diff --git a/CMakeLists.txt b/CMakeLists.txt
index 81488582070a7bcd45dc009b9e2cce835d9a4bde..a2a18ce081039e32df522b993c3a60e9e5e78514 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -31,6 +31,14 @@ project(TurTLE)
string(TIMESTAMP BUILD_DATE "%Y-%m-%d")
+#####################################################################################
+## CXX Standard
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+#####################################################################################
+
+
#####################################################################################
## Python and version
@@ -49,33 +57,32 @@ execute_process(
project(TurTLE
VERSION ${TURTLE_VERSION}
LANGUAGES C CXX)
-#####################################################################################
-#####################################################################################
-## CXX Standard
+add_library(TurTLE STATIC "")
-set(CMAKE_CXX_STANDARD 17)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
+target_compile_options(TurTLE PRIVATE $<$<CONFIG:DEBUG>:-O1>)
#####################################################################################
#####################################################################################
## OpenMP
find_package(OpenMP REQUIRED)
+target_link_libraries(TurTLE
+ PRIVATE
+ OpenMP::OpenMP_CXX)
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
#####################################################################################
#####################################################################################
## MPI
find_package(MPI REQUIRED)
+target_link_libraries(TurTLE
+ PRIVATE
+ MPI::MPI_C)
-set(CMAKE_CXX_COMPILE_FLAGS "${CMAKE_CXX_COMPILE_FLAGS} ${MPI_CXX_COMPILE_OPTIONS}")
-set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MPI_CXX_LINK_FLAGS}")
-include_directories(${MPI_CXX_INCLUDE_DIRS})
-add_definitions(${MPI_CXX_COMPILE_DEFINITIONS})
+#include_directories(${MPI_CXX_INCLUDE_DIRS})
+#add_definitions(${MPI_CXX_COMPILE_DEFINITIONS})
# set(CMAKE_CXX_EXTENSIONS OFF)
#####################################################################################
@@ -212,13 +219,19 @@ endif()
set(HDF5_PREFER_PARALLEL TRUE)
set(HDF5_NO_FIND_PACKAGE_CONFIG_FILE TRUE)
-find_package(HDF5 REQUIRED)
+find_package(HDF5 REQUIRED COMPONENTS C)
+target_link_libraries(TurTLE
+ PRIVATE
+ HDF5::HDF5)
+target_include_directories(TurTLE
+ PUBLIC
+ ${HDF5_C_INCLUDE_DIR})
-message(STATUS "HDF5_C_INCLUDE_DIRS ${HDF5_C_INCLUDE_DIRS}")
+#message(STATUS "HDF5_C_INCLUDE_DIRS ${HDF5_C_INCLUDE_DIRS}")
-include_directories(${HDF5_C_INCLUDE_DIRS})
-add_definitions(${HDF5_C_DEFINITIONS})
-list(APPEND TURTLE_LIBS "${HDF5_C_LIBRARIES}")
+#include_directories(${HDF5_C_INCLUDE_DIRS})
+#add_definitions(${HDF5_C_DEFINITIONS})
+#list(APPEND TURTLE_LIBS "${HDF5_C_LIBRARIES}")
option(TURTLE_HDF5_USE_SZIP "Set to on to also link against SZIP" OFF)
@@ -227,7 +240,10 @@ if(TURTLE_HDF5_USE_SZIP)
if(TURTLE_HDF5_SZIP_LIB_PATH)
link_directories(${TURTLE_HDF5_SZIP_LIB_PATH})
endif()
- list(APPEND TURTLE_LIBS "z")
+ #list(APPEND TURTLE_LIBS "z")
+ target_link_libraries(TurTLE
+ PRIVATE
+ z)
endif()
#####################################################################################
@@ -237,8 +253,9 @@ endif()
find_package(GSL)
if (GSL_FOUND)
- include_directories(${GSL_INCLUDE_DIRS})
- list(APPEND TURTLE_LIBS "${GSL_LIBRARIES}")
+ target_link_libraries(TurTLE
+ PRIVATE
+ GSL::gsl)
endif()
#####################################################################################
@@ -252,9 +269,8 @@ if(DEFINED ENV{PINCHECK_ROOT})
HINTS ${PINCHECK_INCLUDE})
if(PINCHECK_HEADER)
message("found pincheck header ${PINCHECK_HEADER}")
- include_directories($ENV{PINCHECK_ROOT}/include)
- #add_definitions(-DPINCHECK_FOUND)
- set(CMAKE_CXX_COMPILE_FLAGS "${CMAKE_CXX_COMPILE_FLAGS} -DPINCHECK_FOUND")
+ target_include_directories(TurTLE PUBLIC $ENV{PINCHECK_ROOT}/include)
+ target_compile_definitions(TurTLE PRIVATE PINCHECK_FOUND)
endif()
endif()
#####################################################################################
@@ -311,9 +327,6 @@ find_library(
set(TURTLE_LIBS ${FFTW_MPI} ${TURTLE_LIBS})
#####################################################################################
-list(APPEND TURTLE_LIBS "${MPI_CXX_LIBRARIES}")
-list(APPEND TURTLE_LIBS "${OpenMP_CXX_LIB_NAMES}")
-
#####################################################################################
## Get the links and include from deps
@@ -322,194 +335,11 @@ get_property(ALL_LINK_DIRS DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY LINK_D
#####################################################################################
#####################################################################################
-## Build the lib
+## Add sources
include_directories(${PROJECT_SOURCE_DIR}/cpp)
-#file(GLOB_RECURSE cpp_for_lib ${PROJECT_SOURCE_DIR}/*.cpp)
-set(cpp_for_lib
- ${PROJECT_SOURCE_DIR}/cpp/full_code/code_base.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/direct_numerical_simulation.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSE.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/static_field.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/kraichnan_field.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/joint_acc_vel_stats.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/pressure_stats.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/filter_test.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/field_test.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/write_filtered_test.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/dealias_test.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/Gauss_field_test.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/symmetrize_test.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/field_output_test.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/phase_shift_test.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test_tracer_set.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/get_rfields.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/get_velocity.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/get_3D_correlations.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/write_rpressure.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/bandpass_stats.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/field_single_to_double.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/resize.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE_field_stats.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/native_binary_to_hdf5.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/postprocess.cpp
- ${PROJECT_SOURCE_DIR}/cpp/base.cpp
- ${PROJECT_SOURCE_DIR}/cpp/field.cpp
- ${PROJECT_SOURCE_DIR}/cpp/kspace.cpp
- ${PROJECT_SOURCE_DIR}/cpp/field_layout.cpp
- ${PROJECT_SOURCE_DIR}/cpp/hdf5_tools.cpp
- ${PROJECT_SOURCE_DIR}/cpp/fftw_tools.cpp
- ${PROJECT_SOURCE_DIR}/cpp/vorticity_equation.cpp
- ${PROJECT_SOURCE_DIR}/cpp/field_binary_IO.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n0.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n1.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n2.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n3.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n4.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n5.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n6.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n7.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n8.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n9.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n10.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/Lagrange_polys.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/field_tinterpolator.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/particle_set.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/rhs/tracer_rhs.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/rhs/tracer_with_collision_counter_rhs.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particle_solver.cpp
- ${PROJECT_SOURCE_DIR}/cpp/scope_timer.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test_interpolation.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEparticles.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEcomplex_particles.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE_Stokes_particles.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEp_extra_sampling.cpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/inner/particles_inner_computer.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/ornstein_uhlenbeck_process.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/ou_vorticity_equation.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test_interpolation_methods.cpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test_particle_integration.cpp)
-
-set(hpp_for_lib
- ${PROJECT_SOURCE_DIR}/cpp/full_code/code_base.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/direct_numerical_simulation.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSE.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/static_field.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/kraichnan_field.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/joint_acc_vel_stats.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/pressure_stats.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/filter_test.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/dealias_test.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/Gauss_field_test.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/field_test.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/write_filtered_test.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/symmetrize_test.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/field_output_test.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/phase_shift_test.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test_tracer_set.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/get_rfields.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/get_velocity.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/get_3D_correlations.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/write_rpressure.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/bandpass_stats.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/field_single_to_double.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/resize.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE_field_stats.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/native_binary_to_hdf5.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/postprocess.hpp
- ${PROJECT_SOURCE_DIR}/cpp/field.hpp
- ${PROJECT_SOURCE_DIR}/cpp/kspace.hpp
- ${PROJECT_SOURCE_DIR}/cpp/field_layout.hpp
- ${PROJECT_SOURCE_DIR}/cpp/hdf5_tools.hpp
- ${PROJECT_SOURCE_DIR}/cpp/fftw_tools.hpp
- ${PROJECT_SOURCE_DIR}/cpp/vorticity_equation.hpp
- ${PROJECT_SOURCE_DIR}/cpp/field_binary_IO.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n0.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n1.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n2.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n3.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n4.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n5.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n6.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n7.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n8.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n9.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/spline_n10.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/Lagrange_polys.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/abstract_particle_set.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/particle_set.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/field_tinterpolator.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/abstract_particle_rhs.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/rhs/tracer_rhs.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/rhs/deformation_tensor_rhs.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particle_solver.hpp
- ${PROJECT_SOURCE_DIR}/cpp/scope_timer.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test_interpolation.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEparticles.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEcomplex_particles.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE_Stokes_particles.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEp_extra_sampling.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/inner/particles_inner_computer.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/inner/particles_inner_computer_2nd_order.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/inner/particles_inner_computer_empty.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/abstract_particles_input.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/abstract_particles_output.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/abstract_particles_system.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/abstract_particles_system_with_p2p.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/alltoall_exchanger.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/lock_free_bool_array.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/p2p/p2p_computer_empty.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/p2p/p2p_computer.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/p2p/p2p_ghost_collisions.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/p2p/p2p_distr_mpi.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/p2p/p2p_tree.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_adams_bashforth.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_distr_mpi.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/particles_field_computer.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/interpolation/particles_generic_interp.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_input_hdf5.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_output_hdf5.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_output_mpiio.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_output_sampling_hdf5.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_sampling.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_system_builder.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_system.hpp
- ${PROJECT_SOURCE_DIR}/cpp/particles/particles_utils.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/main_code.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/codes_with_no_output.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE_no_output.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEparticles_no_output.hpp
- ${PROJECT_SOURCE_DIR}/cpp/base.hpp
- ${PROJECT_SOURCE_DIR}/cpp/env_utils.hpp
- ${PROJECT_SOURCE_DIR}/cpp/fftw_interface.hpp
- ${PROJECT_SOURCE_DIR}/cpp/turtle_timer.hpp
- ${PROJECT_SOURCE_DIR}/cpp/omputils.hpp
- ${PROJECT_SOURCE_DIR}/cpp/shared_array.hpp
- ${PROJECT_SOURCE_DIR}/cpp/spectrum_function.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/ornstein_uhlenbeck_process.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/ou_vorticity_equation.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test_interpolation_methods.hpp
- ${PROJECT_SOURCE_DIR}/cpp/full_code/test_particle_integration.hpp)
-
-if(GSL_FOUND)
- LIST(APPEND cpp_for_lib ${PROJECT_SOURCE_DIR}/cpp/particles/rhs/deformation_tensor_rhs.cpp)
- LIST(APPEND hpp_for_lib ${PROJECT_SOURCE_DIR}/cpp/particles/rhs/deformation_tensor_rhs.hpp)
-endif()
-
-#file(GLOB_RECURSE hpp_for_lib ${PROJECT_SOURCE_DIR}/*.hpp)
-LIST(APPEND source_files ${hpp_for_lib} ${cpp_for_lib})
-
-add_library(TurTLE ${source_files})
-
-target_link_libraries(TurTLE ${TURTLE_LIBS})
-target_compile_options(TurTLE PRIVATE $<$<CONFIG:DEBUG>:-O1>)
+add_subdirectory(cpp)
install(TARGETS TurTLE EXPORT TURTLE_EXPORT DESTINATION lib/ )
install(DIRECTORY ${PROJECT_SOURCE_DIR}/cpp/ DESTINATION include/TurTLE/ FILES_MATCHING PATTERN "*.h*")
diff --git a/TurTLE/_code.py b/TurTLE/_code.py
index 24481fbca5913a103f762b042e8076c744fe672c..fcd6ac5b4181fdf75b27ba920aa43caa28c5ec57 100644
--- a/TurTLE/_code.py
+++ b/TurTLE/_code.py
@@ -205,17 +205,20 @@ class _code(_base):
with open('CMakeLists.txt', 'w') as outfile:
outfile.write('cmake_minimum_required(VERSION 3.10)\n')
outfile.write('cmake_policy(VERSION 3.12)\n')
- outfile.write('project(project_{0} LANGUAGES C CXX)\n'.format(self.name))
outfile.write('set(CMAKE_CXX_STANDARD 17)\n')
outfile.write('set(CMAKE_CXX_STANDARD_REQUIRED ON)\n')
+ outfile.write('project(project_{0} LANGUAGES C CXX)\n'.format(self.name))
+ outfile.write('add_executable({0} {0}.cpp)\n'.format(self.name))
outfile.write('find_package(OpenMP REQUIRED)\n')
- outfile.write('set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")\n')
outfile.write('find_package(MPI REQUIRED)\n')
- outfile.write('set(CMAKE_CXX_COMPILE_FLAGS "${CMAKE_CXX_COMPILE_FLAGS} ${MPI_CXX_COMPILE_OPTIONS}")\n')
- outfile.write('include_directories(${MPI_CXX_INCLUDE_DIRS})\n')
- outfile.write('add_definitions(${MPI_CXX_COMPILE_DEFINITIONS})\n')
- outfile.write('list(APPEND TURTLE_LIBS "${MPI_CXX_LIBRARIES}")\n')
- outfile.write('list(APPEND TURTLE_LIBS "${OpenMP_CXX_LIB_NAMES}")\n')
+ outfile.write('target_link_libraries({0} PRIVATE OpenMP::OpenMP_CXX MPI::MPI_C)\n'.format(self.name))
+ outfile.write('set(HDF5_STATIC ON)\n')
+ outfile.write('set(HDF5_PREFER_PARALLEL TRUE)\n')
+ outfile.write('set(HDF5_NO_FIND_PACKAGE_CONFIG_FILE TRUE)\n')
+ outfile.write('find_package(HDF5 REQUIRED COMPONENTS C)\n')
+ outfile.write('message("found HDF5 include dir at ${HDF5_C_INCLUDE_DIR}")\n')
+ outfile.write('target_link_libraries({0} PRIVATE HDF5::HDF5)\n'.format(self.name))
+ outfile.write('target_include_directories({0} PRIVATE ${{HDF5_C_INCLUDE_DIR}})\n'.format(self.name))
#ideally we should use something like the following 2 lines
#outfile.write('set(CMAKE_CXX_COMPILER ${TURTLE_CXX_COMPILER})\n')
#outfile.write('set(CMAKE_C_COMPILER ${TURTLE_C_COMPILER})\n')
@@ -223,8 +226,6 @@ class _code(_base):
outfile.write('set(CMAKE_CXX_COMPILE_FLAGS "${CMAKE_CXX_COMPILE_FLAGS} ${TURTLE_CXX_COMPILE_FLAGS}")\n')
outfile.write('set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_COMPILE_FLAGS}")\n')
outfile.write('set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${TURTLE_EXE_LINKER_FLAGS}")\n')
- outfile.write('set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MPI_CXX_LINK_FLAGS}")\n')
- outfile.write('set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")\n')
outfile.write('if(NDEBUG)\n')
outfile.write(' add_definitions(-DNDEBUG)\n')
outfile.write('endif()\n')
@@ -234,9 +235,8 @@ class _code(_base):
outfile.write('include_directories(${TURTLE_INCLUDE_DIRECTORIES} ${TURTLE_INCLUDE_DIR}/TurTLE)\n')
outfile.write('link_directories(${TURTLE_LINK_DIRECTORIES} ${TURTLE_LIBRARIES_DIR})\n')
outfile.write('find_library(TURTLE_STATIC_LIBRARY TurTLE HINTS ${TURTLE_LIBRARIES_DIR})\n')
- outfile.write('add_executable({0} {0}.cpp)\n'.format(self.name))
- outfile.write('target_link_libraries(' + self.name + ' ${TURTLE_STATIC_LIBRARY})\n')
- outfile.write('target_link_libraries(' + self.name + ' ${TURTLE_LIBS})\n')
+ outfile.write('target_link_libraries(' + self.name + ' PRIVATE ${TURTLE_STATIC_LIBRARY})\n')
+ outfile.write('target_link_libraries(' + self.name + ' PRIVATE ${TURTLE_LIBS})\n')
fname = self.dns_type + '_extra_cmake.txt'
if os.path.exists(fname):
with open(fname, 'r') as ifile:
diff --git a/TurTLE/test/collisions/stokes_rhs.hpp b/TurTLE/test/collisions/stokes_rhs.hpp
index 582f7089f3ed0759329b172363ac14823e500fdd..41268149f23f590bc1e6bb9f9ce011aba5c34c8c 100644
--- a/TurTLE/test/collisions/stokes_rhs.hpp
+++ b/TurTLE/test/collisions/stokes_rhs.hpp
@@ -43,7 +43,7 @@ class stokes_rhs: public abstract_particle_rhs
public:
stokes_rhs(){}
~stokes_rhs(){}
- const int getStateSize() const
+ int getStateSize() const
{
// 3 numbers for position
// // 9 numbers for components of deformation tensor // 3 numbers to store logarithmic factors
diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6421dd5c13ccd7b17a3c65f239d6e0eda1f50294
--- /dev/null
+++ b/cpp/CMakeLists.txt
@@ -0,0 +1,210 @@
+#######################################################################
+# #
+# Copyright 2019 Max Planck Institute #
+# for Dynamics and Self-Organization #
+# #
+# This file is part of TurTLE. #
+# #
+# TurTLE 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. #
+# #
+# TurTLE 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 TurTLE. If not, see <http://www.gnu.org/licenses/> #
+# #
+# Contact: Cristian.Lalescu@ds.mpg.de #
+# #
+#######################################################################
+
+
+
+set(cpp_for_lib
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/code_base.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/direct_numerical_simulation.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSE.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVE.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/static_field.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/kraichnan_field.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/joint_acc_vel_stats.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/pressure_stats.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/filter_test.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/field_test.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/write_filtered_test.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/dealias_test.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/Gauss_field_test.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/symmetrize_test.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/field_output_test.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/phase_shift_test.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test_tracer_set.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/get_rfields.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/get_velocity.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/get_3D_correlations.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/write_rpressure.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/bandpass_stats.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/field_single_to_double.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/resize.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVE_field_stats.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/native_binary_to_hdf5.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/postprocess.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/base.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/field.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/kspace.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/field_layout.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/hdf5_tools.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/fftw_tools.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/vorticity_equation.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/field_binary_IO.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n0.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n1.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n2.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n3.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n4.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n5.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n6.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n7.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n8.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n9.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n10.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/Lagrange_polys.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/field_tinterpolator.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/particle_set.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/rhs/tracer_rhs.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/rhs/tracer_with_collision_counter_rhs.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particle_solver.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/scope_timer.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test_interpolation.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVEparticles.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVEcomplex_particles.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVE_Stokes_particles.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVEp_extra_sampling.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/inner/particles_inner_computer.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/ornstein_uhlenbeck_process.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/ou_vorticity_equation.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test_interpolation_methods.cpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test_particle_integration.cpp)
+
+set(hpp_for_lib
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/code_base.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/direct_numerical_simulation.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSE.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVE.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/static_field.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/kraichnan_field.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/joint_acc_vel_stats.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/pressure_stats.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/filter_test.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/dealias_test.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/Gauss_field_test.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/field_test.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/write_filtered_test.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/symmetrize_test.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/field_output_test.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/phase_shift_test.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test_tracer_set.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/get_rfields.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/get_velocity.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/get_3D_correlations.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/write_rpressure.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/bandpass_stats.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/field_single_to_double.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/resize.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVE_field_stats.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/native_binary_to_hdf5.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/postprocess.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/field.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/kspace.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/field_layout.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/hdf5_tools.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/fftw_tools.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/vorticity_equation.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/field_binary_IO.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n0.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n1.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n2.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n3.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n4.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n5.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n6.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n7.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n8.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n9.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/spline_n10.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/Lagrange_polys.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/abstract_particle_set.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/particle_set.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/field_tinterpolator.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/abstract_particle_rhs.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/rhs/tracer_rhs.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/rhs/deformation_tensor_rhs.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/rhs/tracer_with_collision_counter_rhs.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particle_solver.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/scope_timer.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test_interpolation.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVEparticles.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVEcomplex_particles.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVE_Stokes_particles.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVEp_extra_sampling.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/inner/particles_inner_computer.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/inner/particles_inner_computer_2nd_order.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/inner/particles_inner_computer_empty.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/abstract_particles_input.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/abstract_particles_output.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/abstract_particles_system.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/abstract_particles_system_with_p2p.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/alltoall_exchanger.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/lock_free_bool_array.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/p2p/p2p_computer_empty.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/p2p/p2p_computer.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/p2p/p2p_ghost_collisions.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/p2p/p2p_distr_mpi.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/p2p/p2p_tree.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_adams_bashforth.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_distr_mpi.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/particles_field_computer.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/interpolation/particles_generic_interp.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_input_hdf5.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_output_hdf5.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_output_mpiio.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_output_sampling_hdf5.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_sampling.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_system_builder.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_system.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/particles/particles_utils.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/main_code.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/codes_with_no_output.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVE_no_output.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/NSVEparticles_no_output.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/base.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/env_utils.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/fftw_interface.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/turtle_timer.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/omputils.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/shared_array.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/spectrum_function.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/ornstein_uhlenbeck_process.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/ou_vorticity_equation.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test_interpolation_methods.hpp
+ ${CMAKE_CURRENT_LIST_DIR}/full_code/test_particle_integration.hpp)
+
+if(GSL_FOUND)
+ LIST(APPEND cpp_for_lib ${CMAKE_CURRENT_LIST_DIR}/particles/rhs/deformation_tensor_rhs.cpp)
+ LIST(APPEND hpp_for_lib ${CMAKE_CURRENT_LIST_DIR}/particles/rhs/deformation_tensor_rhs.hpp)
+endif()
+
+LIST(APPEND source_files ${hpp_for_lib} ${cpp_for_lib})
+
+target_sources(TurTLE
+ PRIVATE
+ ${source_files})
+
+#EOF
+
diff --git a/cpp/base.cpp b/cpp/base.cpp
index b80b08ec51b36cd7c83aa312aa667cb2334f5fc3..1ad16d3794e7632a3e107f04b65320bf8283c85b 100644
--- a/cpp/base.cpp
+++ b/cpp/base.cpp
@@ -14,7 +14,8 @@ int read_maximum_MPI_tag_value()
&flag);
if (flag){
maximum_MPI_tag_value = *((int*)(max_tag));
- std::cerr << "Maximum MPI tag value queried is " << maximum_MPI_tag_value << std::endl;
+ if (myrank == 0)
+ std::cerr << "Maximum MPI tag value queried from rank 0 is " << maximum_MPI_tag_value << std::endl;
}
else{
std::cerr << "TurTLE error: couldn't get maximum MPI tag value." << std::endl;
diff --git a/cpp/field.cpp b/cpp/field.cpp
index 16091a6bdc3ae2dfb3627f467fdf2bff0f0206cf..078f59c6145c1d84eaf1c6e2619ba9723be8710f 100644
--- a/cpp/field.cpp
+++ b/cpp/field.cpp
@@ -993,11 +993,13 @@ void field<rnumber, be, fc>::compute_rspace_stats(
const hid_t group,
const std::string dset_name,
const hsize_t toffset,
- const std::vector<double> max_estimate)
+ const std::vector<double> max_estimate,
+ const unsigned int maximum_moment)
{
TIMEZONE("field::compute_rspace_stats");
assert(this->real_space_representation);
const unsigned int nmoments = 10;
+ assert(maximum_moment < nmoments);
int nvals, nbins;
if (this->myrank == 0)
{
@@ -1017,6 +1019,13 @@ void field<rnumber, be, fc>::compute_rspace_stats(
// dset_name.c_str());
assert(ndims == int(ndim(fc))-1);
assert(dims[1] == nmoments);
+ // gcc complains about the following code, when ndim(fc)-1 is too small
+ // since I already assert what the value of ndims is, I know the code
+ // is safe, so I just tell GCC to ignore the apparent problem with this
+ // pragma. See link below for more info:
+ // https://gcc.gnu.org/onlinedocs/gcc/Diagnostic-Pragmas.html
+#pragma GCC diagnostic ignored "-Warray-bounds"
+#pragma GCC diagnostic push
switch(ndims)
{
case 2:
@@ -1029,6 +1038,7 @@ void field<rnumber, be, fc>::compute_rspace_stats(
nvals = dims[2]*dims[3];
break;
}
+#pragma GCC diagnostic pop
H5Sclose(wspace);
H5Dclose(dset);
dset = H5Dopen(group, ("histograms/" + dset_name).c_str(), H5P_DEFAULT);
@@ -1113,8 +1123,8 @@ void field<rnumber, be, fc>::compute_rspace_stats(
if (bin >= 0 && bin < nbins)
local_hist[bin*nvals+i]++;
}
- for (int n=1; n < int(nmoments)-1; n++){
- for (int i=0; i<nvals; i++){
+ for (unsigned int n=1; n < maximum_moment; n++){
+ for (auto i=0; i<nvals; i++){
local_moments[n*nvals + i] += (pow_tmp[i] = val_tmp[i]*pow_tmp[i]);
}
}
diff --git a/cpp/field.hpp b/cpp/field.hpp
index f6c69a7d1e10d6751e0be0055518b1fa4c2d2e6c..eb79f5b74237efa7d98f5f889b5a64af763849c8 100644
--- a/cpp/field.hpp
+++ b/cpp/field.hpp
@@ -139,7 +139,8 @@ class field
const hid_t group,
const std::string dset_name,
const hsize_t toffset,
- const std::vector<double> max_estimate);
+ const std::vector<double> max_estimate,
+ const unsigned int maximum_moment = 9);
void compute_rspace_zaverage(
const hid_t group,
diff --git a/cpp/full_code/NSVE.cpp b/cpp/full_code/NSVE.cpp
index 5c0d360c0cdced78c17b72b11b30d813239d75c8..20591057555de5989742d6d1d25066ed4be64c71 100644
--- a/cpp/full_code/NSVE.cpp
+++ b/cpp/full_code/NSVE.cpp
@@ -84,7 +84,7 @@ int NSVE<rnumber>::initialize(void)
this->fs->fk0 = fk0;
this->fs->fk1 = fk1;
this->fs->dt = dt;
- strncpy(this->fs->forcing_type, forcing_type, 128);
+ this->fs->forcing_type = forcing_type;
this->fs->iteration = this->iteration;
this->fs->checkpoint = this->checkpoint;
@@ -193,8 +193,7 @@ int NSVE<rnumber>::read_parameters(void)
this->histogram_bins = hdf5_tools::read_value<int>(parameter_file, "parameters/histogram_bins");
this->max_velocity_estimate = hdf5_tools::read_value<double>(parameter_file, "parameters/max_velocity_estimate");
this->max_vorticity_estimate = hdf5_tools::read_value<double>(parameter_file, "parameters/max_vorticity_estimate");
- std::string tmp = hdf5_tools::read_string(parameter_file, "parameters/forcing_type");
- snprintf(this->forcing_type, 511, "%s", tmp.c_str());
+ this->forcing_type = hdf5_tools::read_string(parameter_file, "parameters/forcing_type");
this->fftw_plan_rigor = hdf5_tools::read_string(parameter_file, "parameters/fftw_plan_rigor");
H5Fclose(parameter_file);
// the following ensures the file is free after exiting this method
diff --git a/cpp/full_code/NSVE.hpp b/cpp/full_code/NSVE.hpp
index 15a388dc4f8e7fdd1db8e11b3cff1806094e18d3..60809a88e6278643b37299490c2d5a8da2e6655f 100644
--- a/cpp/full_code/NSVE.hpp
+++ b/cpp/full_code/NSVE.hpp
@@ -28,12 +28,13 @@
#define NSVE_HPP
-
-#include <cstdlib>
#include "base.hpp"
#include "vorticity_equation.hpp"
#include "full_code/direct_numerical_simulation.hpp"
+#include <cstdlib>
+#include <string>
+
/** \brief Navier-Stokes solver.
*
* Solves the vorticity equation for a Navier-Stokes fluid.
@@ -58,7 +59,7 @@ class NSVE: public direct_numerical_simulation
double energy;
double injection_rate;
int fmode;
- char forcing_type[512];
+ std::string forcing_type;
int histogram_bins;
double max_velocity_estimate;
double max_vorticity_estimate;
diff --git a/cpp/full_code/postprocess.cpp b/cpp/full_code/postprocess.cpp
index 2fe20c34ef524419e6e591b6d381421f12944d3b..2c136a7baa01e8e0e4bdbaf063cff3a06fca7f3a 100644
--- a/cpp/full_code/postprocess.cpp
+++ b/cpp/full_code/postprocess.cpp
@@ -73,8 +73,7 @@ int postprocess::read_parameters()
this->variation_time_scale = hdf5_tools::read_value<double>(parameter_file, "parameters/variation_time_scale");
this->energy = hdf5_tools::read_value<double>(parameter_file, "parameters/energy");
this->injection_rate = hdf5_tools::read_value<double>(parameter_file, "parameters/injection_rate");
- std::string tmp = hdf5_tools::read_string(parameter_file, "parameters/forcing_type");
- snprintf(this->forcing_type, 511, "%s", tmp.c_str());
+ this->forcing_type = hdf5_tools::read_string(parameter_file, "parameters/forcing_type");
H5Fclose(parameter_file);
MPI_Barrier(this->comm);
return EXIT_SUCCESS;
@@ -96,7 +95,7 @@ int postprocess::copy_parameters_into(
dst->friction_coefficient = this->friction_coefficient;
dst->variation_strength = this->variation_strength;
dst->variation_time_scale = this->variation_time_scale;
- strncpy(dst->forcing_type, this->forcing_type, 128);
+ dst->forcing_type = this->forcing_type;
return EXIT_SUCCESS;
}
diff --git a/cpp/full_code/postprocess.hpp b/cpp/full_code/postprocess.hpp
index 4a8fab396149ccddc008d15dedbc15ce968b8a70..52826cf7acf436823ad200e28ca29534bcf5e355 100644
--- a/cpp/full_code/postprocess.hpp
+++ b/cpp/full_code/postprocess.hpp
@@ -27,13 +27,14 @@
#ifndef POSTPROCESS_HPP
#define POSTPROCESS_HPP
+#include "full_code/code_base.hpp"
+#include "vorticity_equation.hpp"
+#include "base.hpp"
+
#include <cstdlib>
#include <sys/types.h>
#include <sys/stat.h>
#include <vector>
-#include "base.hpp"
-#include "vorticity_equation.hpp"
-#include "full_code/code_base.hpp"
class postprocess: public code_base
{
@@ -56,7 +57,7 @@ class postprocess: public code_base
double variation_strength;
double variation_time_scale;
int fmode;
- char forcing_type[512];
+ std::string forcing_type;
double nu;
postprocess(
diff --git a/cpp/hdf5_tools.cpp b/cpp/hdf5_tools.cpp
index 9a92c459cf368de3a66b456bffef502fcc9478cb..e75070b40ac56f5e2d248194430cd8ff250a6cce 100644
--- a/cpp/hdf5_tools.cpp
+++ b/cpp/hdf5_tools.cpp
@@ -1,7 +1,7 @@
#include "hdf5_tools.hpp"
#include "scope_timer.hpp"
-#include <cfloat>
-#include <climits>
+
+#include <limits>
template <> hid_t hdf5_tools::hdf5_type_id<char>()
{
@@ -208,13 +208,7 @@ std::vector<number> hdf5_tools::read_vector(
hsize_t vector_length;
// first, read size of array
hid_t dset, dspace;
- hid_t mem_dtype;
- if (typeid(number) == typeid(int))
- mem_dtype = H5Tcopy(H5T_NATIVE_INT);
- else if (typeid(number) == typeid(double))
- mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
- else
- return result;
+ hid_t mem_dtype = H5Tcopy(hdf5_tools::hdf5_type_id<number>());
dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
dspace = H5Dget_space(dset);
assert(H5Sget_simple_extent_ndims(dspace) == 1);
@@ -235,15 +229,7 @@ number hdf5_tools::read_value(
TIMEZONE("hdf5_tools::read_value");
number result;
hid_t dset;
- hid_t mem_dtype;
- if (typeid(number) == typeid(int))
- mem_dtype = H5Tcopy(H5T_NATIVE_INT);
- else if (typeid(number) == typeid(long long int))
- mem_dtype = H5Tcopy(H5T_NATIVE_LLONG);
- else if (typeid(number) == typeid(double))
- mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
- else
- return result;
+ hid_t mem_dtype = H5Tcopy(hdf5_tools::hdf5_type_id<number>());
if (H5Lexists(group, dset_name.c_str(), H5P_DEFAULT))
{
dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
@@ -258,12 +244,7 @@ number hdf5_tools::read_value(
{
DEBUG_MSG("attempted to read dataset %s which does not exist.\n",
dset_name.c_str());
- if (typeid(number) == typeid(int))
- result = INT_MAX;
- else if (typeid(number) == typeid(long long int))
- result = -1;
- else if (typeid(number) == typeid(double))
- result = number(DBL_MAX);
+ result = std::numeric_limits<number>::max();
}
H5Tclose(mem_dtype);
return result;
@@ -275,13 +256,10 @@ int hdf5_tools::write_value_with_single_rank(
const std::string dset_name,
const number value)
{
+ assert(typeid(number) == typeid(int) ||
+ typeid(number) == typeid(double));
hid_t dset, mem_dtype;
- if (typeid(number) == typeid(int))
- mem_dtype = H5Tcopy(H5T_NATIVE_INT);
- else if (typeid(number) == typeid(double))
- mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
- else
- return EXIT_FAILURE;
+ mem_dtype = H5Tcopy(hdf5_tools::hdf5_type_id<number>());
if (H5Lexists(group, dset_name.c_str(), H5P_DEFAULT))
{
dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
diff --git a/cpp/kspace.cpp b/cpp/kspace.cpp
index b1f40ae446e469888ae645d0dd751aae4635817d..3628893df9d19561260d09eba882e0944491108b 100644
--- a/cpp/kspace.cpp
+++ b/cpp/kspace.cpp
@@ -172,7 +172,9 @@ kspace<be, dt>::kspace(
// I chose the last option because there's no reason to optimize this
// loop. Furthermore, it seems like the solution that's most readable,
// and with the least amount of side effects.
- # pragma novector
+ #if defined(__INTEL_COMPILER)
+ #pragma novector
+ #endif
for (int n=0; n<this->nshells; n++){
if (this->nshell[n] > 0)
this->kshell[n] /= this->nshell[n];
diff --git a/cpp/particles/abstract_particle_rhs.hpp b/cpp/particles/abstract_particle_rhs.hpp
index 947e152430cb14bc439021d83e48860411c2c175..a0c68816c4e8879d3a72fee5aff8a168a3142916 100644
--- a/cpp/particles/abstract_particle_rhs.hpp
+++ b/cpp/particles/abstract_particle_rhs.hpp
@@ -49,7 +49,7 @@ class abstract_particle_rhs
/** Probe the dimension of the ODE
*/
- virtual const int getStateSize() const = 0;
+ virtual int getStateSize() const = 0;
/** Compute right-hand-side of the ODE
diff --git a/cpp/particles/rhs/deformation_tensor_rhs.hpp b/cpp/particles/rhs/deformation_tensor_rhs.hpp
index 0835f9869645d14eacedea5990562dffbd0203e4..43b75cb934003606d7f35889da7911769bdbab80 100644
--- a/cpp/particles/rhs/deformation_tensor_rhs.hpp
+++ b/cpp/particles/rhs/deformation_tensor_rhs.hpp
@@ -48,7 +48,7 @@ class deformation_tensor_rhs: public abstract_particle_rhs
deformation_tensor_rhs(){}
~deformation_tensor_rhs() noexcept(false){}
- const int getStateSize() const
+ int getStateSize() const
{
// 3 numbers for position
// 9 numbers for components of deformation tensor
diff --git a/cpp/particles/rhs/tracer_rhs.hpp b/cpp/particles/rhs/tracer_rhs.hpp
index 680b46fdbc330d3bd892a1343094dd066c1f83a5..eca90024144f2a598bcad860c050173245175a13 100644
--- a/cpp/particles/rhs/tracer_rhs.hpp
+++ b/cpp/particles/rhs/tracer_rhs.hpp
@@ -43,7 +43,7 @@ class tracer_rhs: public abstract_particle_rhs
tracer_rhs(){}
~tracer_rhs() noexcept(false){}
- const int getStateSize() const
+ int getStateSize() const
{
return 3;
}
diff --git a/cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp b/cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp
index 5aa15213d02702eb96c198fab0e333584efb1598..4fdc0686586003b913f3ef09dd70bba69365b5e4 100644
--- a/cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp
+++ b/cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp
@@ -44,7 +44,7 @@ class tracer_with_collision_counter_rhs: public tracer_rhs<rnumber, be, tt>
tracer_with_collision_counter_rhs(){}
~tracer_with_collision_counter_rhs() noexcept(false){}
- virtual const int getStateSize() const
+ virtual int getStateSize() const
{
return 3;
}
diff --git a/cpp/vorticity_equation.cpp b/cpp/vorticity_equation.cpp
index c32c03319d1e35796a847a30d1b9590999d3678a..7ce50a766ff3ed0c50d47b0da0b99787159e8518 100644
--- a/cpp/vorticity_equation.cpp
+++ b/cpp/vorticity_equation.cpp
@@ -289,12 +289,12 @@ void vorticity_equation<rnumber, be>::add_forcing(
double t)
{
TIMEZONE("vorticity_equation::add_forcing");
- if (strcmp(this->forcing_type, "Kolmogorov") == 0)
+ if (this->forcing_type == std::string("Kolmogorov"))
{
this->add_Kolmogorov_forcing(dst, this->fmode, this->famplitude);
return;
}
- if (strcmp(this->forcing_type, "2Kolmogorov") == 0)
+ if (this->forcing_type == std::string("2Kolmogorov"))
{
// 2 Kolmogorov forces
// first one wavenumber fk0, amplitude 1 - A
@@ -307,7 +307,7 @@ void vorticity_equation<rnumber, be>::add_forcing(
this->add_Kolmogorov_forcing(dst, fmode, amplitude);
return;
}
- if (strcmp(this->forcing_type, "Kolmogorov_and_drag") == 0)
+ if (this->forcing_type == std::string("Kolmogorov_and_drag"))
{
this->add_Kolmogorov_forcing(dst, this->fmode, this->famplitude);
this->add_field_band(
@@ -316,7 +316,7 @@ void vorticity_equation<rnumber, be>::add_forcing(
-this->friction_coefficient);
return;
}
- if (strcmp(this->forcing_type, "Kolmogorov_and_compensated_drag") == 0)
+ if (this->forcing_type == std::string("Kolmogorov_and_compensated_drag"))
{
double amplitude = this->famplitude * (
1 + this->friction_coefficient / sqrt(this->fmode * this->famplitude));
@@ -327,7 +327,7 @@ void vorticity_equation<rnumber, be>::add_forcing(
-this->friction_coefficient);
return;
}
- if (strcmp(this->forcing_type, "linear") == 0)
+ if (this->forcing_type == std::string("linear"))
{
this->add_field_band(
dst, vort_field,
@@ -335,9 +335,9 @@ void vorticity_equation<rnumber, be>::add_forcing(
this->famplitude);
return;
}
- if ((strcmp(this->forcing_type, "fixed_energy_injection_rate") == 0) ||
- (strcmp(this->forcing_type, "fixed_energy_injection_rate_and_drag") == 0) ||
- (strcmp(this->forcing_type, "sinusoidal_energy_injection_rate") == 0))
+ if (this->forcing_type == std::string("fixed_energy_injection_rate") ||
+ this->forcing_type == std::string("fixed_energy_injection_rate_and_drag") ||
+ this->forcing_type == std::string("sinusoidal_energy_injection_rate"))
{
// first, compute energy in shell
shared_array<double> local_energy_in_shell(1);
@@ -377,7 +377,7 @@ void vorticity_equation<rnumber, be>::add_forcing(
if (energy_in_shell < 10*std::numeric_limits<rnumber>::epsilon())
energy_in_shell = 1;
double temp_famplitude = 0;
- if (strcmp(this->forcing_type, "sinusoidal_energy_injection_rate") == 0){
+ if (this->forcing_type == std::string("sinusoidal_energy_injection_rate")){
temp_famplitude = (this->injection_rate + this->variation_strength
*sin(t/this->variation_time_scale))
/ energy_in_shell;
@@ -389,18 +389,18 @@ void vorticity_equation<rnumber, be>::add_forcing(
this->fk0, this->fk1,
temp_famplitude);
// and add drag if desired
- if (strcmp(this->forcing_type, "fixed_energy_injection_rate_and_drag") == 0)
+ if (this->forcing_type == std::string("fixed_energy_injection_rate_and_drag"))
this->add_field_band(
dst, vort_field,
this->fmode, this->fmode + (this->fk1 - this->fk0),
-this->friction_coefficient);
return;
}
- if (strcmp(this->forcing_type, "fixed_energy") == 0)
+ if (this->forcing_type == std::string("fixed_energy"))
return;
else
{
- DEBUG_MSG("unknown forcing type printed on next line\n%s", this->forcing_type);
+ DEBUG_MSG("unknown forcing type printed on next line\n%s", this->forcing_type.c_str());
throw std::invalid_argument("unknown forcing type");
}
}
@@ -412,7 +412,7 @@ void vorticity_equation<rnumber, be>::impose_forcing(
field<rnumber, be, THREE> *oold)
{
TIMEZONE("vorticity_equation::impose_forcing");
- if (strcmp(this->forcing_type, "fixed_energy") == 0)
+ if (this->forcing_type == std::string("fixed_energy"))
{
// first, compute energy in shell
shared_array<double> local_energy_in_shell(1);
@@ -802,7 +802,7 @@ void vorticity_equation<rnumber, be>::compute_Eulerian_acceleration(
for (int i=0; i<2; i++)
acceleration->get_cdata()[tindex+cc][i] = \
- this->nu*k2*this->cvelocity->get_cdata()[tindex+cc][i];
- if (strcmp(this->forcing_type, "linear") == 0)
+ if (this->forcing_type == std::string("linear"))
{
double knorm = sqrt(k2);
if ((this->fk0 <= knorm) &&
diff --git a/cpp/vorticity_equation.hpp b/cpp/vorticity_equation.hpp
index 90803b4b29a65951cac5afe93bfdd49cccf722da..e48196f31505c75eda2f0d7b6d72e9fe46b2443c 100644
--- a/cpp/vorticity_equation.hpp
+++ b/cpp/vorticity_equation.hpp
@@ -27,12 +27,14 @@
#ifndef VORTICITY_EQUATION
#define VORTICITY_EQUATION
+#include "field.hpp"
+
#include <sys/stat.h>
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
+#include <string>
-#include "field.hpp"
extern int myrank, nprocs;
@@ -79,7 +81,7 @@ class vorticity_equation
double friction_coefficient; // for Kolmogorov_and_drag
double variation_strength; // for time-varying forcing
double variation_time_scale; // for time-varying forcing
- char forcing_type[128];
+ std::string forcing_type;
/* constructor, destructor */
vorticity_equation(