Implemented fibers support for meshes with same refinement levels. Te…

…sts are still needed.
rsachetto · Jun 23, 2020 · 5d5273c · 5d5273c
1 parent 6aaa00c
commit 5d5273c
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Showing 42 changed files with 6,753 additions and 3,169 deletions.
diff --git a/.clang-format b/.clang-format
@@ -4,7 +4,7 @@ AllowShortFunctionsOnASingleLine: None
 AllowShortLoopsOnASingleLine: false
 BinPackParameters: true
 BreakBeforeBinaryOperators: None
-ColumnLimit: 120
+ColumnLimit: 160
 IndentWidth: 4
 Language: Cpp
 SpaceBeforeAssignmentOperators: true

diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
diff --git a/bsbash/build_functions.sh b/bsbash/build_functions.sh
@@ -110,6 +110,17 @@ CLEAN_PROJECT () {
 
 }
 
+CLEAN_PROJECT_LIBS () {
+
+  DIR_NAME="${DEFAULT_BUILD_DIR}${1}"
+
+    for DIR in "${DIR_NAME}"/lib*; do
+        ECHO_AND_EXEC_COMMAND "find ${DIR} -name "*.o" -exec rm -rf {} \\";
+        ECHO_AND_EXEC_COMMAND "find ${DIR} -name "*.a" -exec rm -rf {} \\";
+        ECHO_AND_EXEC_COMMAND "find ${DIR} -name ".*last_compiled_time_bbash" -exec rm -rf {} \\";
+    done
+}
+
 PRINT_INFO () {
 	if [ -z "$QUIET" ]; then
   		printf "[INFO] ${INFO}%s${NC}\n" "$1"	

diff --git a/build.sh b/build.sh
@@ -19,6 +19,7 @@ fi
 COMPILE_GUI=''
 COMPILE_MPI=''
 COMPILE_CONVERTER=''
+COMPILE_FIBER_CONVERTER=''
 COMPILE_SIMULATOR=''
 COMPILE_WITH_DDM=''
 
@@ -55,6 +56,7 @@ for i in "${BUILD_ARGS[@]}"; do
         COMPILE_MPI='y'
         COMPILE_SIMULATOR='y'
         COMPILE_CONVERTER='y'
+        COMPILE_FIBER_CONVERTER='y'
     fi
 
     if [ "$i" == "simulator" ]; then        
@@ -204,6 +206,10 @@ if [ -n "$COMPILE_CONVERTER" ]; then
     COMPILE_EXECUTABLE "MonoAlg3D_converter" "src/main_converter.c" "" "$STATIC_DEPS" "$DYNAMIC_DEPS" "$EXTRA_LIB_PATH $LIBRARY_OUTPUT_DIRECTORY"
 fi
 
+if [ -n "$COMPILE_FIBER_CONVERTER" ]; then
+    COMPILE_EXECUTABLE "MonoAlg3D_fiber_converter" "src/main_fiber_converter.c" "" "$STATIC_DEPS" "$DYNAMIC_DEPS" "$EXTRA_LIB_PATH $LIBRARY_OUTPUT_DIRECTORY"
+fi
+
 FIND_CRITERION
 
 if [ -n "$CRITERION_FOUND" ]; then

diff --git a/example_configs/benchmark_config_example.ini b/example_configs/benchmark_config_example.ini
@@ -1,22 +1,22 @@
 [main]
 num_threads=6
-dt_pde=0.05
+dt_pde=0.005
 simulation_time=150
 abort_on_no_activity=false
 vm_threshold=-86.0
-use_adaptivity=true
+use_adaptivity=false
 start_adapting_at=1.2
 
 [update_monodomain]
 main_function=update_monodomain_default
 
 [save_result]
 ;/////mandatory/////////
-print_rate=0
-output_dir=outputs/9versions_benchmark_250_500
-main_function=save_as_text_or_binary
-#init_function=init_save_as_vtk_or_vtu
-#end_function=end_save_as_vtk_or_vtu
+print_rate=200
+output_dir=outputs/9versions_benchmark_200
+main_function=save_as_vtk
+init_function=init_save_as_vtk_or_vtu
+end_function=end_save_as_vtk_or_vtu
 ;binary=true
 ;save_pvd=true
 ;compress=true
@@ -32,23 +32,23 @@ derefine_each = 1
 
 [assembly_matrix]
 init_function=set_initial_conditions_fvm
-sigma_x=0.0000176
-sigma_y=0.0001334
+sigma_x=0.0001334
+sigma_y=0.0000176
 sigma_z=0.0000176
 library_file=shared_libs/libdefault_matrix_assembly.so
 main_function=homogeneous_sigma_assembly_matrix
 
 [linear_system_solver]
 tolerance=1e-15
-use_preconditioner=yes
 max_iterations=100
+use_gpu=true
 library_file=shared_libs/libdefault_linear_system_solver.so
 init_function=init_conjugate_gradient
 end_function=end_conjugate_gradient
 main_function=conjugate_gradient
 
 [ode_solver]
-dt=0.01
+dt=0.005
 use_gpu=true
 gpu_id=0
 library_file=shared_libs/libten_tusscher_2006.so

diff --git a/example_configs/domino_mesh.ini b/example_configs/domino_mesh.ini
@@ -1,7 +1,7 @@
 [main]
 num_threads=2
 dt_pde=0.02
-simulation_time=400.0
+simulation_time=0.02
 abort_on_no_activity=false
 use_adaptivity=false
 
@@ -42,8 +42,8 @@ refine_each = 1
 derefine_each = 1
 
 [domain]
-name=Plain Mesh
-main_function=domino_mesh
+name = Domino mesh
+main_function=initialize_grid_with_domino_mesh
 
 [ode_solver]
 dt=0.02