Merge pull request #26 from ulgltas/lacroix

Py3 and PFEM3D Support

Author: rboman

.gitignore

@@ -18,3 +18,7 @@ ccupydo/*.so
 ccupydo/CCupydo*
 
 .vscode/
+
+run.bat
+compile.bat
+compile.sh

CMake/FindMpi4Py.cmake

@@ -38,7 +38,7 @@ IF(NOT PYTHON_EXECUTABLE)
 
 ELSE(NOT PYTHON_EXECUTABLE)
     EXECUTE_PROCESS(
-        COMMAND ${PYTHON_EXECUTABLE} -c "import distutils.sysconfig as cg; print cg.get_python_lib(1,0)"
+        COMMAND ${PYTHON_EXECUTABLE} -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0))"
         OUTPUT_VARIABLE PYTHON_SITEDIR
         OUTPUT_STRIP_TRAILING_WHITESPACE
     )
@@ -54,8 +54,14 @@ ELSE(NOT PYTHON_EXECUTABLE)
     FIND_PACKAGE_HANDLE_STANDARD_ARGS(Mpi4Py DEFAULT_MSG MPI4PY_INCLUDE_DIR  )
 
     IF(MPI4PY_FOUND)  
+        EXECUTE_PROCESS( # Find name of MPI .so
+            COMMAND ${PYTHON_EXECUTABLE} -c "from mpi4py import MPI; from sys import stdout; from os import path; stdout.write(path.basename(MPI.__file__))"
+            OUTPUT_VARIABLE MPI4PY_LIB_NAME
+            RESULT_VARIABLE MPI4PY_NOT_FOUND
+            OUTPUT_STRIP_TRAILING_WHITESPACE
+        )
         EXECUTE_PROCESS(  
-            COMMAND ${PYTHON_EXECUTABLE} -c "import mpi4py; print mpi4py.__version__"
+            COMMAND ${PYTHON_EXECUTABLE} -c "import mpi4py; print(mpi4py.__version__)"
             OUTPUT_VARIABLE MPI4PY_VERSION  
             RESULT_VARIABLE  MPI4PY_NOT_FOUND  
             OUTPUT_STRIP_TRAILING_WHITESPACE  
@@ -71,7 +77,7 @@ ELSE(NOT PYTHON_EXECUTABLE)
         IF(NOT MPI4PY_SWIG_FILE)  
             MESSAGE(STATUS "mpi4py.i not found !")  
         ENDIF(NOT MPI4PY_SWIG_FILE)  
-        FIND_FILE(MPI4PY_LIBRARIES MPI.so HINTS ${MPI4PY_INCLUDE_DIR}/.. ${PYTHON_SITEDIR}/mpi4py)
+        FIND_FILE(MPI4PY_LIBRARIES NAMES ${MPI4PY_LIB_NAME} HINTS ${MPI4PY_INCLUDE_DIR}/.. ${PYTHON_SITEDIR}/mpi4py)
     ELSE(MPI4PY_FOUND)  
         IF(MPI4PY_FIND_REQUIRED)  
             MESSAGE(FATAL_ERROR "mpi4py not found !")  

CMake/FindNUMPY.cmake

@@ -46,7 +46,7 @@ ELSE(NOT PYTHON_EXECUTABLE)
 
     IF(NUMPY_FOUND)
         EXECUTE_PROCESS(
-            COMMAND ${PYTHON_EXECUTABLE} -c "import numpy; print numpy.__version__"
+            COMMAND ${PYTHON_EXECUTABLE} -c "import numpy; print(numpy.__version__)"
             OUTPUT_VARIABLE NUMPY_VERSION
             RESULT_VARIABLE  NUMPY_NOT_FOUND
             OUTPUT_STRIP_TRAILING_WHITESPACE

CMake/FindPETSc4Py.cmake

@@ -38,7 +38,7 @@ IF(NOT PYTHON_EXECUTABLE)
 
 ELSE(NOT PYTHON_EXECUTABLE)
     EXECUTE_PROCESS(
-        COMMAND ${PYTHON_EXECUTABLE} -c "import distutils.sysconfig as cg; print cg.get_python_lib(1,0)"
+        COMMAND ${PYTHON_EXECUTABLE} -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0))"
         OUTPUT_VARIABLE PYTHON_SITEDIR
         OUTPUT_STRIP_TRAILING_WHITESPACE
     )
@@ -54,8 +54,14 @@ ELSE(NOT PYTHON_EXECUTABLE)
     FIND_PACKAGE_HANDLE_STANDARD_ARGS(PETSc4Py DEFAULT_MSG PETSC4PY_INCLUDE_DIR)
 
     IF(PETSC4PY_FOUND)
+        EXECUTE_PROCESS( # Find name of PETSc .so
+            COMMAND ${PYTHON_EXECUTABLE} -c "from petsc4py import PETSc; from sys import stdout; from os import path; stdout.write(path.basename(PETSc.__file__))"
+            OUTPUT_VARIABLE PETSC4PY_LIB_NAME
+            RESULT_VARIABLE PETSC4PY_NOT_FOUND
+            OUTPUT_STRIP_TRAILING_WHITESPACE
+        )
         EXECUTE_PROCESS(
-            COMMAND ${PYTHON_EXECUTABLE} -c "import petsc4py; print petsc4py.__version__"
+            COMMAND ${PYTHON_EXECUTABLE} -c "import petsc4py; print(petsc4py.__version__)"
             OUTPUT_VARIABLE PETSC4PY_VERSION
             RESULT_VARIABLE PETSC4PY_NOT_FOUND
             OUTPUT_STRIP_TRAILING_WHITESPACE
@@ -71,7 +77,7 @@ ELSE(NOT PYTHON_EXECUTABLE)
         IF(NOT PETSC4PY_SWIG_FILE)
             MESSAGE(STATUS "petsc4py.i not found !")
         ENDIF(NOT PETSC4PY_SWIG_FILE)
-        FIND_FILE(PETSC4PY_LIBRARIES PETSc.so HINTS ${PETSC4PY_INCLUDE_DIR}/../lib ${PETSC4PY_INCLUDE_DIR}/../lib/$ENV{PETSC_ARCH} ${PYTHON_SITEDIR}/petsc4py/lib ${PYTHON_SITEDIR}/petsc4py/lib/$ENV{PETSC_ARCH})
+        FIND_FILE(PETSC4PY_LIBRARIES NAMES ${PETSC4PY_LIB_NAME} HINTS ${PETSC4PY_INCLUDE_DIR}/../lib ${PETSC4PY_INCLUDE_DIR}/../lib/$ENV{PETSC_ARCH} ${PYTHON_SITEDIR}/petsc4py/lib ${PYTHON_SITEDIR}/petsc4py/lib/$ENV{PETSC_ARCH})
     ELSE(PETSC4PY_FOUND)
         IF(PETSC4PY_FIND_REQUIRED)
             MESSAGE(FATAL_ERROR "petsc4py headers missing")

CMake/cupyMacros.cmake

@@ -9,7 +9,7 @@ MACRO(MACRO_AddTest srcDir)
     #message(STATUS "tfiles=${tfiles}")
     foreach(tfile ${tfiles})
         set(spath ${srcDir}/${tfile})
-        if(NOT IS_DIRECTORY ${spath} AND ${spath} MATCHES ".+\\fsi.py$")
+        if((NOT IS_DIRECTORY ${spath}) AND (${spath} MATCHES ".+\\fsi.py$" OR ${spath} MATCHES ".+\\fsi_adj.py$"))
             string(REPLACE "${PROJECT_SOURCE_DIR}/" "" strip ${spath}) 
             message(STATUS "Adding test ${strip}")
             add_test(NAME ${strip} 

CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright 2018 University of Liège
+# Copyright 2021 University of Liège
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -14,85 +14,109 @@
 
 # Main CMake file.
 # Configure the compilation of the C++ core of CUPyDO and the Py wrapper.
-#
-# Authors : D. THOMAS.
 
 CMAKE_MINIMUM_REQUIRED(VERSION 3.1)
 PROJECT(CUPyDO)
 
-LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/CMake")
-
-# macros/fcts
-INCLUDE(cupyMacros)
+SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH "")
+SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH "")
+MARK_AS_ADVANCED(LIBRARY_OUTPUT_PATH EXECUTABLE_OUTPUT_PATH)
 
-# Type of build
-IF( NOT CMAKE_BUILD_TYPE )
-    SET( CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE )
+IF(NOT CMAKE_BUILD_TYPE)
+    SET( CMAKE_BUILD_TYPE "Release" CACHE STRING "" FORCE)
 ENDIF()
-MESSAGE(STATUS "Build type : ${CMAKE_BUILD_TYPE}")
+
+LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/CMake")
 
 # Options
 OPTION(WITH_MPI "Build for parallel run" OFF)
 
+# macros/fcts
+INCLUDE(cupyMacros)
+
 # -- C++11
-SET(CMAKE_CXX_STANDARD 11) # newer way to set C++11 (requires cmake>=3.1)
+SET(CMAKE_CXX_STANDARD 11)
 SET(CMAKE_CXX_STANDARD_REQUIRED ON)
 
-# Add warnings during compilation when build type is Debug
-IF(CMAKE_BUILD_TYPE MATCHES Debug)
-    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra")
+# Set specific compiler flags
+MESSAGE(STATUS "CMAKE_CXX_COMPILER_ID=${CMAKE_CXX_COMPILER_ID}")
+IF(CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_BUILD_TYPE MATCHES Debug)
+    # Add warnings during compilation when build type is Debug
+    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall - Wextra")
 ENDIF()
 
+# -- Search for Python
+IF (CMAKE_VERSION VERSION_LESS 3.12.0)
+    FIND_PACKAGE(PythonInterp 3.6 REQUIRED)
+    FIND_PACKAGE(PythonLibs 3.6 REQUIRED)
+ELSE()
+    find_package (Python3 COMPONENTS Interpreter Development)
+    # use Python3_ROOT_DIR if wrong python found (e.g. anaconda)
+    SET(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
+    SET(PYTHON_LIBRARIES ${Python3_LIBRARIES})
+    SET(PYTHON_INCLUDE_PATH ${Python3_INCLUDE_DIRS}) 
+    SET(PYTHONLIBS_VERSION_STRING ${Python3_VERSION})     
+ENDIF()
+MESSAGE(STATUS "PYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}")
+MESSAGE(STATUS "PYTHON_LIBRARIES:FILEPATH=${PYTHON_LIBRARIES}")
+MESSAGE(STATUS "PYTHON_INCLUDE_PATH:FILEPATH=${PYTHON_INCLUDE_PATH}")
+MESSAGE(STATUS "PYTHON_FRAMEWORK_INCLUDES=${PYTHON_FRAMEWORK_INCLUDES}")
+MESSAGE(STATUS "PYTHONLIBS_VERSION_STRING=${PYTHONLIBS_VERSION_STRING}")
+MESSAGE(STATUS "Python_FRAMEWORKS=${Python_FRAMEWORKS}")
+INCLUDE_DIRECTORIES( ${PYTHON_INCLUDE_PATH} )
+
+# numpy
+FIND_PACKAGE(NUMPY REQUIRED)
+INCLUDE_DIRECTORIES( ${NUMPY_INCLUDE_DIR} )
+
+# -- Search for SWIG
+FIND_PACKAGE(SWIG REQUIRED)
+IF(CMAKE_GENERATOR MATCHES "Visual Studio")
+    # SET(CMAKE_SWIG_OUTDIR "${EXECUTABLE_OUTPUT_PATH}/$(Configuration)/") # INSTALL does not work
+    SET(CMAKE_SWIG_OUTDIR "${EXECUTABLE_OUTPUT_PATH}")
+ELSE()
+    SET(CMAKE_SWIG_OUTDIR "${EXECUTABLE_OUTPUT_PATH}")
+ENDIF()
+MESSAGE(STATUS "CMAKE_SWIG_OUTDIR=${CMAKE_SWIG_OUTDIR}")
+
 # Build for parallel run using MPI (default is OFF)
 IF(WITH_MPI)
     FIND_PACKAGE(MPI REQUIRED)
-    IF(MPI_FOUND)
-        MESSAGE(STATUS "MPI_INCLUDE_PATH=${MPI_INCLUDE_PATH}")
-        MESSAGE(STATUS "MPI_LIBRARIES=${MPI_LIBRARIES}")
-        ADD_DEFINITIONS(-DHAVE_MPI)
-        FIND_PACKAGE(PETSc REQUIRED)
-    ENDIF(MPI_FOUND)
-ENDIF(WITH_MPI)
+    MESSAGE(STATUS "MPI_INCLUDE_PATH=${MPI_INCLUDE_PATH}")
+    MESSAGE(STATUS "MPI_LIBRARIES=${MPI_LIBRARIES}")
+    ADD_DEFINITIONS(-DHAVE_MPI)
+    MESSAGE(STATUS "MPI_INCLUDE_PATH=${MPI_INCLUDE_PATH}")
+    INCLUDE_DIRECTORIES( ${MPI_INCLUDE_PATH} )
+
+    FIND_PACKAGE(PETSc REQUIRED)
+    MESSAGE(STATUS "PETSC_INCLUDE_PATH=${PETSC_INCLUDE_PATH}")
+    INCLUDE_DIRECTORIES( ${PETSC_INCLUDE_PATH} )
 
-# Python/SWIG
-FIND_PACKAGE(PythonInterp 2.7 REQUIRED)
-FIND_PACKAGE(PythonLibs 2.7 REQUIRED)
-MESSAGE(STATUS "PYTHONINTERP_FOUND=${PYTHONINTERP_FOUND}")
-MESSAGE(STATUS "PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}")
-MESSAGE(STATUS "PYTHONLIBS_FOUND=${PYTHONLIBS_FOUND}")
-MESSAGE(STATUS "PYTHON_LIBRARIES=${PYTHON_LIBRARIES}")
-MESSAGE(STATUS "PYTHON_INCLUDE_PATH=${PYTHON_INCLUDE_PATH}")
-FIND_PACKAGE(NUMPY REQUIRED)
-FIND_PACKAGE(SWIG REQUIRED)
-SET(CMAKE_SWIG_OUTDIR "${EXECUTABLE_OUTPUT_PATH}")
-MESSAGE(STATUS "SWIG_EXECUTABLE=${SWIG_EXECUTABLE}")
-IF(WITH_MPI)
     FIND_PACKAGE(PETSc4Py REQUIRED)
+    MESSAGE(STATUS "PETSC4PY_INCLUDE_DIR=${PETSC4PY_INCLUDE_DIR}")
+    INCLUDE_DIRECTORIES( ${PETSC4PY_INCLUDE_DIR} )
+
     FIND_PACKAGE(Mpi4Py REQUIRED)
+    MESSAGE(STATUS "MPI4PY_INCLUDE_DIR=${MPI4PY_INCLUDE_DIR}")
+    INCLUDE_DIRECTORIES( ${MPI4PY_INCLUDE_DIR} )
 ENDIF(WITH_MPI)
 
-INCLUDE_DIRECTORIES( ${MPI_INCLUDE_PATH} ${PETSC_INCLUDE_PATH} )
-
 SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 #-------------------------------------------------------------
 INCLUDE(${SWIG_USE_FILE})
 
-INCLUDE_DIRECTORIES(  ${PROJECT_SOURCE_DIR}/src 
-                      ${PYTHON_INCLUDE_PATH} 
-                      ${NUMPY_INCLUDE_DIR} 
-                      ${PETSC4PY_INCLUDE_DIR} 
-                      ${MPI4PY_INCLUDE_DIR})
+INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/src )
 
 FILE(GLOB SRCS src/*.h src/*.cpp)
 
 FILE(GLOB ISRCS _src/*.i)
 
 IF(WITH_MPI)
     SET(CMAKE_SWIG_FLAGS "-DHAVE_MPI")
-ELSE(WITH_MPI)
+ELSE()
     SET(CMAKE_SWIG_FLAGS "")
-ENDIF(WITH_MPI)
+ENDIF()
 
 SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
 
@@ -105,17 +129,18 @@ IF(${CMAKE_VERSION} VERSION_LESS "3.8.0")
 ELSE()
     SWIG_ADD_LIBRARY(CCupydo
                      LANGUAGE python
-                     SOURCES ${ISRCS} ${SRCS})
+                     SOURCES ${PROJECT_SOURCE_DIR}/_src/CCupydo.i ${SRCS})
 ENDIF()
 
 SWIG_LINK_LIBRARIES(CCupydo ${PYTHON_LIBRARIES} ${MPI_LIBRARIES} ${PETSC_LIBRARIES})
 
 # --- Install ---
+# note: [RB] this is not how INSTALL is supposed to be used!
 SET(CMAKE_INSTALL_PREFIX "${PROJECT_SOURCE_DIR}")
 MESSAGE(STATUS "Installation directory : ${CMAKE_INSTALL_PREFIX}")
 
 INSTALL_TARGETS(/ccupydo _CCupydo)
-INSTALL_FILES(/ccupydo FILES "${PROJECT_BINARY_DIR}/CCupydo.py")
+INSTALL_FILES(/ccupydo FILES "${CMAKE_SWIG_OUTDIR}/CCupydo.py")
 
 # --- Enable CTest ---
 ENABLE_TESTING()

NOTICE.txt

@@ -3,7 +3,7 @@
 =========================================================================
 
 CUPyDO
-Copyright 2018-2019 University of Liège.
+Copyright 2018-2021 University of Liège.
 
 This software was developed at the University of Liège (Belgium) by: 
 

README.md

@@ -3,18 +3,44 @@ FSI tools for partinioned coupling between generic solid and fluid solvers.
 
 [![Apache License Version 2.0](https://img.shields.io/badge/license-Apache_2.0-green.svg)](LICENSE)
 
-## Features
+## Solvers
 CUPyDO currently features interfaces for the following solvers:
-- Solid:
-  - Metafor --> A Nonlinear Finite Element solid solver developed at the University of Liège (http://metafor.ltas.ulg.ac.be/dokuwiki/)
-  - RBM --> A dynamic 2dof pitch/plunge solid solver developed at the University of Liège (https://github.com/ulgltas/NativeSolid)
-  - modali -> A static/dynamic modal solver developed at the University of Liège (https://github.com/ulgltas/modali)
-  - GetDP --> A free finite element software and a general environment for the treatment of discrete problems, developed at University of Liège (http://getdp.info/)
-- Fluid:
-  - PFEM --> Particle Finite Element Method fluid solver developed at the University of Liège (https://gitlab.uliege.be/am-dept/PFEM)
-  - SU2 --> Open-source CFD code developed at Stanford University (https://su2code.github.io/)
-  - Flow --> A Full Potential Finite Element fluid solver, part of the waves project, developed at the University of Liège (https://gitlab.uliege.be/am-dept/waves)
-  - VLM --> A Vortex Lattice Method, developed at the University of Liège (https://github.com/ulgltas/VLM)
+- **Solid**
+  - Metafor **[v3492]** (http://metafor.ltas.ulg.ac.be/dokuwiki/start)
+  - A Nonlinear Finite Element solid solver developed at the University of Liège.
+  ---
+  - RBMI **[1.1]** (https://github.com/ulgltas/NativeSolid)
+  - A dynamic 2dof pitch/plunge solid solver developed at the University of Liège.
+  ---
+  - SU2 **[X]** (https://su2code.github.io/)
+  - Open-source CFD code developed at Stanford University.
+  ---
+  - Modali **[v2.0]** (https://github.com/ulgltas/modali)
+  - A static/dynamic modal solver developed at the University of Liège.
+  ---
+  - GetDP **[X]** (http://getdp.info/)
+  - A free finite element software and a general environment for the treatment of discrete problems, developed at University of Liège.
+  ---
+  - pyBeam **[0.1]** (https://github.com/pyBeam/pyBeam)
+  - A nonlinear beam finite element solver developed for aeronautical design applications.
+  ---
+- **Fluid**
+  - PFEM **[v1.19]** (https://gitlab.uliege.be/am-dept/PFEM)
+  - Particle Finite Element Method fluid solver developed at the University of Liège.
+  ---
+  - SU2 **[7.1.1\*]** (https://github.com/ulgltas/SU2/tree/fix_wrap_strong)
+  - Open-source CFD code developed at Stanford University.
+  ---
+  - Flow **[v2.1.1]** (https://gitlab.uliege.be/am-dept/waves)
+  - A Full Potential Finite Element fluid solver, part of the waves project, developed at the University of Liège.
+  ---
+  - VLM **[v2.0]** (https://github.com/ulgltas/VLM)
+  - A Vortex Lattice Method, developed at the University of Liège.
+  ---
+  - PFEM3D **[2.0.0]** (https://github.com/ImperatorS79/PFEM3D)
+  - A 3D Particle Finite Element Method fluid solver developed at the University of Liège.
+
+##  Features
 
 Furthermore, CUPyDO features two interpolation alogrithms:
 - Radial Basis Functions (RBF)

_src/CCupydo.i

@@ -35,6 +35,11 @@ threads="1"
 #include "cLinearSolver.h"
 %}
 
+// Problem with Swig & Python 3 for np.int64
+%begin %{
+#define SWIG_PYTHON_CAST_MODE
+%}
+
 // petite bidouille pour pouvoir compiler avec "threads=1" et iterer sur des std_vector
 // (sinon ca explose � la destruction de l'iterateur)
 %nothread swig::SwigPyIterator::~SwigPyIterator();