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Merge branch 'python' into unittests-refactor

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jngrad committed Jun 7, 2019
2 parents f8b0364 + 1db3e66 commit e621b89df7335f6aa27d53fd6e455c7fc50ef405
Showing with 6,107 additions and 624 deletions.
  1. +2 −2 CMakeLists.txt
  2. +44 −31 cmake/FindSphinx.cmake
  3. +841 −0 doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
  4. +874 −0 doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
  5. +3,137 −0 doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
  6. +16 −0 doc/tutorials/11-ferrofluid/CMakeLists.txt
  7. BIN doc/tutorials/11-ferrofluid/figures/Electro-Steric_Stabilization.jpg
  8. BIN doc/tutorials/11-ferrofluid/figures/Ferrofluid_Magnet_under_glass_edit.jpg
  9. BIN doc/tutorials/11-ferrofluid/figures/headtotailconf.png
  10. +10 −1 doc/tutorials/CMakeLists.txt
  11. +2 −1 maintainer/CI/build_cmake.sh
  12. +1 −1 requirements.txt
  13. +1 −1 src/core/grid_based_algorithms/electrokinetics_cuda.cu
  14. +7 −17 src/core/grid_based_algorithms/lbgpu_cuda.cu
  15. +1 −0 src/core/observables/ComForce.hpp
  16. +1 −0 src/core/observables/ComPosition.hpp
  17. +1 −0 src/core/observables/ComVelocity.hpp
  18. +1 −0 src/core/observables/Current.hpp
  19. +5 −2 src/core/observables/CylindricalDensityProfile.hpp
  20. +3 −2 src/core/observables/CylindricalFluxDensityProfile.hpp
  21. +3 −3 src/core/observables/CylindricalLBFluxDensityProfileAtParticlePositions.cpp
  22. +2 −0 src/core/observables/CylindricalLBFluxDensityProfileAtParticlePositions.hpp
  23. +41 −9 src/core/observables/CylindricalLBProfileObservable.hpp
  24. +15 −32 src/core/observables/CylindricalLBVelocityProfile.cpp
  25. +1 −0 src/core/observables/CylindricalLBVelocityProfile.hpp
  26. +3 −3 src/core/observables/CylindricalLBVelocityProfileAtParticlePositions.cpp
  27. +1 −0 src/core/observables/CylindricalLBVelocityProfileAtParticlePositions.hpp
  28. +13 −2 src/core/observables/CylindricalPidProfileObservable.hpp
  29. +10 −6 src/core/observables/{CylindricalProfileObservable.hpp → CylindricalProfile.hpp}
  30. +3 −2 src/core/observables/CylindricalVelocityProfile.hpp
  31. +1 −0 src/core/observables/DensityProfile.hpp
  32. +1 −0 src/core/observables/DipoleMoment.hpp
  33. +1 −0 src/core/observables/FluxDensityProfile.hpp
  34. +1 −0 src/core/observables/ForceDensityProfile.hpp
  35. +0 −62 src/core/observables/LBObservable.hpp
  36. +51 −2 src/core/observables/LBProfileObservable.hpp
  37. +4 −19 src/core/observables/LBVelocityProfile.cpp
  38. +1 −0 src/core/observables/LBVelocityProfile.hpp
  39. +1 −0 src/core/observables/MagneticDipoleMoment.hpp
  40. +1 −0 src/core/observables/ParticleAngles.hpp
  41. +1 −0 src/core/observables/ParticleAngularVelocities.hpp
  42. +1 −0 src/core/observables/ParticleBodyAngularVelocities.hpp
  43. +1 −0 src/core/observables/ParticleBodyVelocities.hpp
  44. +1 −0 src/core/observables/ParticleDihedrals.hpp
  45. +1 −0 src/core/observables/ParticleDistances.hpp
  46. +1 −0 src/core/observables/ParticleForces.hpp
  47. +1 −0 src/core/observables/ParticlePositions.hpp
  48. +1 −0 src/core/observables/ParticleVelocities.hpp
  49. +2 −1 src/core/observables/PidObservable.hpp
  50. +9 −6 src/core/observables/PidProfileObservable.hpp
  51. +6 −3 src/core/observables/ProfileObservable.hpp
  52. +6 −2 src/core/particle_data.cpp
  53. +1 −1 src/core/polymer.cpp
  54. +1 −1 src/core/rotate_system.cpp
  55. +14 −26 src/python/espressomd/observables.py
  56. +1 −1 src/python/espressomd/polymer.pyx
  57. +2 −0 src/python/espressomd/script_interface.pxd
  58. +24 −18 src/python/espressomd/script_interface.pyx
  59. +79 −122 src/script_interface/observables/CylindricalLBProfileObservable.hpp
  60. +12 −8 src/script_interface/observables/CylindricalPidProfileObservable.hpp
  61. +12 −7 src/script_interface/observables/LBProfileObservable.hpp
  62. +14 −14 src/script_interface/observables/PidObservable.hpp
  63. +9 −1 src/script_interface/observables/PidProfileObservable.hpp
  64. +3 −1 src/script_interface/observables/ProfileObservable.hpp
  65. +5 −0 src/script_interface/observables/initialize.cpp
  66. +1 −1 src/utils/include/utils/Vector.hpp
  67. +0 −79 src/utils/include/utils/coordinate_transformation.hpp
  68. +86 −0 src/utils/include/utils/math/coordinate_transformation.hpp
  69. +17 −2 src/utils/include/utils/{ → math}/vec_rotate.hpp
  70. +91 −0 src/utils/include/utils/sampling.hpp
  71. +2 −1 src/utils/tests/CMakeLists.txt
  72. +1 −0 src/utils/tests/Vector_test.cpp
  73. +85 −0 src/utils/tests/coordinate_transformation.cpp
  74. +63 −0 src/utils/tests/sampling_test.cpp
  75. +1 −1 src/utils/tests/vec_rotate_test.cpp
  76. +1 −0 testsuite/python/CMakeLists.txt
  77. +226 −0 testsuite/python/lb_poiseuille_cylinder.py
  78. +24 −3 testsuite/python/observable_cylindrical.py
  79. +57 −126 testsuite/python/observable_cylindricalLB.py
  80. +2 −1 testsuite/python/observable_profileLB.py
  81. +3 −0 testsuite/scripts/tutorials/CMakeLists.txt
  82. +42 −0 testsuite/scripts/tutorials/test_11-ferrofluid_1.py
  83. +45 −0 testsuite/scripts/tutorials/test_11-ferrofluid_2.py
  84. +51 −0 testsuite/scripts/tutorials/test_11-ferrofluid_3.py
@@ -209,10 +209,10 @@ if(WITH_CUDA)

set(CUDA_LINK_LIBRARIES_KEYWORD PUBLIC)

set(CUDA_NVCC_FLAGS_DEBUG "${CUDA_NVCC_FLAGS_DEBUG} -g -G")
set(CUDA_NVCC_FLAGS_DEBUG "${CUDA_NVCC_FLAGS_DEBUG} -g")
set(CUDA_NVCC_FLAGS_RELEASE "${CUDA_NVCC_FLAGS_RELEASE} -O3 -DNDEBUG")
set(CUDA_NVCC_FLAGS_MINSIZEREL "${CUDA_NVCC_FLAGS_MINSIZEREL} -Os -DNDEBUG")
set(CUDA_NVCC_FLAGS_RELWITHDEBINFO "${CUDA_NVCC_FLAGS_RELWITHDEBINFO} -g -G -O2")
set(CUDA_NVCC_FLAGS_RELWITHDEBINFO "${CUDA_NVCC_FLAGS_RELWITHDEBINFO} -g -O2")
set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} -gencode=arch=compute_30,code=sm_30 -gencode=arch=compute_52,code=sm_52 -gencode=arch=compute_52,code=compute_52")
list(APPEND CUDA_NVCC_FLAGS "-std=c++14")
SET(CUDA_PROPAGATE_HOST_FLAGS OFF)
@@ -1,44 +1,57 @@
include(FindPackageHandleStandardArgs)

find_program(SPHINX_EXECUTABLE NAMES sphinx-build sphinx-build-${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
HINTS
$ENV{SPHINX_DIR}
PATHS /opt/local/ /usr/local/ $ENV{HOME}/Library/Python/2.7/
PATH_SUFFIXES bin
DOC "Sphinx documentation generator."
)

find_program(SPHINX_API_DOC_EXE NAMES sphinx-apidoc sphinx-apidoc-${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
HINTS
PATH_SUFFIXES bin
PATHS /opt/local/ /usr/local/ $ENV{HOME}/Library/Python/2.7/
DOC "Sphinx api-doc executable."
)
find_program(SPHINX_EXECUTABLE
NAMES sphinx-build
sphinx-build-${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
HINTS $ENV{SPHINX_DIR}
PATHS /opt/local/ /usr/local/ $ENV{HOME}/Library/Python/2.7/
PATH_SUFFIXES bin
DOC "Sphinx documentation generator.")

find_program(SPHINX_API_DOC_EXE
NAMES sphinx-apidoc
sphinx-apidoc-${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
HINTS
PATH_SUFFIXES bin
PATHS /opt/local/ /usr/local/ $ENV{HOME}/Library/Python/2.7/
DOC "Sphinx api-doc executable.")

if(Sphinx_FIND_VERSION)
execute_process(COMMAND "${SPHINX_EXECUTABLE}" --version
OUTPUT_VARIABLE QUERY_VERSION_OUT
ERROR_VARIABLE QUERY_VERSION_ERR
RESULT_VARIABLE QUERY_VERSION_RESULT)

# Sphinx switched at some point from returning ther version
# on stdout to printing it at stderr. Since we do not know
# ther version yet, we use stdout if it matches a version
# regex, or stderr otherwise.
OUTPUT_VARIABLE QUERY_VERSION_OUT
ERROR_VARIABLE QUERY_VERSION_ERR
RESULT_VARIABLE QUERY_VERSION_RESULT)

# Sphinx switched at some point from returning ther version on stdout to
# printing it at stderr. Since we do not know ther version yet, we use stdout
# if it matches a version regex, or stderr otherwise.
if(QUERY_VERSION_OUT MATCHES "[0-9.]+")
set(QUERY_VERSION "${QUERY_VERSION_OUT}")
else()
set(QUERY_VERSION "${QUERY_VERSION_ERR}")
endif()

if(NOT QUERY_VERSION_RESULT)
string(REGEX MATCH "[0-9.]+" AVAILABLE_VERSION "${QUERY_VERSION}")
endif( )
endif( )

find_package_handle_standard_args(Sphinx
REQUIRED_VARS SPHINX_EXECUTABLE SPHINX_API_DOC_EXE
VERSION_VAR AVAILABLE_VERSION
)

string(REGEX MATCH
"[0-9.]+"
SPHINX_VERSION
"${QUERY_VERSION}")
endif()

set(SPHINX_VERSION_COMPATIBLE TRUE)
# Blacklist broken version
if("${SPHINX_VERSION}" VERSION_EQUAL "2.1.0")
message(WARNING "Sphinx version 2.1.0 is not compatible.")
set(SPHINX_VERSION_COMPATIBLE FALSE)
endif()
endif()

find_package_handle_standard_args(Sphinx
REQUIRED_VARS
SPHINX_EXECUTABLE
SPHINX_API_DOC_EXE
SPHINX_VERSION_COMPATIBLE
VERSION_VAR
SPHINX_VERSION)

mark_as_advanced(SPHINX_EXECUTABLE)

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