Merge branch 'python' into cells

Author: RudolfWeeber

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:8a7d258889d87dcc9c96a200784b30b532d45b33
+image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:e583d4b2eb8eedd10068957f952bd67008475ee5
 
 stages:
   - prepare
@@ -114,7 +114,7 @@ no_rotation:
 ubuntu:wo-dependencies:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-wo-dependencies:fc7628d32de0fce605976ba9edebe7eff186e618
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-wo-dependencies:e583d4b2eb8eedd10068957f952bd67008475ee5
   script:
     - export myconfig=maxset with_cuda=false make_check_unit_tests=false make_check_python=false
     - bash maintainer/CI/build_cmake.sh
@@ -199,6 +199,24 @@ clang-sanitizer:
     - linux
     - cuda
 
+cuda11-maxset:
+  <<: *global_job_definition
+  stage: build
+  image: docker.pkg.github.com/espressomd/docker/cuda:e583d4b2eb8eedd10068957f952bd67008475ee5
+  variables:
+     CC: 'gcc-9'
+     CXX: 'g++-9'
+  script:
+    - export myconfig=maxset with_cuda=true with_coverage=false test_timeout=900 srcdir=${CI_PROJECT_DIR}
+    - export with_scafacos=true with_stokesian_dynamics=true
+    - bash maintainer/CI/build_cmake.sh
+  tags:
+    - docker
+    - linux
+    - cuda
+  only:
+    - schedules
+
 cuda10-maxset:
   <<: *global_job_definition
   stage: build
@@ -230,11 +248,6 @@ cuda9-maxset:
     - export myconfig=maxset with_cuda=true with_coverage=true test_timeout=900 srcdir=${CI_PROJECT_DIR}
     - export with_scafacos=true with_stokesian_dynamics=true
     - bash maintainer/CI/build_cmake.sh
-  artifacts:
-    paths:
-    - build/
-    expire_in: 1 week
-  when: on_success
   tags:
     - docker
     - linux
@@ -354,7 +367,7 @@ empty:
 rocm-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/rocm:d496478230db4e5c286680e3bdc1621af1fccffc
+  image: docker.pkg.github.com/espressomd/docker/rocm:cb775a82f49a7f6d4a806f17358caec797f48f73
   script:
     - export myconfig=maxset with_cuda=true with_cuda_compiler=hip
     - export with_stokesian_dynamics=false
@@ -457,7 +470,7 @@ check_cuda_maxset_no_gpu:
   <<: *global_job_definition
   stage: additional_checks
   when: on_success
-  needs: 
+  needs:
     - cuda10-maxset
   script:
     - export CUDA_VISIBLE_DEVICES=""
@@ -470,9 +483,9 @@ check_cuda_maxset_no_gpu:
 
 check_with_odd_no_of_processors:
   <<: *global_job_definition
-  stage: additional_checks 
+  stage: additional_checks
   when: on_success
-  needs: 
+  needs:
     - cuda10-maxset
   script:
     - cd ${CI_PROJECT_DIR}/build
@@ -507,7 +520,7 @@ deploy_sphinx_documentation:
   dependencies:
     - check_sphinx
   script:
-    - cd ${CI_PROJECT_DIR}/build/doc/sphinx/html && 
+    - cd ${CI_PROJECT_DIR}/build/doc/sphinx/html &&
       rsync -avz --delete -e "ssh -i ${HOME}/.ssh/espresso_rsa" ./ [email protected]:/home/espresso/public_html/html/doc
 
 deploy_doxygen_documentation:

CMakeLists.txt

@@ -18,7 +18,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-cmake_minimum_required(VERSION 3.10)
+cmake_minimum_required(VERSION 3.11)
 message(STATUS "CMake version: ${CMAKE_VERSION}")
 if(POLICY CMP0076)
   # make target_sources() convert relative paths to absolute
@@ -166,7 +166,7 @@ if(WITH_CUDA)
   endif()
 endif(WITH_CUDA)
 
-find_package(PythonInterp 3.5 REQUIRED)
+find_package(PythonInterp 3.6 REQUIRED)
 
 if(WITH_PYTHON)
   find_package(Cython 0.26 REQUIRED)
@@ -278,7 +278,6 @@ endif(WITH_STOKESIAN_DYNAMICS)
 if(WITH_STOKESIAN_DYNAMICS)
   set(CMAKE_INSTALL_LIBDIR
       "${CMAKE_INSTALL_PREFIX}/${PYTHON_INSTDIR}/espressomd")
-  cmake_minimum_required(VERSION 3.11)
   include(FetchContent)
   FetchContent_Declare(
     stokesian_dynamics
@@ -485,6 +484,9 @@ if(WITH_TESTS)
   if(WITH_PYTHON)
     add_subdirectory(testsuite)
   endif(WITH_PYTHON)
+  set(CTEST_ARGS ""
+      CACHE STRING
+            "Extra arguments to give to ctest calls (separated by semicolons)")
 endif(WITH_TESTS)
 
 if(WITH_BENCHMARKS)

cmake/FindCUDACompilerHIP.cmake

@@ -27,21 +27,26 @@ find_package(HIP ${CUDACompilerHIP_FIND_VERSION} MODULE REQUIRED)
 # patch HCC_PATH environment variable and reload HIP
 if(HIP_VERSION VERSION_LESS 3.1)
   set(HCC_PATH "${HIP_ROOT_DIR}")
-else()
+elseif(HIP_VERSION VERSION_LESS 3.5)
   set(HCC_PATH "${ROCM_HOME}/hcc")
+else()
+  set(HIP_HIPCC_CMAKE_LINKER_HELPER "${HIP_HIPCC_EXECUTABLE}")
+  unset(HCC_PATH)
 endif()
 find_package(HIP ${CUDACompilerHIP_FIND_VERSION} MODULE REQUIRED)
 
 set(CUDA 1)
 set(HIP 1)
 
-list(APPEND HIP_HCC_FLAGS
+list(APPEND HIP_HIPCC_FLAGS
        -std=c++${CMAKE_CUDA_STANDARD} -pedantic -Wall -Wextra
        -Wno-sign-compare -Wno-unused-function -Wno-unused-variable
        -Wno-unused-parameter -Wno-missing-braces -Wno-gnu-anonymous-struct
        -Wno-nested-anon-types -Wno-gnu-zero-variadic-macro-arguments
        -Wno-c99-designator -Wno-macro-redefined -Wno-duplicate-decl-specifier
        $<$<VERSION_GREATER_EQUAL:${HIP_VERSION},3.3>:-Wno-deprecated-copy>
+       $<$<VERSION_GREATER_EQUAL:${HIP_VERSION},3.7>:-Wno-c++17-extensions>
+       $<$<VERSION_GREATER_EQUAL:${HIP_VERSION},3.7>:-Wno-unused-command-line-argument>
        $<$<BOOL:${WARNINGS_ARE_ERRORS}>:-Werror>)
 
 list(APPEND HIP_HIPCC_FLAGS_DEBUG -g)

cmake/FindCUDACompilerNVCC.cmake

@@ -50,8 +50,11 @@ list(APPEND CUDA_NVCC_FLAGS_MINSIZEREL -O2 -Xptxas=-O2 -Xcompiler=-Os -DNDEBUG)
 list(APPEND CUDA_NVCC_FLAGS_RELWITHDEBINFO -O2 -g -Xptxas=-O2 -Xcompiler=-O2,-g -DNDEBUG)
 list(APPEND CUDA_NVCC_FLAGS_COVERAGE -O3 -g -Xptxas=-O3 -Xcompiler=-Og,-g)
 list(APPEND CUDA_NVCC_FLAGS_RELWITHASSERT -O3 -g -Xptxas=-O3 -Xcompiler=-O3,-g)
+if(CMAKE_CUDA_COMPILER_VERSION VERSION_LESS 11)
+  list(APPEND CUDA_NVCC_FLAGS -gencode=arch=compute_30,code=sm_30)
+endif()
 list(APPEND CUDA_NVCC_FLAGS
-       -gencode=arch=compute_30,code=sm_30 -gencode=arch=compute_52,code=sm_52
+       -gencode=arch=compute_52,code=sm_52
        -gencode=arch=compute_52,code=compute_52 -std=c++${CMAKE_CUDA_STANDARD}
        $<$<BOOL:${WARNINGS_ARE_ERRORS}>:-Xcompiler=-Werror;-Xptxas=-Werror>
        $<$<BOOL:${CMAKE_OSX_SYSROOT}>:-Xcompiler=-isysroot;-Xcompiler=${CMAKE_OSX_SYSROOT}>)
@@ -60,6 +63,7 @@ function(find_gpu_library)
   cmake_parse_arguments(LIBRARY "REQUIRED" "NAMES;VARNAME" "" ${ARGN})
   list(APPEND LIBRARY_PATHS
        ${CUDA_TOOLKIT_ROOT_DIR}/lib64 ${CUDA_TOOLKIT_ROOT_DIR}/lib
+       ${CUDA_TOOLKIT_ROOT_DIR}/compat
        /usr/local/nvidia/lib /usr/lib/x86_64-linux-gnu)
   if(LIBRARY_REQUIRED)
     find_library(${LIBRARY_VARNAME} NAMES ${LIBRARY_NAMES} PATHS ${LIBRARY_PATHS} NO_DEFAULT_PATH REQUIRED)

cmake/FindFFTW3.cmake

@@ -28,7 +28,6 @@ if(FFTW3_INCLUDE_DIR)
 endif(FFTW3_INCLUDE_DIR)
 
 find_path(FFTW3_INCLUDE_DIR fftw3.h)
-
 find_library(FFTW3_LIBRARIES NAMES fftw3)
 
 # handle the QUIETLY and REQUIRED arguments and set FFTW_FOUND to TRUE if all
@@ -38,3 +37,9 @@ find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARIES
                                   FFTW3_INCLUDE_DIR)
 
 mark_as_advanced(FFTW3_LIBRARIES FFTW3_INCLUDE_DIR)
+
+if(FFTW3_FOUND AND NOT TARGET FFTW3::FFTW3)
+  add_library(FFTW3::FFTW3 INTERFACE IMPORTED)
+  target_include_directories(FFTW3::FFTW3 INTERFACE "${FFTW3_INCLUDE_DIR}")
+  target_link_libraries(FFTW3::FFTW3 INTERFACE "${FFTW3_LIBRARIES}")
+endif()

doc/sphinx/advanced_methods.rst

@@ -28,7 +28,7 @@ Several modes are available for different types of binding.
     import espressomd
     from espressomd.interactions import HarmonicBond
 
-    system = espressomd.System()
+    system = espressomd.System(box_l=[1, 1, 1])
     bond_centers = HarmonicBond(k=1000, r_0=<CUTOFF>)
     system.bonded_inter.add(bond_centers)
     system.collision_detection.set_params(mode="bind_centers", distance=<CUTOFF>,

doc/sphinx/constraints.rst

@@ -167,7 +167,7 @@ Available shapes
 Python syntax::
 
     import espressomd from espressomd.shapes import <SHAPE>
-    system = espressomd.System()
+    system = espressomd.System(box_l=[1, 1, 1])
 
 ``<SHAPE>`` can be any of the available shapes.
 

doc/sphinx/electrostatics.rst

@@ -35,20 +35,22 @@ Note that using the electrostatic interaction also requires assigning charges to
 the particles via the particle property
 :py:attr:`espressomd.particle_data.ParticleHandle.q`.
 
-This example shows the general usage of an electrostatic method ``<SOLVER>``.
-All of them need the Bjerrum length and a set of other required parameters.
-First, an instance of the solver is created and only after adding it to the actors
-list, it is activated. Internally the method calls a tuning routine on
-activation to achieve the given accuracy::
+All solvers need a prefactor and a set of other required parameters.
+This example shows the general usage of the electrostatic method ``P3M``.
+An instance of the solver is created and added to the actors list, at which
+point it will be automatically activated. This activation will internally
+call a tuning function to achieve the requested accuracy::
 
     import espressomd
-    from espressomd import electrostatics
+    import espressomd.electrostatics
 
-    system = espressomd.System()
-    solver = electrostatics.<SOLVER>(prefactor=C, <ADDITIONAL REQUIRED PARAMETERS>)
+    system = espressomd.System(box_l=[10, 10, 10])
+    system.time_step = 0.01
+    system.part.add(pos=[[0, 0, 0], [1, 1, 1]], q=[-1, 1])
+    solver = espressomd.electrostatics.P3M(prefactor=2, accuracy=1e-3)
     system.actors.add(solver)
 
-where the prefactor :math:`C` is defined as in Eqn. :eq:`coulomb_prefactor`
+where the prefactor is defined as :math:`C` in Eqn. :eq:`coulomb_prefactor`.
 
 .. _Coulomb P3M:
 
@@ -60,9 +62,10 @@ Coulomb P3M
 For this feature to work, you need to have the ``fftw3`` library
 installed on your system. In |es|, you can check if it is compiled in by
 checking for the feature ``FFTW`` with ``espressomd.features``.
-P3M requires full periodicity (1 1 1). Make sure that you know the relevance of the
-P3M parameters before using P3M! If you are not sure, read the following
-references:
+P3M requires full periodicity (1 1 1). When using a non-metallic dielectric
+constant (``epsilon != 0.0``), the box must be cubic.
+Make sure that you know the relevance of the P3M parameters before using P3M!
+If you are not sure, read the following references:
 :cite:`ewald21,hockney88,kolafa92,deserno98a,deserno98b,deserno00,deserno00a,cerda08d`.
 
 .. _Tuning Coulomb P3M:

doc/sphinx/installation.rst

@@ -89,7 +89,11 @@ are required:
 .. code-block:: bash
 
     sudo apt install python3-matplotlib python3-scipy ipython3 jupyter-notebook
-    sudo pip3 install 'pint>=0.9'
+    pip3 install --user 'pint>=0.9' 'jupyter_contrib_nbextensions==0.5.1' \
+                        'sphinx>=1.6.7,!=2.1.0,!=3.0.0' 'sphinxcontrib-bibtex>=0.3.5'
+    jupyter contrib nbextension install --user
+    jupyter nbextension enable rubberband/main
+    jupyter nbextension enable exercise2/main
 
 Nvidia GPU acceleration
 """""""""""""""""""""""
@@ -829,10 +833,10 @@ to actually write a simulation script for |es|.
 Running an interactive notebook
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Running the Jupyter interpreter requires using the ``ipypresso`` script, which
+Running a Jupyter session requires using the ``ipypresso`` script, which
 is also located in the build directory (its name comes from the IPython
 interpreter, today known as Jupyter). To run the tutorials, you will need
-to start the Jupyter interpreter in notebook mode:
+to start a Jupyter session:
 
 .. code-block:: bash
 
@@ -858,11 +862,16 @@ will exit the Python interpreter and Jupyter will notify you that the current
 Python kernel stopped. If a cell takes too long to execute, you may interrupt
 it with the stop button.
 
-To close the Jupyter notebook, go to the terminal where it was started and use
+Solutions cells are created using the ``exercise2`` plugin from nbextensions.
+To prevent solution code cells from running when clicking on "Run All", these
+code cells need to be converted to Markdown cells and fenced with `````python``
+and ```````.
+
+To close the Jupyter session, go to the terminal where it was started and use
 the keyboard shortcut Ctrl+C twice.
 
-When starting the Jupyter interpreter in notebook mode, you may see the
-following warning in the terminal:
+When starting a Jupyter session, you may see the following warning in the
+terminal:
 
 .. code-block:: none
 

doc/sphinx/inter_non-bonded.rst

@@ -620,7 +620,7 @@ that the Thole correction acts between all dipoles, intra- and intermolecular.
 Again, the accuracy is related to the P3M accuracy and the split between
 short-range and long-range electrostatics interaction. It is configured by::
 
-    system = espressomd.System()
+    system = espressomd.System(box_l=[1, 1, 1])
     system.non_bonded_inter[type_1,type_2].thole.set_params(scaling_coeff=<float>, q1q2=<float>)
 
 with parameters:

doc/sphinx/io.rst

@@ -211,7 +211,7 @@ capabilities. The usage is quite simple:
 .. code:: python
 
     from espressomd.io.mppiio import mpiio
-    system = espressomd.System()
+    system = espressomd.System(box_l=[1, 1, 1])
     # ... add particles here
     mpiio.write("/tmp/mydata", positions=True, velocities=True, types=True, bonds=True)
 

doc/sphinx/magnetostatics.rst

@@ -27,9 +27,15 @@ relative permittivity of the background material, respectively.
 
 Magnetostatic interactions are activated via the actor framework::
 
-    from espressomd.magnetostatics import DipolarDirectSumCpu
+    import espressomd
+    import espressomd.magnetostatics
 
-    direct_sum = DipolarDirectSumCpu(prefactor=1)
+    system = espressomd.System(box_l=[10, 10, 10])
+    system.time_step = 0.01
+    system.part.add(pos=[[0, 0, 0], [1, 1, 1]],
+                    rotation=2 * [(1, 1, 1)], dip=2 * [(1, 0, 0)])
+
+    direct_sum = espressomd.magnetostatics.DipolarDirectSumCpu(prefactor=1)
     system.actors.add(direct_sum)
     # ...
     system.actors.remove(direct_sum)
@@ -49,7 +55,8 @@ Dipolar P3M
 This is the dipolar version of the P3M algorithm, described in :cite:`cerda08d`.
 
 Make sure that you know the relevance of the P3M parameters before using
-P3M! If you are not sure, read the following references
+P3M! If you are not sure, read the following references:
+:cite:`ewald21,hockney88,kolafa92,deserno98a,deserno98b,deserno00,deserno00a,cerda08d`.
 
 Note that dipolar P3M does not work with non-cubic boxes.