From 274c4e0d6f1c09d072298211d1dde326d230993a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Dagand?= <timothee.dagand@neel.cnrs.com>
Date: Tue, 5 May 2026 09:47:48 +0200
Subject: [PATCH] Move sources to new src directory

---
 CMakeLists.txt                                | 47 +------------------
 Doxyfile                                      |  2 +-
 ci-tests/full_test.py                         |  4 +-
 src/CMakeLists.txt                            | 44 +++++++++++++++++
 {algebra => src/algebra}/algebra.h            |  0
 {algebra => src/algebra}/algebraCore.h        |  0
 {algebra => src/algebra}/bicg.h               |  0
 {algebra => src/algebra}/cg.h                 |  0
 {algebra => src/algebra}/iter.h               |  0
 {algebra => src/algebra}/sparseMat.h          |  2 +-
 chronometer.cpp => src/chronometer.cpp        |  0
 chronometer.h => src/chronometer.h            |  0
 config.h.in => src/config.h.in                |  0
 .../default-settings.yml                      |  0
 .../electrostatSolver.cpp                     |  0
 .../electrostatSolver.h                       |  0
 element.h => src/element.h                    |  0
 energy.cpp => src/energy.cpp                  |  0
 .../expression_parser.cpp                     |  0
 .../expression_parser.h                       |  0
 facette.cpp => src/facette.cpp                |  0
 facette.h => src/facette.h                    |  0
 fem.h => src/fem.h                            |  0
 fmm_demag.h => src/fmm_demag.h                |  0
 linear_algebra.cpp => src/linear_algebra.cpp  |  0
 linear_algebra.h => src/linear_algebra.h      |  0
 log-stats.h => src/log-stats.h                |  0
 main.cpp => src/main.cpp                      |  0
 mesh.cpp => src/mesh.cpp                      |  0
 mesh.h => src/mesh.h                          |  0
 meshUtils.h => src/meshUtils.h                |  0
 node.h => src/node.h                          |  0
 read.cpp => src/read.cpp                      |  0
 recentering.cpp => src/recentering.cpp        |  0
 save.cpp => src/save.cpp                      |  0
 settings.cpp => src/settings.cpp              |  0
 settings.h => src/settings.h                  |  0
 solver.cpp => src/solver.cpp                  |  0
 solver.h => src/solver.h                      |  0
 .../spinAccumulationSolver.cpp                |  0
 .../spinAccumulationSolver.h                  |  0
 tags.cpp => src/tags.cpp                      |  0
 tags.h => src/tags.h                          |  0
 tetra.cpp => src/tetra.cpp                    |  0
 tetra.h => src/tetra.h                        |  0
 .../time_integration.cpp                      |  0
 time_integration.h => src/time_integration.h  |  0
 unit-tests/CMakeLists.txt                     | 22 ++++-----
 unit-tests/sparse_matrix.h                    |  2 +-
 unit-tests/ut_algebra.cpp                     |  6 +--
 50 files changed, 65 insertions(+), 64 deletions(-)
 create mode 100644 src/CMakeLists.txt
 rename {algebra => src/algebra}/algebra.h (100%)
 rename {algebra => src/algebra}/algebraCore.h (100%)
 rename {algebra => src/algebra}/bicg.h (100%)
 rename {algebra => src/algebra}/cg.h (100%)
 rename {algebra => src/algebra}/iter.h (100%)
 rename {algebra => src/algebra}/sparseMat.h (99%)
 rename chronometer.cpp => src/chronometer.cpp (100%)
 rename chronometer.h => src/chronometer.h (100%)
 rename config.h.in => src/config.h.in (100%)
 rename default-settings.yml => src/default-settings.yml (100%)
 rename electrostatSolver.cpp => src/electrostatSolver.cpp (100%)
 rename electrostatSolver.h => src/electrostatSolver.h (100%)
 rename element.h => src/element.h (100%)
 rename energy.cpp => src/energy.cpp (100%)
 rename expression_parser.cpp => src/expression_parser.cpp (100%)
 rename expression_parser.h => src/expression_parser.h (100%)
 rename facette.cpp => src/facette.cpp (100%)
 rename facette.h => src/facette.h (100%)
 rename fem.h => src/fem.h (100%)
 rename fmm_demag.h => src/fmm_demag.h (100%)
 rename linear_algebra.cpp => src/linear_algebra.cpp (100%)
 rename linear_algebra.h => src/linear_algebra.h (100%)
 rename log-stats.h => src/log-stats.h (100%)
 rename main.cpp => src/main.cpp (100%)
 rename mesh.cpp => src/mesh.cpp (100%)
 rename mesh.h => src/mesh.h (100%)
 rename meshUtils.h => src/meshUtils.h (100%)
 rename node.h => src/node.h (100%)
 rename read.cpp => src/read.cpp (100%)
 rename recentering.cpp => src/recentering.cpp (100%)
 rename save.cpp => src/save.cpp (100%)
 rename settings.cpp => src/settings.cpp (100%)
 rename settings.h => src/settings.h (100%)
 rename solver.cpp => src/solver.cpp (100%)
 rename solver.h => src/solver.h (100%)
 rename spinAccumulationSolver.cpp => src/spinAccumulationSolver.cpp (100%)
 rename spinAccumulationSolver.h => src/spinAccumulationSolver.h (100%)
 rename tags.cpp => src/tags.cpp (100%)
 rename tags.h => src/tags.h (100%)
 rename tetra.cpp => src/tetra.cpp (100%)
 rename tetra.h => src/tetra.h (100%)
 rename time_integration.cpp => src/time_integration.cpp (100%)
 rename time_integration.h => src/time_integration.h (100%)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ccf89080..cf315bd0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -109,50 +109,7 @@ if(${ENABLE_LTO})
     set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
 endif()
 
-set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fopenmp")
-
-SET(HEADERS config.h node.h expression_parser.h mesh.h electrostatSolver.h
-    spinAccumulationSolver.h time_integration.h settings.h tetra.h
-    facette.h linear_algebra.h log-stats.h tags.h chronometer.h element.h)
-
-SET(SOURCES settings.cpp time_integration.cpp solver.cpp electrostatSolver.cpp
-    spinAccumulationSolver.cpp read.cpp save.cpp linear_algebra.cpp recentering.cpp tetra.cpp
-    energy.cpp facette.cpp expression_parser.cpp chronometer.cpp
-    tags.cpp mesh.cpp)
-
-configure_file(config.h.in ./config.h)
-
-add_custom_command(
-    OUTPUT default-settings.o
-    COMMAND ld -r -b binary -z noexecstack default-settings.yml -o default-settings.o
-    DEPENDS default-settings.yml)
-
-#===========================================================================
-# Compiler options
-#===========================================================================
-# -ffast-math -msse4.2 -mfpmath=sse (on X86 -mfpmath=sse set by default) or -mavx
-# -fsanitize=address leak null undefined # both compiler and linker
-#===========================================================================
-
-include_directories (${CMAKE_SOURCE_DIR} ${GMSH_INC})
-
-ADD_EXECUTABLE(feellgood main.cpp ${HEADERS} ${SOURCES} default-settings.o)
-target_compile_options( feellgood PUBLIC -Wall -Wextra -O3 -march=native ${MKL_CFLAGS} )
-target_compile_definitions(feellgood PUBLIC
-        -DNDEBUG -DTBB_SUPPRESS_DEPRECATED_MESSAGES ${EIGEN_MKL_CFLAGS} )
-
-if (MKL_FOUND)
-    #option --no-as-needed for mkl, see
-    # https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-link-line-advisor.html
-    target_link_options(feellgood PUBLIC "-Wl,--no-as-needed" )
-    # not sure we really need it since --no-as-needed is default value, though there might be
-    # a --as-needed before
-    TARGET_LINK_LIBRARIES(feellgood yaml-cpp duktape ann OpenMP::OpenMP_CXX ${TBB_LINK}
-            Eigen3::Eigen ${MKL_TARGET} ${GMSH_LIB})
-else()
-    TARGET_LINK_LIBRARIES(feellgood yaml-cpp duktape ann OpenMP::OpenMP_CXX ${TBB_LINK}
-            Eigen3::Eigen ${GMSH_LIB})
-endif()
+add_subdirectory(src)
 
 #===========================================================================
 # Find where to install the Python modules.
@@ -226,7 +183,7 @@ else()
 endif()
 
 if(${ENABLE_UTESTS})
-    configure_file(./unit-tests/ut_config.h.in ./unit-tests/ut_config.h)
+    configure_file(unit-tests/ut_config.h.in unit-tests/ut_config.h)
     include(CTest)
     add_subdirectory(unit-tests)
 endif()
diff --git a/Doxyfile b/Doxyfile
index 92400a91..da3354ce 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -765,7 +765,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = . algebra
+INPUT                  = . src src/algebra
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
diff --git a/ci-tests/full_test.py b/ci-tests/full_test.py
index 0cf9ef0d..f30601ec 100755
--- a/ci-tests/full_test.py
+++ b/ci-tests/full_test.py
@@ -43,7 +43,7 @@ def distance_R3(v1, v2):
 }
 
 # Expected outcome. It depends on whether feeLLGood was compiled in ONE_GAUSS_POINT mode.
-val = subprocess.check_output(["../feellgood","--version"])
+val = subprocess.check_output(["../src/feellgood","--version"])
 if b'ONE_GAUSS_POINT=ON' in val:
     expected = { "m": [0.307432, 0.476202, -0.823843], "E_tot": -4.446980e-19 }
 else:
@@ -51,7 +51,7 @@ def distance_R3(v1, v2):
 
 # Run the simulation.
 sys.stdout.flush()
-val = subprocess.run(["../feellgood", "--seed", "2", "-"], input=json.dumps(settings), text=True)
+val = subprocess.run(["../src/feellgood", "--seed", "2", "-"], input=json.dumps(settings), text=True)
 
 #(devNote) to avoid -fsanitize=leak ASLR bug, we turn off address randomizer
 #val = subprocess.run(["setarch", "--addr-no-randomize", "../feellgood", "--seed", "2", "-"],
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 00000000..977cb045
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,44 @@
+SET(HEADERS config.h node.h expression_parser.h mesh.h electrostatSolver.h
+        spinAccumulationSolver.h time_integration.h settings.h tetra.h
+        facette.h linear_algebra.h log-stats.h tags.h chronometer.h element.h)
+
+SET(SOURCES settings.cpp time_integration.cpp solver.cpp electrostatSolver.cpp
+        spinAccumulationSolver.cpp read.cpp save.cpp linear_algebra.cpp recentering.cpp tetra.cpp
+        energy.cpp facette.cpp expression_parser.cpp chronometer.cpp
+        tags.cpp mesh.cpp)
+
+configure_file(config.h.in ./config.h)
+
+set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fopenmp")
+
+add_custom_command(
+    OUTPUT default-settings.o
+    COMMAND ld -r -b binary -z noexecstack default-settings.yml -o default-settings.o
+    DEPENDS default-settings.yml)
+
+#===========================================================================
+# Compiler options
+#===========================================================================
+# -ffast-math -msse4.2 -mfpmath=sse (on X86 -mfpmath=sse set by default) or -mavx
+# -fsanitize=address leak null undefined # both compiler and linker
+#===========================================================================
+
+include_directories (${CMAKE_SOURCE_DIR} ${GMSH_INC})
+
+ADD_EXECUTABLE(feellgood main.cpp ${HEADERS} ${SOURCES} default-settings.o)
+target_compile_options( feellgood PUBLIC -Wall -Wextra -O3 -march=native ${MKL_CFLAGS} )
+target_compile_definitions(feellgood PUBLIC
+        -DNDEBUG -DTBB_SUPPRESS_DEPRECATED_MESSAGES ${EIGEN_MKL_CFLAGS} )
+
+if (MKL_FOUND)
+    #option --no-as-needed for mkl, see
+    # https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-link-line-advisor.html
+    target_link_options(feellgood PUBLIC "-Wl,--no-as-needed" )
+    # not sure we really need it since --no-as-needed is default value, though there might be
+    # a --as-needed before
+    TARGET_LINK_LIBRARIES(feellgood yaml-cpp duktape ann OpenMP::OpenMP_CXX ${TBB_LINK}
+            Eigen3::Eigen ${MKL_TARGET} ${GMSH_LIB})
+else()
+    TARGET_LINK_LIBRARIES(feellgood yaml-cpp duktape ann OpenMP::OpenMP_CXX ${TBB_LINK}
+            Eigen3::Eigen ${GMSH_LIB})
+endif()
diff --git a/algebra/algebra.h b/src/algebra/algebra.h
similarity index 100%
rename from algebra/algebra.h
rename to src/algebra/algebra.h
diff --git a/algebra/algebraCore.h b/src/algebra/algebraCore.h
similarity index 100%
rename from algebra/algebraCore.h
rename to src/algebra/algebraCore.h
diff --git a/algebra/bicg.h b/src/algebra/bicg.h
similarity index 100%
rename from algebra/bicg.h
rename to src/algebra/bicg.h
diff --git a/algebra/cg.h b/src/algebra/cg.h
similarity index 100%
rename from algebra/cg.h
rename to src/algebra/cg.h
diff --git a/algebra/iter.h b/src/algebra/iter.h
similarity index 100%
rename from algebra/iter.h
rename to src/algebra/iter.h
diff --git a/algebra/sparseMat.h b/src/algebra/sparseMat.h
similarity index 99%
rename from algebra/sparseMat.h
rename to src/algebra/sparseMat.h
index f68eedab..04630b00 100644
--- a/algebra/sparseMat.h
+++ b/src/algebra/sparseMat.h
@@ -25,7 +25,7 @@ reconstructing the matrix from scratch.
 #include <execution>
 #include <mutex>
 
-#include "config.h"
+#include "../config.h"
 #include "algebraCore.h"
 
 namespace algebra
diff --git a/chronometer.cpp b/src/chronometer.cpp
similarity index 100%
rename from chronometer.cpp
rename to src/chronometer.cpp
diff --git a/chronometer.h b/src/chronometer.h
similarity index 100%
rename from chronometer.h
rename to src/chronometer.h
diff --git a/config.h.in b/src/config.h.in
similarity index 100%
rename from config.h.in
rename to src/config.h.in
diff --git a/default-settings.yml b/src/default-settings.yml
similarity index 100%
rename from default-settings.yml
rename to src/default-settings.yml
diff --git a/electrostatSolver.cpp b/src/electrostatSolver.cpp
similarity index 100%
rename from electrostatSolver.cpp
rename to src/electrostatSolver.cpp
diff --git a/electrostatSolver.h b/src/electrostatSolver.h
similarity index 100%
rename from electrostatSolver.h
rename to src/electrostatSolver.h
diff --git a/element.h b/src/element.h
similarity index 100%
rename from element.h
rename to src/element.h
diff --git a/energy.cpp b/src/energy.cpp
similarity index 100%
rename from energy.cpp
rename to src/energy.cpp
diff --git a/expression_parser.cpp b/src/expression_parser.cpp
similarity index 100%
rename from expression_parser.cpp
rename to src/expression_parser.cpp
diff --git a/expression_parser.h b/src/expression_parser.h
similarity index 100%
rename from expression_parser.h
rename to src/expression_parser.h
diff --git a/facette.cpp b/src/facette.cpp
similarity index 100%
rename from facette.cpp
rename to src/facette.cpp
diff --git a/facette.h b/src/facette.h
similarity index 100%
rename from facette.h
rename to src/facette.h
diff --git a/fem.h b/src/fem.h
similarity index 100%
rename from fem.h
rename to src/fem.h
diff --git a/fmm_demag.h b/src/fmm_demag.h
similarity index 100%
rename from fmm_demag.h
rename to src/fmm_demag.h
diff --git a/linear_algebra.cpp b/src/linear_algebra.cpp
similarity index 100%
rename from linear_algebra.cpp
rename to src/linear_algebra.cpp
diff --git a/linear_algebra.h b/src/linear_algebra.h
similarity index 100%
rename from linear_algebra.h
rename to src/linear_algebra.h
diff --git a/log-stats.h b/src/log-stats.h
similarity index 100%
rename from log-stats.h
rename to src/log-stats.h
diff --git a/main.cpp b/src/main.cpp
similarity index 100%
rename from main.cpp
rename to src/main.cpp
diff --git a/mesh.cpp b/src/mesh.cpp
similarity index 100%
rename from mesh.cpp
rename to src/mesh.cpp
diff --git a/mesh.h b/src/mesh.h
similarity index 100%
rename from mesh.h
rename to src/mesh.h
diff --git a/meshUtils.h b/src/meshUtils.h
similarity index 100%
rename from meshUtils.h
rename to src/meshUtils.h
diff --git a/node.h b/src/node.h
similarity index 100%
rename from node.h
rename to src/node.h
diff --git a/read.cpp b/src/read.cpp
similarity index 100%
rename from read.cpp
rename to src/read.cpp
diff --git a/recentering.cpp b/src/recentering.cpp
similarity index 100%
rename from recentering.cpp
rename to src/recentering.cpp
diff --git a/save.cpp b/src/save.cpp
similarity index 100%
rename from save.cpp
rename to src/save.cpp
diff --git a/settings.cpp b/src/settings.cpp
similarity index 100%
rename from settings.cpp
rename to src/settings.cpp
diff --git a/settings.h b/src/settings.h
similarity index 100%
rename from settings.h
rename to src/settings.h
diff --git a/solver.cpp b/src/solver.cpp
similarity index 100%
rename from solver.cpp
rename to src/solver.cpp
diff --git a/solver.h b/src/solver.h
similarity index 100%
rename from solver.h
rename to src/solver.h
diff --git a/spinAccumulationSolver.cpp b/src/spinAccumulationSolver.cpp
similarity index 100%
rename from spinAccumulationSolver.cpp
rename to src/spinAccumulationSolver.cpp
diff --git a/spinAccumulationSolver.h b/src/spinAccumulationSolver.h
similarity index 100%
rename from spinAccumulationSolver.h
rename to src/spinAccumulationSolver.h
diff --git a/tags.cpp b/src/tags.cpp
similarity index 100%
rename from tags.cpp
rename to src/tags.cpp
diff --git a/tags.h b/src/tags.h
similarity index 100%
rename from tags.h
rename to src/tags.h
diff --git a/tetra.cpp b/src/tetra.cpp
similarity index 100%
rename from tetra.cpp
rename to src/tetra.cpp
diff --git a/tetra.h b/src/tetra.h
similarity index 100%
rename from tetra.h
rename to src/tetra.h
diff --git a/time_integration.cpp b/src/time_integration.cpp
similarity index 100%
rename from time_integration.cpp
rename to src/time_integration.cpp
diff --git a/time_integration.h b/src/time_integration.h
similarity index 100%
rename from time_integration.h
rename to src/time_integration.h
diff --git a/unit-tests/CMakeLists.txt b/unit-tests/CMakeLists.txt
index 5fd389b9..b6a09933 100644
--- a/unit-tests/CMakeLists.txt
+++ b/unit-tests/CMakeLists.txt
@@ -16,7 +16,7 @@ if(NOT GMSH_INC)
   message(FATAL_ERROR "Could not find gmsh.h")
 endif()
 
-include_directories (${CMAKE_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${GMSH_INC})
+include_directories (${CMAKE_SOURCE_DIR}/src ${Boost_INCLUDE_DIRS} ${GMSH_INC})
 
 set( BOOST_TEST_LOG_LEVEL "all" )
 
@@ -32,39 +32,39 @@ add_executable (test_ut_algebra ut_algebra.cpp)
 
 add_executable (test_ut_OMP_solver ut_OMP_solver.cpp)
 
-add_executable(test_ut_dukTapeParser ../expression_parser.cpp ut_dukTapeParser.cpp)
+add_executable(test_ut_dukTapeParser ../src/expression_parser.cpp ut_dukTapeParser.cpp)
 
 add_executable (test_ut_node ut_node.cpp)
 
 add_executable (test_ut_index ut_index.cpp)
 
-SET(SOURCES ../facette.cpp ../tetra.cpp ut_element.cpp)
+SET(SOURCES ../src/facette.cpp ../src/tetra.cpp ut_element.cpp)
 add_executable (test_ut_element ${SOURCES})
 
-SET(SOURCES ../facette.cpp ut_facette.cpp)
+SET(SOURCES ../src/facette.cpp ut_facette.cpp)
 add_executable (test_ut_facette ${SOURCES})
 
-SET(SOURCES ../facette.cpp ut_fac_charges.cpp)
+SET(SOURCES ../src/facette.cpp ut_fac_charges.cpp)
 add_executable (test_ut_fac_charges ${SOURCES})
 
-SET(SOURCES ../tetra.cpp ut_tetra.cpp)
+SET(SOURCES ../src/tetra.cpp ut_tetra.cpp)
 add_executable (test_ut_tetra ${SOURCES})
 
-SET(SOURCES ../tetra.cpp ut_tet_lumping.cpp)
+SET(SOURCES ../src/tetra.cpp ut_tet_lumping.cpp)
 add_executable (test_ut_tet_lumping ${SOURCES})
 
-SET(SOURCES ../tetra.cpp ut_tet_charges.cpp)
+SET(SOURCES ../src/tetra.cpp ut_tet_charges.cpp)
 add_executable (test_ut_tet_charges ${SOURCES})
 
-SET(SOURCES ../tetra.cpp ut_energy.cpp ../facette.cpp)
+SET(SOURCES ../src/tetra.cpp ut_energy.cpp ../src/facette.cpp)
 add_executable (test_ut_energy ${SOURCES})
 
-SET(SOURCES ../tetra.cpp ut_anisotropy.cpp)
+SET(SOURCES ../src/tetra.cpp ut_anisotropy.cpp)
 add_executable (test_ut_anisotropy ${SOURCES})
 
 add_executable (test_ut_tiny ut_tiny.cpp)
 
-set(SOURCES ../tetra.cpp ut_time_int.cpp)
+set(SOURCES ../src/tetra.cpp ut_time_int.cpp)
 add_executable (test_ut_time_int ${SOURCES})
 
 add_executable (test_ut_log-stats ut_log-stats.cpp)
diff --git a/unit-tests/sparse_matrix.h b/unit-tests/sparse_matrix.h
index 10a4603b..517e89d7 100644
--- a/unit-tests/sparse_matrix.h
+++ b/unit-tests/sparse_matrix.h
@@ -7,7 +7,7 @@
 
 #include <vector>
 
-#include "../algebra/sparseMat.h"
+#include "algebra/sparseMat.h"
 
 using algebra::SparseMatrix;
 using algebra::MatrixShape;
diff --git a/unit-tests/ut_algebra.cpp b/unit-tests/ut_algebra.cpp
index de70f57e..6bbefe14 100644
--- a/unit-tests/ut_algebra.cpp
+++ b/unit-tests/ut_algebra.cpp
@@ -7,9 +7,9 @@
 
 #include "ut_config.h"  // for tolerance UT_TOL macro
 #include "sparse_matrix.h"
-#include "../algebra/algebra.h"
-#include "../algebra/cg.h"
-#include "../algebra/bicg.h"
+#include "algebra/algebra.h"
+#include "algebra/cg.h"
+#include "algebra/bicg.h"
 
 using namespace algebra;