Merge branch 'python' into fix-4008

.gitlab-ci.yml

@@ -33,7 +33,7 @@ variables:
 status_pending:
   <<: *notification_job_definition
   stage: prepare
-  script: bash maintainer/gh_post_status.sh pending
+  script: sh maintainer/gh_post_status.sh pending
 
 style:
   <<: *global_job_definition
@@ -42,7 +42,7 @@ style:
   before_script:
     - git submodule deinit .
   script:
-    - maintainer/CI/fix_style.sh
+    - sh maintainer/CI/fix_style.sh
   tags:
     - docker
     - linux
@@ -515,7 +515,7 @@ check_with_odd_no_of_processors:
   script:
     - cd ${CI_PROJECT_DIR}/build
     - cmake -DTEST_NP=3 .
-    - make -t && make check_python_parallel_odd
+    - make -t && make check_unit_tests && make check_python_parallel_odd
   tags:
     - docker
     - linux
@@ -572,27 +572,27 @@ deploy_tutorials:
 status_success:
   <<: *notification_job_definition
   stage: result
-  script: bash maintainer/gh_post_status.sh success
+  script: sh maintainer/gh_post_status.sh success
   when: on_success
 
 status_failure:
   <<: *notification_job_definition
   stage: result
-  script: bash maintainer/gh_post_status.sh failure
+  script: sh maintainer/gh_post_status.sh failure
   when: on_failure
 
 notify_success:
   <<: *notification_job_definition
   stage: result
-  script: bash maintainer/gh_close_issue.sh
+  script: sh maintainer/gh_close_issue.sh
   when: on_success
   only:
     - python
 
 notify_failure:
   <<: *notification_job_definition
   stage: result
-  script: bash maintainer/gh_create_issue.sh
+  script: sh maintainer/gh_create_issue.sh
   when: on_failure
   only:
     - python

.pre-commit-config.yaml

@@ -9,6 +9,7 @@ repos:
         language: system
         always_run: false
         files: '.*\.(cpp|hpp|cu|cuh)'
+        exclude: '^libs/'
         args: ["-i", "-style=file"]
 
     -   id: autopep8
@@ -17,15 +18,16 @@ repos:
         language: system
         always_run: false
         files: '.*\.(py|pyx|pxd)'
-        exclude: '\.pylintrc|.*.\.py\.in'
-        args: ["--ignore=E266,E701,W291,W293", "--in-place", "--aggressive"]
+        exclude: '\.pylintrc|.*.\.py\.in|^libs/'
+        args: ["--ignore=E266,E402,E701,W291,W293", "--in-place", "--aggressive"]
 
     -   id: cmake-format
         name: cmake-format
         entry: sh maintainer/format/cmake-format.sh
         language: system
         always_run: false
         files: 'CMakeLists.txt'
+        exclude: '^libs/h5xx/|^libs/Random123-1\.09/'
         args: ["-i"]
 
     -   id: ex-flags

AUTHORS

@@ -10,13 +10,14 @@ The following people have contributed to ESPResSo:
 
 Core developers
 ---------------
-Florian Weik
 Rudolf Weeber
 Kai Szuttor
 Jean-Noël Grad
+Alexander Reinauer
 
 Former Core Developers
 ----------------------
+Florian Weik
 Georg Rempfer
 Stefan Kesselheim
 Bernward Mann (deceased 2006)
@@ -57,6 +58,7 @@ Frank Mühlbach
 Gizem Inci
 Gregoria Illya
 Hamid Zaheri
+Hao Lu
 Henri Menke
 Igor Pasichnyk
 Ingo Tischler
@@ -103,6 +105,7 @@ Pedro Ojeda
 Pedro Sanchez
 Peter Košovan
 Pierre de Buyl
+Riccardo Frenner
 Robert Kaufmann
 Robin Bardakcioglu
 Sam Foley

CMakeLists.txt

@@ -306,29 +306,6 @@ endif(WITH_VALGRIND_INSTRUMENTATION)
 
 find_package(MPI 3.0 REQUIRED)
 
-# CMake < 3.9
-if(NOT TARGET MPI::MPI_CXX)
-  add_library(MPI::MPI_CXX IMPORTED INTERFACE)
-
-  # Workaround for https://gitlab.kitware.com/cmake/cmake/issues/18349
-  foreach(_MPI_FLAG ${MPI_CXX_COMPILE_FLAGS})
-    set_property(TARGET MPI::MPI_CXX PROPERTY INTERFACE_COMPILE_OPTIONS
-                                              ${_MPI_FLAG})
-  endforeach()
-
-  set_property(TARGET MPI::MPI_CXX PROPERTY INTERFACE_INCLUDE_DIRECTORIES
-                                            "${MPI_CXX_INCLUDE_PATH}")
-
-  # Workaround for https://gitlab.kitware.com/cmake/cmake/issues/18349
-  foreach(_MPI_FLAG ${MPI_CXX_LINK_FLAGS})
-    set_property(TARGET MPI::MPI_CXX PROPERTY INTERFACE_LINK_LIBRARIES
-                                              ${_MPI_FLAG})
-  endforeach()
-
-  set_property(TARGET MPI::MPI_CXX PROPERTY INTERFACE_LINK_LIBRARIES
-                                            ${MPI_CXX_LIBRARIES})
-endif()
-
 # ##############################################################################
 # Boost
 # ##############################################################################
@@ -473,16 +450,14 @@ endif()
 
 if(WITH_TESTS)
   enable_testing()
-  if(Boost_UNIT_TEST_FRAMEWORK_FOUND)
-    set(WITH_UNIT_TESTS ON)
-  endif(Boost_UNIT_TEST_FRAMEWORK_FOUND)
   add_custom_target(check)
-  if(WITH_PYTHON)
-    add_subdirectory(testsuite)
-  endif(WITH_PYTHON)
   set(CTEST_ARGS ""
       CACHE STRING
             "Extra arguments to give to ctest calls (separated by semicolons)")
+  set(TEST_NP "4" CACHE STRING "Maximal number of MPI ranks to use per test")
+  if(WITH_PYTHON)
+    add_subdirectory(testsuite)
+  endif(WITH_PYTHON)
 endif(WITH_TESTS)
 
 if(WITH_BENCHMARKS)

cmake/FindCUDACompilerNVCC.cmake

@@ -63,7 +63,6 @@ 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/unit_test.cmake

@@ -1,12 +1,3 @@
-if(NOT DEFINED TEST_NP)
-  include(ProcessorCount)
-  processorcount(NP)
-  math(EXPR TEST_NP "${NP}/2 + 1")
-  if(${TEST_NP} GREATER 4)
-    set(TEST_NP 4)
-  endif()
-endif()
-
 if(EXISTS ${MPIEXEC})
   # OpenMPI 2.0 and higher checks the number of processes against the number of
   # CPUs

doc/sphinx/advanced_methods.rst

@@ -1894,7 +1894,7 @@ The call of ``add_reaction`` define the insertion :math:`\mathrm{\emptyset \to t
 Multiple reactions for the insertions of different types can be added to the same ``WidomInsertion`` instance.
 Measuring the excess chemical potential using the insertion method is done via calling ``widom.measure_excess_chemical_potential(0)``.
 If another particle insertion is defined, then the excess chemical potential for this insertion can be measured by calling ``widom.measure_excess_chemical_potential(1)``.
-Be aware that the implemented method only works for the canonical ensemble. If the numbers of particles fluctuate (i.e. in a semi grand canonical simulation) one has to adapt the formulas from which the excess chemical potential is calculated! This is not implemented. Also in a isobaric-isothermal simulation (NPT) the corresponding formulas for the excess chemical potentials need to be adapted. This is not implemented.
+Be aware that the implemented method only works for the canonical ensemble. If the numbers of particles fluctuate (i.e. in a semi grand canonical simulation) one has to adapt the formulas from which the excess chemical potential is calculated! This is not implemented. Also in a isobaric-isothermal simulation (NpT) the corresponding formulas for the excess chemical potentials need to be adapted. This is not implemented.
 
 The implementation can also deal with the simultaneous insertion of multiple particles and can therefore measure the change of excess free energy of multiple particles like e.g.:
 

doc/sphinx/electrostatics.rst

@@ -318,7 +318,7 @@ MMM1D is used with::
 
 where the prefactor :math:`C` is defined in Eqn. :eq:`coulomb_prefactor`.
 MMM1D Coulomb method for systems with periodicity (0 0 1). Needs the
-nsquared cell system (see section :ref:`Cellsystems`). The first form sets parameters
+N-squared cell system (see section :ref:`Cellsystems`). The first form sets parameters
 manually. The switch radius determines at which xy-distance the force
 calculation switches from the near to the far formula. The Bessel cutoff
 does not need to be specified as it is automatically determined from the
@@ -336,7 +336,7 @@ MMM1D on GPU
 :class:`espressomd.electrostatics.MMM1DGPU`
 
 MMM1D is also available in a GPU implementation. Unlike its CPU
-counterpart, it does not need the nsquared cell system.
+counterpart, it does not need the N-squared cell system.
 
 ::
 

doc/sphinx/installation.rst

@@ -352,9 +352,9 @@ General features
 In addition, there are switches that enable additional features in the
 integrator or thermostat:
 
--  ``NPT`` Enables an on-the-fly NPT integration scheme.
+-  ``NPT`` Enables an on-the-fly NpT integration scheme.
 
-   .. seealso:: :ref:`Isotropic NPT thermostat`
+   .. seealso:: :ref:`Isotropic NpT thermostat`
 
 -  ``ENGINE``
 

doc/sphinx/introduction.rst

@@ -448,7 +448,7 @@ report so to the developers using the instructions in :ref:`Contributing`.
 +--------------------------------+------------------------+------------------+------------+
 | Langevin Thermostat            | Core                   | Core             | Yes        |
 +--------------------------------+------------------------+------------------+------------+
-| Isotropic NPT                  | Experimental           | None             | Yes        |
+| Isotropic NpT                  | Experimental           | None             | Yes        |
 +--------------------------------+------------------------+------------------+------------+
 | Quaternion Integrator          | Core                   | Good             | Yes        |
 +--------------------------------+------------------------+------------------+------------+