From 01fd875a868fb6b6d436aa7bfe5e3f1163bb485e Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@ds.mpg.de>
Date: Mon, 11 Mar 2019 17:12:36 +0100
Subject: [PATCH] python package is built in cmake build tree
---
CMakeLists.txt | 11 ++--
{bfps/cpp => cpp}/Lagrange_polys.cpp | 0
{bfps/cpp => cpp}/Lagrange_polys.hpp | 0
{bfps/cpp => cpp}/base.hpp | 0
{bfps/cpp => cpp}/bfps_timer.hpp | 0
{bfps/cpp => cpp}/fftw_interface.hpp | 0
{bfps/cpp => cpp}/fftw_tools.cpp | 0
{bfps/cpp => cpp}/fftw_tools.hpp | 0
{bfps/cpp => cpp}/field.cpp | 0
{bfps/cpp => cpp}/field.hpp | 0
{bfps/cpp => cpp}/field_binary_IO.cpp | 0
{bfps/cpp => cpp}/field_binary_IO.hpp | 0
{bfps/cpp => cpp}/field_layout.cpp | 0
{bfps/cpp => cpp}/field_layout.hpp | 0
{bfps/cpp => cpp}/full_code/NSVE.cpp | 0
{bfps/cpp => cpp}/full_code/NSVE.hpp | 0
.../full_code/NSVE_field_stats.cpp | 0
.../full_code/NSVE_field_stats.hpp | 0
.../cpp => cpp}/full_code/NSVE_no_output.hpp | 0
.../full_code/NSVEcomplex_particles.cpp | 0
.../full_code/NSVEcomplex_particles.hpp | 0
.../full_code/NSVEp_extra_sampling.cpp | 0
.../full_code/NSVEp_extra_sampling.hpp | 0
{bfps/cpp => cpp}/full_code/NSVEparticles.cpp | 0
{bfps/cpp => cpp}/full_code/NSVEparticles.hpp | 0
.../full_code/NSVEparticles_no_output.hpp | 0
{bfps/cpp => cpp}/full_code/code_base.cpp | 0
{bfps/cpp => cpp}/full_code/code_base.hpp | 0
.../full_code/codes_with_no_output.hpp | 0
.../full_code/direct_numerical_simulation.cpp | 0
.../full_code/direct_numerical_simulation.hpp | 0
.../full_code/field_output_test.cpp | 0
.../full_code/field_output_test.hpp | 0
.../full_code/field_single_to_double.cpp | 0
.../full_code/field_single_to_double.hpp | 0
{bfps/cpp => cpp}/full_code/field_test.cpp | 0
{bfps/cpp => cpp}/full_code/field_test.hpp | 0
{bfps/cpp => cpp}/full_code/filter_test.cpp | 0
{bfps/cpp => cpp}/full_code/filter_test.hpp | 0
{bfps/cpp => cpp}/full_code/get_rfields.cpp | 0
{bfps/cpp => cpp}/full_code/get_rfields.hpp | 0
.../full_code/joint_acc_vel_stats.cpp | 0
.../full_code/joint_acc_vel_stats.hpp | 0
{bfps/cpp => cpp}/full_code/main_code.hpp | 0
.../full_code/native_binary_to_hdf5.cpp | 0
.../full_code/native_binary_to_hdf5.hpp | 0
{bfps/cpp => cpp}/full_code/postprocess.cpp | 0
{bfps/cpp => cpp}/full_code/postprocess.hpp | 0
{bfps/cpp => cpp}/full_code/resize.cpp | 0
{bfps/cpp => cpp}/full_code/resize.hpp | 0
.../cpp => cpp}/full_code/symmetrize_test.cpp | 0
.../cpp => cpp}/full_code/symmetrize_test.hpp | 0
{bfps/cpp => cpp}/full_code/test.cpp | 0
{bfps/cpp => cpp}/full_code/test.hpp | 0
.../full_code/test_interpolation.cpp | 0
.../full_code/test_interpolation.hpp | 0
{bfps/cpp => cpp}/hdf5_tools.cpp | 0
{bfps/cpp => cpp}/hdf5_tools.hpp | 0
{bfps/cpp => cpp}/kspace.cpp | 0
{bfps/cpp => cpp}/kspace.hpp | 0
{bfps/cpp => cpp}/omputils.hpp | 0
{bfps/cpp => cpp}/particles/.tocompile | 0
.../particles/abstract_particles_input.hpp | 0
.../particles/abstract_particles_output.hpp | 0
.../particles/abstract_particles_system.hpp | 0
.../particles/alltoall_exchanger.hpp | 0
{bfps/cpp => cpp}/particles/env_utils.hpp | 0
.../particles/lock_free_bool_array.hpp | 0
{bfps/cpp => cpp}/particles/p2p_computer.hpp | 0
.../particles/p2p_computer_empty.hpp | 0
{bfps/cpp => cpp}/particles/p2p_distr_mpi.hpp | 0
{bfps/cpp => cpp}/particles/p2p_tree.hpp | 0
.../particles/particles_adams_bashforth.hpp | 0
.../particles/particles_distr_mpi.hpp | 0
.../particles/particles_field_computer.hpp | 0
.../particles/particles_generic_interp.hpp | 0
.../particles/particles_inner_computer.cpp | 0
.../particles/particles_inner_computer.hpp | 0
.../particles_inner_computer_empty.hpp | 0
.../particles/particles_input_hdf5.hpp | 0
.../particles/particles_output_hdf5.hpp | 0
.../particles/particles_output_mpiio.hpp | 0
.../particles_output_sampling_hdf5.hpp | 0
.../particles/particles_sampling.hpp | 0
.../particles/particles_system.hpp | 0
.../particles/particles_system_builder.hpp | 0
.../cpp => cpp}/particles/particles_utils.hpp | 0
{bfps/cpp => cpp}/scope_timer.cpp | 0
{bfps/cpp => cpp}/scope_timer.hpp | 0
{bfps/cpp => cpp}/shared_array.hpp | 0
{bfps/cpp => cpp}/spline.hpp | 0
{bfps/cpp => cpp}/spline_n1.cpp | 0
{bfps/cpp => cpp}/spline_n1.hpp | 0
{bfps/cpp => cpp}/spline_n10.cpp | 0
{bfps/cpp => cpp}/spline_n10.hpp | 0
{bfps/cpp => cpp}/spline_n2.cpp | 0
{bfps/cpp => cpp}/spline_n2.hpp | 0
{bfps/cpp => cpp}/spline_n3.cpp | 0
{bfps/cpp => cpp}/spline_n3.hpp | 0
{bfps/cpp => cpp}/spline_n4.cpp | 0
{bfps/cpp => cpp}/spline_n4.hpp | 0
{bfps/cpp => cpp}/spline_n5.cpp | 0
{bfps/cpp => cpp}/spline_n5.hpp | 0
{bfps/cpp => cpp}/spline_n6.cpp | 0
{bfps/cpp => cpp}/spline_n6.hpp | 0
{bfps/cpp => cpp}/spline_n7.cpp | 0
{bfps/cpp => cpp}/spline_n7.hpp | 0
{bfps/cpp => cpp}/spline_n8.cpp | 0
{bfps/cpp => cpp}/spline_n8.hpp | 0
{bfps/cpp => cpp}/spline_n9.cpp | 0
{bfps/cpp => cpp}/spline_n9.hpp | 0
{bfps/cpp => cpp}/vorticity_equation.cpp | 0
{bfps/cpp => cpp}/vorticity_equation.hpp | 0
machine_settings_py.py | 63 -------------------
setup.py | 4 +-
115 files changed, 9 insertions(+), 69 deletions(-)
rename {bfps/cpp => cpp}/Lagrange_polys.cpp (100%)
rename {bfps/cpp => cpp}/Lagrange_polys.hpp (100%)
rename {bfps/cpp => cpp}/base.hpp (100%)
rename {bfps/cpp => cpp}/bfps_timer.hpp (100%)
rename {bfps/cpp => cpp}/fftw_interface.hpp (100%)
rename {bfps/cpp => cpp}/fftw_tools.cpp (100%)
rename {bfps/cpp => cpp}/fftw_tools.hpp (100%)
rename {bfps/cpp => cpp}/field.cpp (100%)
rename {bfps/cpp => cpp}/field.hpp (100%)
rename {bfps/cpp => cpp}/field_binary_IO.cpp (100%)
rename {bfps/cpp => cpp}/field_binary_IO.hpp (100%)
rename {bfps/cpp => cpp}/field_layout.cpp (100%)
rename {bfps/cpp => cpp}/field_layout.hpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVE.cpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVE.hpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVE_field_stats.cpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVE_field_stats.hpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVE_no_output.hpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVEcomplex_particles.cpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVEcomplex_particles.hpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVEp_extra_sampling.cpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVEp_extra_sampling.hpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVEparticles.cpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVEparticles.hpp (100%)
rename {bfps/cpp => cpp}/full_code/NSVEparticles_no_output.hpp (100%)
rename {bfps/cpp => cpp}/full_code/code_base.cpp (100%)
rename {bfps/cpp => cpp}/full_code/code_base.hpp (100%)
rename {bfps/cpp => cpp}/full_code/codes_with_no_output.hpp (100%)
rename {bfps/cpp => cpp}/full_code/direct_numerical_simulation.cpp (100%)
rename {bfps/cpp => cpp}/full_code/direct_numerical_simulation.hpp (100%)
rename {bfps/cpp => cpp}/full_code/field_output_test.cpp (100%)
rename {bfps/cpp => cpp}/full_code/field_output_test.hpp (100%)
rename {bfps/cpp => cpp}/full_code/field_single_to_double.cpp (100%)
rename {bfps/cpp => cpp}/full_code/field_single_to_double.hpp (100%)
rename {bfps/cpp => cpp}/full_code/field_test.cpp (100%)
rename {bfps/cpp => cpp}/full_code/field_test.hpp (100%)
rename {bfps/cpp => cpp}/full_code/filter_test.cpp (100%)
rename {bfps/cpp => cpp}/full_code/filter_test.hpp (100%)
rename {bfps/cpp => cpp}/full_code/get_rfields.cpp (100%)
rename {bfps/cpp => cpp}/full_code/get_rfields.hpp (100%)
rename {bfps/cpp => cpp}/full_code/joint_acc_vel_stats.cpp (100%)
rename {bfps/cpp => cpp}/full_code/joint_acc_vel_stats.hpp (100%)
rename {bfps/cpp => cpp}/full_code/main_code.hpp (100%)
rename {bfps/cpp => cpp}/full_code/native_binary_to_hdf5.cpp (100%)
rename {bfps/cpp => cpp}/full_code/native_binary_to_hdf5.hpp (100%)
rename {bfps/cpp => cpp}/full_code/postprocess.cpp (100%)
rename {bfps/cpp => cpp}/full_code/postprocess.hpp (100%)
rename {bfps/cpp => cpp}/full_code/resize.cpp (100%)
rename {bfps/cpp => cpp}/full_code/resize.hpp (100%)
rename {bfps/cpp => cpp}/full_code/symmetrize_test.cpp (100%)
rename {bfps/cpp => cpp}/full_code/symmetrize_test.hpp (100%)
rename {bfps/cpp => cpp}/full_code/test.cpp (100%)
rename {bfps/cpp => cpp}/full_code/test.hpp (100%)
rename {bfps/cpp => cpp}/full_code/test_interpolation.cpp (100%)
rename {bfps/cpp => cpp}/full_code/test_interpolation.hpp (100%)
rename {bfps/cpp => cpp}/hdf5_tools.cpp (100%)
rename {bfps/cpp => cpp}/hdf5_tools.hpp (100%)
rename {bfps/cpp => cpp}/kspace.cpp (100%)
rename {bfps/cpp => cpp}/kspace.hpp (100%)
rename {bfps/cpp => cpp}/omputils.hpp (100%)
rename {bfps/cpp => cpp}/particles/.tocompile (100%)
rename {bfps/cpp => cpp}/particles/abstract_particles_input.hpp (100%)
rename {bfps/cpp => cpp}/particles/abstract_particles_output.hpp (100%)
rename {bfps/cpp => cpp}/particles/abstract_particles_system.hpp (100%)
rename {bfps/cpp => cpp}/particles/alltoall_exchanger.hpp (100%)
rename {bfps/cpp => cpp}/particles/env_utils.hpp (100%)
rename {bfps/cpp => cpp}/particles/lock_free_bool_array.hpp (100%)
rename {bfps/cpp => cpp}/particles/p2p_computer.hpp (100%)
rename {bfps/cpp => cpp}/particles/p2p_computer_empty.hpp (100%)
rename {bfps/cpp => cpp}/particles/p2p_distr_mpi.hpp (100%)
rename {bfps/cpp => cpp}/particles/p2p_tree.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_adams_bashforth.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_distr_mpi.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_field_computer.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_generic_interp.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_inner_computer.cpp (100%)
rename {bfps/cpp => cpp}/particles/particles_inner_computer.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_inner_computer_empty.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_input_hdf5.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_output_hdf5.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_output_mpiio.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_output_sampling_hdf5.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_sampling.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_system.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_system_builder.hpp (100%)
rename {bfps/cpp => cpp}/particles/particles_utils.hpp (100%)
rename {bfps/cpp => cpp}/scope_timer.cpp (100%)
rename {bfps/cpp => cpp}/scope_timer.hpp (100%)
rename {bfps/cpp => cpp}/shared_array.hpp (100%)
rename {bfps/cpp => cpp}/spline.hpp (100%)
rename {bfps/cpp => cpp}/spline_n1.cpp (100%)
rename {bfps/cpp => cpp}/spline_n1.hpp (100%)
rename {bfps/cpp => cpp}/spline_n10.cpp (100%)
rename {bfps/cpp => cpp}/spline_n10.hpp (100%)
rename {bfps/cpp => cpp}/spline_n2.cpp (100%)
rename {bfps/cpp => cpp}/spline_n2.hpp (100%)
rename {bfps/cpp => cpp}/spline_n3.cpp (100%)
rename {bfps/cpp => cpp}/spline_n3.hpp (100%)
rename {bfps/cpp => cpp}/spline_n4.cpp (100%)
rename {bfps/cpp => cpp}/spline_n4.hpp (100%)
rename {bfps/cpp => cpp}/spline_n5.cpp (100%)
rename {bfps/cpp => cpp}/spline_n5.hpp (100%)
rename {bfps/cpp => cpp}/spline_n6.cpp (100%)
rename {bfps/cpp => cpp}/spline_n6.hpp (100%)
rename {bfps/cpp => cpp}/spline_n7.cpp (100%)
rename {bfps/cpp => cpp}/spline_n7.hpp (100%)
rename {bfps/cpp => cpp}/spline_n8.cpp (100%)
rename {bfps/cpp => cpp}/spline_n8.hpp (100%)
rename {bfps/cpp => cpp}/spline_n9.cpp (100%)
rename {bfps/cpp => cpp}/spline_n9.hpp (100%)
rename {bfps/cpp => cpp}/vorticity_equation.cpp (100%)
rename {bfps/cpp => cpp}/vorticity_equation.hpp (100%)
delete mode 100644 machine_settings_py.py
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2877199e..e125f8ee 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -97,10 +97,10 @@ get_property(ALL_LINK_DIRS DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY LINK_D
#####################################################################################
## Build the lib
-include_directories(${PROJECT_SOURCE_DIR}/bfps/cpp)
+include_directories(${PROJECT_SOURCE_DIR}/cpp)
-file(GLOB_RECURSE cpp_for_lib ${PROJECT_SOURCE_DIR}/bfps/*.cpp)
-file(GLOB_RECURSE hpp_for_lib ${PROJECT_SOURCE_DIR}/bfps/*.hpp)
+file(GLOB_RECURSE cpp_for_lib ${PROJECT_SOURCE_DIR}/*.cpp)
+file(GLOB_RECURSE hpp_for_lib ${PROJECT_SOURCE_DIR}/*.hpp)
LIST(APPEND source_files ${hpp_for_lib} ${cpp_for_lib})
add_library(bfps ${source_files})
@@ -108,7 +108,7 @@ add_library(bfps ${source_files})
target_link_libraries(bfps ${BFPS_LIBS})
install(TARGETS bfps EXPORT BFPS_EXPORT DESTINATION lib/ )
-install(DIRECTORY ${PROJECT_SOURCE_DIR}/bfps/cpp DESTINATION include/bfps/ FILES_MATCHING PATTERN "*.h*")
+install(DIRECTORY ${PROJECT_SOURCE_DIR}/cpp DESTINATION include/bfps/ FILES_MATCHING PATTERN "*.h*")
#####################################################################################
## Export the configuration
@@ -122,5 +122,6 @@ install(EXPORT BFPS_EXPORT DESTINATION lib/)
#####################################################################################
## Install the python wrapper
-install(CODE "execute_process(COMMAND python setup.py install --force --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})")
+file(COPY ${PROJECT_SOURCE_DIR}/bfps DESTINATION ${PROJECT_BINARY_DIR}/python/)
+install(CODE "execute_process(COMMAND python ${PROJECT_SOURCE_DIR}/setup.py install --force --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/python/)")
diff --git a/bfps/cpp/Lagrange_polys.cpp b/cpp/Lagrange_polys.cpp
similarity index 100%
rename from bfps/cpp/Lagrange_polys.cpp
rename to cpp/Lagrange_polys.cpp
diff --git a/bfps/cpp/Lagrange_polys.hpp b/cpp/Lagrange_polys.hpp
similarity index 100%
rename from bfps/cpp/Lagrange_polys.hpp
rename to cpp/Lagrange_polys.hpp
diff --git a/bfps/cpp/base.hpp b/cpp/base.hpp
similarity index 100%
rename from bfps/cpp/base.hpp
rename to cpp/base.hpp
diff --git a/bfps/cpp/bfps_timer.hpp b/cpp/bfps_timer.hpp
similarity index 100%
rename from bfps/cpp/bfps_timer.hpp
rename to cpp/bfps_timer.hpp
diff --git a/bfps/cpp/fftw_interface.hpp b/cpp/fftw_interface.hpp
similarity index 100%
rename from bfps/cpp/fftw_interface.hpp
rename to cpp/fftw_interface.hpp
diff --git a/bfps/cpp/fftw_tools.cpp b/cpp/fftw_tools.cpp
similarity index 100%
rename from bfps/cpp/fftw_tools.cpp
rename to cpp/fftw_tools.cpp
diff --git a/bfps/cpp/fftw_tools.hpp b/cpp/fftw_tools.hpp
similarity index 100%
rename from bfps/cpp/fftw_tools.hpp
rename to cpp/fftw_tools.hpp
diff --git a/bfps/cpp/field.cpp b/cpp/field.cpp
similarity index 100%
rename from bfps/cpp/field.cpp
rename to cpp/field.cpp
diff --git a/bfps/cpp/field.hpp b/cpp/field.hpp
similarity index 100%
rename from bfps/cpp/field.hpp
rename to cpp/field.hpp
diff --git a/bfps/cpp/field_binary_IO.cpp b/cpp/field_binary_IO.cpp
similarity index 100%
rename from bfps/cpp/field_binary_IO.cpp
rename to cpp/field_binary_IO.cpp
diff --git a/bfps/cpp/field_binary_IO.hpp b/cpp/field_binary_IO.hpp
similarity index 100%
rename from bfps/cpp/field_binary_IO.hpp
rename to cpp/field_binary_IO.hpp
diff --git a/bfps/cpp/field_layout.cpp b/cpp/field_layout.cpp
similarity index 100%
rename from bfps/cpp/field_layout.cpp
rename to cpp/field_layout.cpp
diff --git a/bfps/cpp/field_layout.hpp b/cpp/field_layout.hpp
similarity index 100%
rename from bfps/cpp/field_layout.hpp
rename to cpp/field_layout.hpp
diff --git a/bfps/cpp/full_code/NSVE.cpp b/cpp/full_code/NSVE.cpp
similarity index 100%
rename from bfps/cpp/full_code/NSVE.cpp
rename to cpp/full_code/NSVE.cpp
diff --git a/bfps/cpp/full_code/NSVE.hpp b/cpp/full_code/NSVE.hpp
similarity index 100%
rename from bfps/cpp/full_code/NSVE.hpp
rename to cpp/full_code/NSVE.hpp
diff --git a/bfps/cpp/full_code/NSVE_field_stats.cpp b/cpp/full_code/NSVE_field_stats.cpp
similarity index 100%
rename from bfps/cpp/full_code/NSVE_field_stats.cpp
rename to cpp/full_code/NSVE_field_stats.cpp
diff --git a/bfps/cpp/full_code/NSVE_field_stats.hpp b/cpp/full_code/NSVE_field_stats.hpp
similarity index 100%
rename from bfps/cpp/full_code/NSVE_field_stats.hpp
rename to cpp/full_code/NSVE_field_stats.hpp
diff --git a/bfps/cpp/full_code/NSVE_no_output.hpp b/cpp/full_code/NSVE_no_output.hpp
similarity index 100%
rename from bfps/cpp/full_code/NSVE_no_output.hpp
rename to cpp/full_code/NSVE_no_output.hpp
diff --git a/bfps/cpp/full_code/NSVEcomplex_particles.cpp b/cpp/full_code/NSVEcomplex_particles.cpp
similarity index 100%
rename from bfps/cpp/full_code/NSVEcomplex_particles.cpp
rename to cpp/full_code/NSVEcomplex_particles.cpp
diff --git a/bfps/cpp/full_code/NSVEcomplex_particles.hpp b/cpp/full_code/NSVEcomplex_particles.hpp
similarity index 100%
rename from bfps/cpp/full_code/NSVEcomplex_particles.hpp
rename to cpp/full_code/NSVEcomplex_particles.hpp
diff --git a/bfps/cpp/full_code/NSVEp_extra_sampling.cpp b/cpp/full_code/NSVEp_extra_sampling.cpp
similarity index 100%
rename from bfps/cpp/full_code/NSVEp_extra_sampling.cpp
rename to cpp/full_code/NSVEp_extra_sampling.cpp
diff --git a/bfps/cpp/full_code/NSVEp_extra_sampling.hpp b/cpp/full_code/NSVEp_extra_sampling.hpp
similarity index 100%
rename from bfps/cpp/full_code/NSVEp_extra_sampling.hpp
rename to cpp/full_code/NSVEp_extra_sampling.hpp
diff --git a/bfps/cpp/full_code/NSVEparticles.cpp b/cpp/full_code/NSVEparticles.cpp
similarity index 100%
rename from bfps/cpp/full_code/NSVEparticles.cpp
rename to cpp/full_code/NSVEparticles.cpp
diff --git a/bfps/cpp/full_code/NSVEparticles.hpp b/cpp/full_code/NSVEparticles.hpp
similarity index 100%
rename from bfps/cpp/full_code/NSVEparticles.hpp
rename to cpp/full_code/NSVEparticles.hpp
diff --git a/bfps/cpp/full_code/NSVEparticles_no_output.hpp b/cpp/full_code/NSVEparticles_no_output.hpp
similarity index 100%
rename from bfps/cpp/full_code/NSVEparticles_no_output.hpp
rename to cpp/full_code/NSVEparticles_no_output.hpp
diff --git a/bfps/cpp/full_code/code_base.cpp b/cpp/full_code/code_base.cpp
similarity index 100%
rename from bfps/cpp/full_code/code_base.cpp
rename to cpp/full_code/code_base.cpp
diff --git a/bfps/cpp/full_code/code_base.hpp b/cpp/full_code/code_base.hpp
similarity index 100%
rename from bfps/cpp/full_code/code_base.hpp
rename to cpp/full_code/code_base.hpp
diff --git a/bfps/cpp/full_code/codes_with_no_output.hpp b/cpp/full_code/codes_with_no_output.hpp
similarity index 100%
rename from bfps/cpp/full_code/codes_with_no_output.hpp
rename to cpp/full_code/codes_with_no_output.hpp
diff --git a/bfps/cpp/full_code/direct_numerical_simulation.cpp b/cpp/full_code/direct_numerical_simulation.cpp
similarity index 100%
rename from bfps/cpp/full_code/direct_numerical_simulation.cpp
rename to cpp/full_code/direct_numerical_simulation.cpp
diff --git a/bfps/cpp/full_code/direct_numerical_simulation.hpp b/cpp/full_code/direct_numerical_simulation.hpp
similarity index 100%
rename from bfps/cpp/full_code/direct_numerical_simulation.hpp
rename to cpp/full_code/direct_numerical_simulation.hpp
diff --git a/bfps/cpp/full_code/field_output_test.cpp b/cpp/full_code/field_output_test.cpp
similarity index 100%
rename from bfps/cpp/full_code/field_output_test.cpp
rename to cpp/full_code/field_output_test.cpp
diff --git a/bfps/cpp/full_code/field_output_test.hpp b/cpp/full_code/field_output_test.hpp
similarity index 100%
rename from bfps/cpp/full_code/field_output_test.hpp
rename to cpp/full_code/field_output_test.hpp
diff --git a/bfps/cpp/full_code/field_single_to_double.cpp b/cpp/full_code/field_single_to_double.cpp
similarity index 100%
rename from bfps/cpp/full_code/field_single_to_double.cpp
rename to cpp/full_code/field_single_to_double.cpp
diff --git a/bfps/cpp/full_code/field_single_to_double.hpp b/cpp/full_code/field_single_to_double.hpp
similarity index 100%
rename from bfps/cpp/full_code/field_single_to_double.hpp
rename to cpp/full_code/field_single_to_double.hpp
diff --git a/bfps/cpp/full_code/field_test.cpp b/cpp/full_code/field_test.cpp
similarity index 100%
rename from bfps/cpp/full_code/field_test.cpp
rename to cpp/full_code/field_test.cpp
diff --git a/bfps/cpp/full_code/field_test.hpp b/cpp/full_code/field_test.hpp
similarity index 100%
rename from bfps/cpp/full_code/field_test.hpp
rename to cpp/full_code/field_test.hpp
diff --git a/bfps/cpp/full_code/filter_test.cpp b/cpp/full_code/filter_test.cpp
similarity index 100%
rename from bfps/cpp/full_code/filter_test.cpp
rename to cpp/full_code/filter_test.cpp
diff --git a/bfps/cpp/full_code/filter_test.hpp b/cpp/full_code/filter_test.hpp
similarity index 100%
rename from bfps/cpp/full_code/filter_test.hpp
rename to cpp/full_code/filter_test.hpp
diff --git a/bfps/cpp/full_code/get_rfields.cpp b/cpp/full_code/get_rfields.cpp
similarity index 100%
rename from bfps/cpp/full_code/get_rfields.cpp
rename to cpp/full_code/get_rfields.cpp
diff --git a/bfps/cpp/full_code/get_rfields.hpp b/cpp/full_code/get_rfields.hpp
similarity index 100%
rename from bfps/cpp/full_code/get_rfields.hpp
rename to cpp/full_code/get_rfields.hpp
diff --git a/bfps/cpp/full_code/joint_acc_vel_stats.cpp b/cpp/full_code/joint_acc_vel_stats.cpp
similarity index 100%
rename from bfps/cpp/full_code/joint_acc_vel_stats.cpp
rename to cpp/full_code/joint_acc_vel_stats.cpp
diff --git a/bfps/cpp/full_code/joint_acc_vel_stats.hpp b/cpp/full_code/joint_acc_vel_stats.hpp
similarity index 100%
rename from bfps/cpp/full_code/joint_acc_vel_stats.hpp
rename to cpp/full_code/joint_acc_vel_stats.hpp
diff --git a/bfps/cpp/full_code/main_code.hpp b/cpp/full_code/main_code.hpp
similarity index 100%
rename from bfps/cpp/full_code/main_code.hpp
rename to cpp/full_code/main_code.hpp
diff --git a/bfps/cpp/full_code/native_binary_to_hdf5.cpp b/cpp/full_code/native_binary_to_hdf5.cpp
similarity index 100%
rename from bfps/cpp/full_code/native_binary_to_hdf5.cpp
rename to cpp/full_code/native_binary_to_hdf5.cpp
diff --git a/bfps/cpp/full_code/native_binary_to_hdf5.hpp b/cpp/full_code/native_binary_to_hdf5.hpp
similarity index 100%
rename from bfps/cpp/full_code/native_binary_to_hdf5.hpp
rename to cpp/full_code/native_binary_to_hdf5.hpp
diff --git a/bfps/cpp/full_code/postprocess.cpp b/cpp/full_code/postprocess.cpp
similarity index 100%
rename from bfps/cpp/full_code/postprocess.cpp
rename to cpp/full_code/postprocess.cpp
diff --git a/bfps/cpp/full_code/postprocess.hpp b/cpp/full_code/postprocess.hpp
similarity index 100%
rename from bfps/cpp/full_code/postprocess.hpp
rename to cpp/full_code/postprocess.hpp
diff --git a/bfps/cpp/full_code/resize.cpp b/cpp/full_code/resize.cpp
similarity index 100%
rename from bfps/cpp/full_code/resize.cpp
rename to cpp/full_code/resize.cpp
diff --git a/bfps/cpp/full_code/resize.hpp b/cpp/full_code/resize.hpp
similarity index 100%
rename from bfps/cpp/full_code/resize.hpp
rename to cpp/full_code/resize.hpp
diff --git a/bfps/cpp/full_code/symmetrize_test.cpp b/cpp/full_code/symmetrize_test.cpp
similarity index 100%
rename from bfps/cpp/full_code/symmetrize_test.cpp
rename to cpp/full_code/symmetrize_test.cpp
diff --git a/bfps/cpp/full_code/symmetrize_test.hpp b/cpp/full_code/symmetrize_test.hpp
similarity index 100%
rename from bfps/cpp/full_code/symmetrize_test.hpp
rename to cpp/full_code/symmetrize_test.hpp
diff --git a/bfps/cpp/full_code/test.cpp b/cpp/full_code/test.cpp
similarity index 100%
rename from bfps/cpp/full_code/test.cpp
rename to cpp/full_code/test.cpp
diff --git a/bfps/cpp/full_code/test.hpp b/cpp/full_code/test.hpp
similarity index 100%
rename from bfps/cpp/full_code/test.hpp
rename to cpp/full_code/test.hpp
diff --git a/bfps/cpp/full_code/test_interpolation.cpp b/cpp/full_code/test_interpolation.cpp
similarity index 100%
rename from bfps/cpp/full_code/test_interpolation.cpp
rename to cpp/full_code/test_interpolation.cpp
diff --git a/bfps/cpp/full_code/test_interpolation.hpp b/cpp/full_code/test_interpolation.hpp
similarity index 100%
rename from bfps/cpp/full_code/test_interpolation.hpp
rename to cpp/full_code/test_interpolation.hpp
diff --git a/bfps/cpp/hdf5_tools.cpp b/cpp/hdf5_tools.cpp
similarity index 100%
rename from bfps/cpp/hdf5_tools.cpp
rename to cpp/hdf5_tools.cpp
diff --git a/bfps/cpp/hdf5_tools.hpp b/cpp/hdf5_tools.hpp
similarity index 100%
rename from bfps/cpp/hdf5_tools.hpp
rename to cpp/hdf5_tools.hpp
diff --git a/bfps/cpp/kspace.cpp b/cpp/kspace.cpp
similarity index 100%
rename from bfps/cpp/kspace.cpp
rename to cpp/kspace.cpp
diff --git a/bfps/cpp/kspace.hpp b/cpp/kspace.hpp
similarity index 100%
rename from bfps/cpp/kspace.hpp
rename to cpp/kspace.hpp
diff --git a/bfps/cpp/omputils.hpp b/cpp/omputils.hpp
similarity index 100%
rename from bfps/cpp/omputils.hpp
rename to cpp/omputils.hpp
diff --git a/bfps/cpp/particles/.tocompile b/cpp/particles/.tocompile
similarity index 100%
rename from bfps/cpp/particles/.tocompile
rename to cpp/particles/.tocompile
diff --git a/bfps/cpp/particles/abstract_particles_input.hpp b/cpp/particles/abstract_particles_input.hpp
similarity index 100%
rename from bfps/cpp/particles/abstract_particles_input.hpp
rename to cpp/particles/abstract_particles_input.hpp
diff --git a/bfps/cpp/particles/abstract_particles_output.hpp b/cpp/particles/abstract_particles_output.hpp
similarity index 100%
rename from bfps/cpp/particles/abstract_particles_output.hpp
rename to cpp/particles/abstract_particles_output.hpp
diff --git a/bfps/cpp/particles/abstract_particles_system.hpp b/cpp/particles/abstract_particles_system.hpp
similarity index 100%
rename from bfps/cpp/particles/abstract_particles_system.hpp
rename to cpp/particles/abstract_particles_system.hpp
diff --git a/bfps/cpp/particles/alltoall_exchanger.hpp b/cpp/particles/alltoall_exchanger.hpp
similarity index 100%
rename from bfps/cpp/particles/alltoall_exchanger.hpp
rename to cpp/particles/alltoall_exchanger.hpp
diff --git a/bfps/cpp/particles/env_utils.hpp b/cpp/particles/env_utils.hpp
similarity index 100%
rename from bfps/cpp/particles/env_utils.hpp
rename to cpp/particles/env_utils.hpp
diff --git a/bfps/cpp/particles/lock_free_bool_array.hpp b/cpp/particles/lock_free_bool_array.hpp
similarity index 100%
rename from bfps/cpp/particles/lock_free_bool_array.hpp
rename to cpp/particles/lock_free_bool_array.hpp
diff --git a/bfps/cpp/particles/p2p_computer.hpp b/cpp/particles/p2p_computer.hpp
similarity index 100%
rename from bfps/cpp/particles/p2p_computer.hpp
rename to cpp/particles/p2p_computer.hpp
diff --git a/bfps/cpp/particles/p2p_computer_empty.hpp b/cpp/particles/p2p_computer_empty.hpp
similarity index 100%
rename from bfps/cpp/particles/p2p_computer_empty.hpp
rename to cpp/particles/p2p_computer_empty.hpp
diff --git a/bfps/cpp/particles/p2p_distr_mpi.hpp b/cpp/particles/p2p_distr_mpi.hpp
similarity index 100%
rename from bfps/cpp/particles/p2p_distr_mpi.hpp
rename to cpp/particles/p2p_distr_mpi.hpp
diff --git a/bfps/cpp/particles/p2p_tree.hpp b/cpp/particles/p2p_tree.hpp
similarity index 100%
rename from bfps/cpp/particles/p2p_tree.hpp
rename to cpp/particles/p2p_tree.hpp
diff --git a/bfps/cpp/particles/particles_adams_bashforth.hpp b/cpp/particles/particles_adams_bashforth.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_adams_bashforth.hpp
rename to cpp/particles/particles_adams_bashforth.hpp
diff --git a/bfps/cpp/particles/particles_distr_mpi.hpp b/cpp/particles/particles_distr_mpi.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_distr_mpi.hpp
rename to cpp/particles/particles_distr_mpi.hpp
diff --git a/bfps/cpp/particles/particles_field_computer.hpp b/cpp/particles/particles_field_computer.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_field_computer.hpp
rename to cpp/particles/particles_field_computer.hpp
diff --git a/bfps/cpp/particles/particles_generic_interp.hpp b/cpp/particles/particles_generic_interp.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_generic_interp.hpp
rename to cpp/particles/particles_generic_interp.hpp
diff --git a/bfps/cpp/particles/particles_inner_computer.cpp b/cpp/particles/particles_inner_computer.cpp
similarity index 100%
rename from bfps/cpp/particles/particles_inner_computer.cpp
rename to cpp/particles/particles_inner_computer.cpp
diff --git a/bfps/cpp/particles/particles_inner_computer.hpp b/cpp/particles/particles_inner_computer.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_inner_computer.hpp
rename to cpp/particles/particles_inner_computer.hpp
diff --git a/bfps/cpp/particles/particles_inner_computer_empty.hpp b/cpp/particles/particles_inner_computer_empty.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_inner_computer_empty.hpp
rename to cpp/particles/particles_inner_computer_empty.hpp
diff --git a/bfps/cpp/particles/particles_input_hdf5.hpp b/cpp/particles/particles_input_hdf5.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_input_hdf5.hpp
rename to cpp/particles/particles_input_hdf5.hpp
diff --git a/bfps/cpp/particles/particles_output_hdf5.hpp b/cpp/particles/particles_output_hdf5.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_output_hdf5.hpp
rename to cpp/particles/particles_output_hdf5.hpp
diff --git a/bfps/cpp/particles/particles_output_mpiio.hpp b/cpp/particles/particles_output_mpiio.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_output_mpiio.hpp
rename to cpp/particles/particles_output_mpiio.hpp
diff --git a/bfps/cpp/particles/particles_output_sampling_hdf5.hpp b/cpp/particles/particles_output_sampling_hdf5.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_output_sampling_hdf5.hpp
rename to cpp/particles/particles_output_sampling_hdf5.hpp
diff --git a/bfps/cpp/particles/particles_sampling.hpp b/cpp/particles/particles_sampling.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_sampling.hpp
rename to cpp/particles/particles_sampling.hpp
diff --git a/bfps/cpp/particles/particles_system.hpp b/cpp/particles/particles_system.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_system.hpp
rename to cpp/particles/particles_system.hpp
diff --git a/bfps/cpp/particles/particles_system_builder.hpp b/cpp/particles/particles_system_builder.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_system_builder.hpp
rename to cpp/particles/particles_system_builder.hpp
diff --git a/bfps/cpp/particles/particles_utils.hpp b/cpp/particles/particles_utils.hpp
similarity index 100%
rename from bfps/cpp/particles/particles_utils.hpp
rename to cpp/particles/particles_utils.hpp
diff --git a/bfps/cpp/scope_timer.cpp b/cpp/scope_timer.cpp
similarity index 100%
rename from bfps/cpp/scope_timer.cpp
rename to cpp/scope_timer.cpp
diff --git a/bfps/cpp/scope_timer.hpp b/cpp/scope_timer.hpp
similarity index 100%
rename from bfps/cpp/scope_timer.hpp
rename to cpp/scope_timer.hpp
diff --git a/bfps/cpp/shared_array.hpp b/cpp/shared_array.hpp
similarity index 100%
rename from bfps/cpp/shared_array.hpp
rename to cpp/shared_array.hpp
diff --git a/bfps/cpp/spline.hpp b/cpp/spline.hpp
similarity index 100%
rename from bfps/cpp/spline.hpp
rename to cpp/spline.hpp
diff --git a/bfps/cpp/spline_n1.cpp b/cpp/spline_n1.cpp
similarity index 100%
rename from bfps/cpp/spline_n1.cpp
rename to cpp/spline_n1.cpp
diff --git a/bfps/cpp/spline_n1.hpp b/cpp/spline_n1.hpp
similarity index 100%
rename from bfps/cpp/spline_n1.hpp
rename to cpp/spline_n1.hpp
diff --git a/bfps/cpp/spline_n10.cpp b/cpp/spline_n10.cpp
similarity index 100%
rename from bfps/cpp/spline_n10.cpp
rename to cpp/spline_n10.cpp
diff --git a/bfps/cpp/spline_n10.hpp b/cpp/spline_n10.hpp
similarity index 100%
rename from bfps/cpp/spline_n10.hpp
rename to cpp/spline_n10.hpp
diff --git a/bfps/cpp/spline_n2.cpp b/cpp/spline_n2.cpp
similarity index 100%
rename from bfps/cpp/spline_n2.cpp
rename to cpp/spline_n2.cpp
diff --git a/bfps/cpp/spline_n2.hpp b/cpp/spline_n2.hpp
similarity index 100%
rename from bfps/cpp/spline_n2.hpp
rename to cpp/spline_n2.hpp
diff --git a/bfps/cpp/spline_n3.cpp b/cpp/spline_n3.cpp
similarity index 100%
rename from bfps/cpp/spline_n3.cpp
rename to cpp/spline_n3.cpp
diff --git a/bfps/cpp/spline_n3.hpp b/cpp/spline_n3.hpp
similarity index 100%
rename from bfps/cpp/spline_n3.hpp
rename to cpp/spline_n3.hpp
diff --git a/bfps/cpp/spline_n4.cpp b/cpp/spline_n4.cpp
similarity index 100%
rename from bfps/cpp/spline_n4.cpp
rename to cpp/spline_n4.cpp
diff --git a/bfps/cpp/spline_n4.hpp b/cpp/spline_n4.hpp
similarity index 100%
rename from bfps/cpp/spline_n4.hpp
rename to cpp/spline_n4.hpp
diff --git a/bfps/cpp/spline_n5.cpp b/cpp/spline_n5.cpp
similarity index 100%
rename from bfps/cpp/spline_n5.cpp
rename to cpp/spline_n5.cpp
diff --git a/bfps/cpp/spline_n5.hpp b/cpp/spline_n5.hpp
similarity index 100%
rename from bfps/cpp/spline_n5.hpp
rename to cpp/spline_n5.hpp
diff --git a/bfps/cpp/spline_n6.cpp b/cpp/spline_n6.cpp
similarity index 100%
rename from bfps/cpp/spline_n6.cpp
rename to cpp/spline_n6.cpp
diff --git a/bfps/cpp/spline_n6.hpp b/cpp/spline_n6.hpp
similarity index 100%
rename from bfps/cpp/spline_n6.hpp
rename to cpp/spline_n6.hpp
diff --git a/bfps/cpp/spline_n7.cpp b/cpp/spline_n7.cpp
similarity index 100%
rename from bfps/cpp/spline_n7.cpp
rename to cpp/spline_n7.cpp
diff --git a/bfps/cpp/spline_n7.hpp b/cpp/spline_n7.hpp
similarity index 100%
rename from bfps/cpp/spline_n7.hpp
rename to cpp/spline_n7.hpp
diff --git a/bfps/cpp/spline_n8.cpp b/cpp/spline_n8.cpp
similarity index 100%
rename from bfps/cpp/spline_n8.cpp
rename to cpp/spline_n8.cpp
diff --git a/bfps/cpp/spline_n8.hpp b/cpp/spline_n8.hpp
similarity index 100%
rename from bfps/cpp/spline_n8.hpp
rename to cpp/spline_n8.hpp
diff --git a/bfps/cpp/spline_n9.cpp b/cpp/spline_n9.cpp
similarity index 100%
rename from bfps/cpp/spline_n9.cpp
rename to cpp/spline_n9.cpp
diff --git a/bfps/cpp/spline_n9.hpp b/cpp/spline_n9.hpp
similarity index 100%
rename from bfps/cpp/spline_n9.hpp
rename to cpp/spline_n9.hpp
diff --git a/bfps/cpp/vorticity_equation.cpp b/cpp/vorticity_equation.cpp
similarity index 100%
rename from bfps/cpp/vorticity_equation.cpp
rename to cpp/vorticity_equation.cpp
diff --git a/bfps/cpp/vorticity_equation.hpp b/cpp/vorticity_equation.hpp
similarity index 100%
rename from bfps/cpp/vorticity_equation.hpp
rename to cpp/vorticity_equation.hpp
diff --git a/machine_settings_py.py b/machine_settings_py.py
deleted file mode 100644
index 787f1d5a..00000000
--- a/machine_settings_py.py
+++ /dev/null
@@ -1,63 +0,0 @@
-#######################################################################
-# #
-# Copyright 2015 Max Planck Institute #
-# for Dynamics and Self-Organization #
-# #
-# This file is part of bfps. #
-# #
-# bfps is free software: you can redistribute it and/or modify #
-# it under the terms of the GNU General Public License as published #
-# by the Free Software Foundation, either version 3 of the License, #
-# or (at your option) any later version. #
-# #
-# bfps is distributed in the hope that it will be useful, #
-# but WITHOUT ANY WARRANTY; without even the implied warranty of #
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
-# GNU General Public License for more details. #
-# #
-# You should have received a copy of the GNU General Public License #
-# along with bfps. If not, see <http://www.gnu.org/licenses/> #
-# #
-# Contact: Cristian.Lalescu@ds.mpg.de #
-# #
-#######################################################################
-
-
-
-import os
-
-########################################################################
-# these lists should be adapted for your different environment(s)
-# personally, I have access to setups where my home folder is shared
-# between different machines, including cluster and desktop, therefore
-# I check the host name when choosing libraries etc.
-# feel free to do your own thing to the copy of this file placed in
-# ./config/bfps
-########################################################################
-
-hostname = os.getenv('HOSTNAME')
-
-compiler = 'g++'
-extra_compile_args = ['-Wall', '-O2', '-g', '-mtune=native', '-ffast-math', '-std=c++11']
-extra_libraries = ['hdf5']
-include_dirs = []
-library_dirs = []
-
-if hostname == 'chichi-G':
- include_dirs = ['/usr/local/include',
- '/usr/include/mpich']
- library_dirs = ['/usr/local/lib',
- '/usr/lib/mpich']
- extra_libraries += ['mpich']
-
-if hostname in ['tolima', 'misti']:
- local_install_dir = '/scratch.local/chichi/installs'
-
- include_dirs = ['/usr/lib64/mpi/gcc/openmpi/include',
- os.path.join(local_install_dir, 'include')]
-
- library_dirs = ['/usr/lib64/mpi/gcc/openmpi/lib64',
- os.path.join(local_install_dir, 'lib'),
- os.path.join(local_install_dir, 'lib64')]
- extra_libraries += ['mpi_cxx', 'mpi']
-
diff --git a/setup.py b/setup.py
index 2a031518..3d91061d 100644
--- a/setup.py
+++ b/setup.py
@@ -146,9 +146,11 @@ setup(
version = VERSION,
########################################################################
# useless stuff folows
+# if anyone knows how to open the README when calling this script from
+# cmake, please let me know.
########################################################################
description = 'Big Fluid and Particle Simulator',
- long_description = open('README.rst', 'r').read(),
+ #long_description = open('${PROJECT_SOURCE_DIR}/README.rst', 'r').read(),
author = AUTHOR,
author_email = AUTHOR_EMAIL,
license = 'GPL version 3.0')
--
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