTANCE,gNa_VALUE - - INTEGER(CMISSIntg), PARAMETER :: NUMBER_OF_ELEMENTS=25 + + INTEGER(CMISSIntg) :: region_handle + +!mpch INTEGER(CMISSIntg), PARAMETER :: NUMBER_OF_ELEMENTS=100 + INTEGER(CMISSIntg) :: NUMBER_OF_ELEMENTS=25 INTEGER(CMISSIntg) :: OUTPUT_FREQUENCY = 1 REAL(CMISSRP), PARAMETER :: STIM_VALUE = 100.0_CMISSRP REAL(CMISSRP), PARAMETER :: STIM_STOP = 0.10_CMISSRP @@ -148,9 +150,9 @@ PROGRAM MONODOMAINEXAMPLE ! process command line arguments before getting started. NUMBER_OF_ARGUMENTS = COMMAND_ARGUMENT_COUNT() - IF(NUMBER_OF_ARGUMENTS >= 3) THEN +!Mpch IF(NUMBER_OF_ARGUMENTS >= 3) THEN + IF(NUMBER_OF_ARGUMENTS == 5) THEN CALL GET_COMMAND_ARGUMENT(1,COMMAND_ARGUMENT,ARGUMENT_LENGTH,STATUS) - !IF(STATUS>0) CALL HANDLE_ERROR("Error for command argument 1.") READ(COMMAND_ARGUMENT(1:ARGUMENT_LENGTH),*) PDE_TIME_STEP WRITE(*, '("PDE Step Size: ", E14.7)') PDE_TIME_STEP CALL GET_COMMAND_ARGUMENT(2,COMMAND_ARGUMENT,ARGUMENT_LENGTH,STATUS) @@ -160,7 +162,6 @@ PROGRAM MONODOMAINEXAMPLE READ(COMMAND_ARGUMENT(1:ARGUMENT_LENGTH),*) OUTPUT_FREQUENCY WRITE(*, '("Output Frequency: ", I10)') OUTPUT_FREQUENCY CALL GET_COMMAND_ARGUMENT(4,COMMAND_ARGUMENT,ARGUMENT_LENGTH,STATUS) - !IF(STATUS>0) CALL HANDLE_ERROR("Error for command argument 4.") CellmlFile = adjustl(COMMAND_ARGUMENT) WRITE(*, '("CellML File: ", A)') CellmlFile inquire(file=CellmlFile, exist=fileExist) @@ -168,10 +169,14 @@ PROGRAM MONODOMAINEXAMPLE write(*, '(">>ERROR: File does not exist")') stop endif + CALL GET_COMMAND_ARGUMENT(5,COMMAND_ARGUMENT,ARGUMENT_LENGTH,STATUS) + READ(COMMAND_ARGUMENT(1:ARGUMENT_LENGTH),*) NUMBER_OF_ELEMENTS + WRITE(*, '("Number of Elements: ", I5)') NUMBER_OF_ELEMENTS ELSE !If there are not enough arguments die horribly WRITE(*,*) " " - WRITE(*,'(">>USAGE: ",A)') "MonodomainExample " +!mpch WRITE(*,'(">>USAGE: ",A)') "MonodomainExample " + WRITE(*,'(">>USAGE: ",A)') "MonodomainExample <# of elements>" WRITE(*,*) " " STOP ENDIF diff --git a/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py b/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py index 2e3083b8..ba9099cd 100644 --- a/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py +++ b/Bioelectrics/Monodomain/Python/Monodomain2DSquare.py @@ -28,10 +28,10 @@ # Simulation parameters stimValue = 100.0 stimStop = 0.1 -timeStop = 1.5 +timeStop = 1.0 odeTimeStep = 0.00001 pdeTimeStep = 0.001 -outputFrequency = 1 +outputFrequency = 250 #DOC-END parameters #Setup field number handles diff --git a/FiniteElasticity/LargeUniAxialExtension/Python/LargeUniAxialExtensionExample.py b/FiniteElasticity/LargeUniAxialExtension/Python/LargeUniAxialExtensionExample.py index 802cf057..7bb76d7d 100755 --- a/FiniteElasticity/LargeUniAxialExtension/Python/LargeUniAxialExtensionExample.py +++ b/FiniteElasticity/LargeUniAxialExtension/Python/LargeUniAxialExtensionExample.py @@ -49,13 +49,7 @@ #< #> Main script -# Add Python bindings directory to PATH import sys, os -sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) -sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], - 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) - -# Intialise OpenCMISS-Iron from opencmiss.iron import iron # Set problem parameters @@ -85,9 +79,9 @@ #iron.DiagnosticsSetOn(iron.DiagnosticTypes.All,[1,2,3,4,5],"Diagnostics",["DOMAIN_MAPPINGS_LOCAL_FROM_GLOBAL_CALCULATE"]) numberOfLoadIncrements = 2 -numberGlobalXElements = 1 -numberGlobalYElements = 1 -numberGlobalZElements = 1 +numberGlobalXElements = 8 +numberGlobalYElements = 8 +numberGlobalZElements = 8 InterpolationType = 1 if(numberGlobalZElements==0): numberOfXi = 2 @@ -319,27 +313,52 @@ solverEquations.BoundaryConditionsCreateStart(boundaryConditions) #Set x=0 nodes to no x displacment in x. Set x=width nodes to 10% x displacement -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,1,1,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,3,1,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,5,1,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,7,1,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,1,1,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,3,1,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,5,1,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,7,1,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,2,1,iron.BoundaryConditionsTypes.FIXED,0.1*width) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,4,1,iron.BoundaryConditionsTypes.FIXED,0.1*width) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,6,1,iron.BoundaryConditionsTypes.FIXED,0.1*width) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,8,1,iron.BoundaryConditionsTypes.FIXED,0.1*width) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,2,1,iron.BoundaryConditionsTypes.FIXED,0.1*width) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,4,1,iron.BoundaryConditionsTypes.FIXED,0.1*width) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,6,1,iron.BoundaryConditionsTypes.FIXED,0.1*width) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,8,1,iron.BoundaryConditionsTypes.FIXED,0.1*width) # Set y=0 nodes to no y displacement -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,1,2,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,2,2,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,5,2,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,6,2,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,1,2,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,2,2,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,5,2,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,6,2,iron.BoundaryConditionsTypes.FIXED,0.0) # Set z=0 nodes to no y displacement -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,1,3,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,2,3,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,3,3,iron.BoundaryConditionsTypes.FIXED,0.0) -boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,4,3,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,1,3,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,2,3,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,3,3,iron.BoundaryConditionsTypes.FIXED,0.0) +#boundaryConditions.AddNode(dependentField,iron.FieldVariableTypes.U,1,1,4,3,iron.BoundaryConditionsTypes.FIXED,0.0) + +nodes = iron.Nodes() +region.NodesGet(nodes) +eps = 1.0e-12 +version = 1 +derivative = 1 +#constrainedNodes = set() +for node in range(1, nodes.NumberOfNodesGet() + 1): + position = [geometricField.ParameterSetGetNode( + iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, + 1, 1, node, component) + for component in range(1, 4)] + # Fix x=0, y=0, and z=0 faces + for idx, component in enumerate(range(1,4)): + if abs(position[idx]) < eps: + boundaryConditions.AddNode( + dependentField, iron.FieldVariableTypes.U, + version, derivative, node, component, + iron.BoundaryConditionsTypes.FIXED, 0.0) + # Set x=width nodes to 10% x displacement + if abs(position[0]-width) < eps: + boundaryConditions.AddNode( + dependentField, iron.FieldVariableTypes.U, + version, derivative, node, 1, + iron.BoundaryConditionsTypes.FIXED, 0.1*width) solverEquations.BoundaryConditionsCreateFinish() diff --git a/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py b/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py index 1323ccf1..dbf74c05 100644 --- a/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py +++ b/FluidMechanics/NavierStokes/LidDrivenCavity/LidDriven.py @@ -49,11 +49,6 @@ # Add Python bindings directory to PATH import sys, os - -sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], 'python')) ) -sys.path.append( os.sep.join((os.environ['OPENCMISS_INSTALL_DIR'], - 'x86_64_linux/gnu-C5.4-gnu-F5.4/mpich2_release/release/python/RELEASE')) ) - import math import time @@ -376,7 +371,7 @@ def LidDriven(numberOfElements,cavityDimensions,lidVelocity,viscosity,density, #========================================================== dimensions = [1.0,1.0] -elementResolutions = [10] +elementResolutions = [23] ReynoldsNumbers = [1000] lidVelocity = [1.0,0.0] density = 1.0 diff --git a/FluidMechanics/NavierStokes/LidDrivenCavity/output/Re1000Elem10x10_GFEM/expected_results/LidDrivenCavity.part0.exnode b/FluidMechanics/NavierStokes/LidDrivenCavity/output/Re1000Elem10x10_GFEM/expected_results/LidDrivenCavity.part0.exnode deleted file mode 100644 index 1db6a78f..00000000 --- a/FluidMechanics/NavierStokes/LidDrivenCavity/output/Re1000Elem10x10_GFEM/expected_results/LidDrivenCavity.part0.exnode +++ /dev/null @@ -1,8426 +0,0 @@ - Group name: Cavity - #Fields=4 - 1) Coordinate, coordinate, rectangular cartesian, #Components=2 - x. 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You may obtain a copy of the License at -# http://www.mozilla.org/MPL/ -# -# Software distributed under the License is distributed on an "AS IS" -# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the -# License for the specific language governing rights and limitations -# under the License. -# -# The Original Code is OpenCMISS -# -# The Initial Developer of the Original Code is University of Auckland, -# Auckland, New Zealand and University of Oxford, Oxford, United -# Kingdom. Portions created by the University of Auckland and University -# of Oxford are Copyright (C) 2007 by the University of Auckland and -# the University of Oxford. All Rights Reserved. -# -# Contributor(s): -# -# Alternatively, the contents of this file may be used under the terms of -# either the GNU General Public License Version 2 or later (the "GPL"), or -# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), -# in which case the provisions of the GPL or the LGPL are applicable instead -# of those above. If you wish to allow use of your version of this file only -# under the terms of either the GPL or the LGPL, and not to allow others to -# use your version of this file under the terms of the MPL, indicate your -# decision by deleting the provisions above and replace them with the notice -# and other provisions required by the GPL or the LGPL. If you do not delete -# the provisions above, a recipient may use your version of this file under -# the terms of any one of the MPL, the GPL or the LGPL. -# -#---------------------------------------------------------------------------------------------------------------------------------- - -MAKEFLAGS = --no-builtin-rules --warn-undefined-variables - -#---------------------------------------------------------------------------------------------------------------------------------- - -ifndef OPENCMISS_ROOT - OPENCMISS_ROOT := ../../../../.. - GLOBAL_ROOT := $(CURDIR)/../../../../.. -else - GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm -endif - -#---------------------------------------------------------------------------------------------------------------------------------- -USEFIELDML = true - -EXAMPLE_PATH=MultiPhysics/MultiCompTransport/MultiCompAdvectionDiffusion/ - -EXAMPLE_NAME = MonolithicSchemeAdvectionDiffusion_FieldML - -include $(GLOBAL_ROOT)/ExampleMakefile - -# let's assume fluid_mechanics_IO_routines has been built in main_object, copy them over -# redefine preliminaries -preliminaries: $(OBJECT_DIR) $(EXE_DIR) - cp $(MAIN_OBJECT_DIR)/fluid_mechanics_IO_routines.o $(OBJECT_DIR) - cp $(MAIN_OBJECT_DIR)/fluid_mechanics_io_routines.mod $(OBJECT_DIR) - -info: - @echo "OBJECTS:" - @echo $(OBJECTS) - @echo "OBJECT_DIR:" - @echo $(OBJECT_DIR) - @echo "MAIN_OBJECT_DIR:" - @echo $(MAIN_OBJECT_DIR) - @echo "EXAMPLE_SOURCE_DIR:" - @echo $(EXAMPLE_SOURCE_DIR) - @echo "MAIN_SOURCE_DIR:" - @echo $(MAIN_SOURCE_DIR) From 5337f7d3cfef1b6a11aa860f7cb9cf2b6006aa33 Mon Sep 17 00:00:00 2001 From: Mark Cheeseman Date: Wed, 2 Nov 2016 15:06:19 +1300 Subject: [PATCH 28/28] added updated example SLURM job submission file --- scripts/jobscript.sl | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 scripts/jobscript.sl diff --git a/scripts/jobscript.sl b/scripts/jobscript.sl new file mode 100644 index 00000000..445f90b6 --- /dev/null +++ b/scripts/jobscript.sl @@ -0,0 +1,12 @@ +#!/bin/bash +#SBATCH -J Monodomain +#SBATCH -A uoa00379 +#SBATCH -C avx +#SBATCH --time=00:30:00 +#SBATCH --ntasks=32 +#SBATCH --mem-per-cpu=1024 +#SBATCH --workdir=/projects/uoa00379/OpenCMISS-mpch/examples/Bioelectrics/build/Monodomain + +module load intel/2015.02 + +time srun ./monodomain.x 0.001 1 250 n98.xml 125