Merging Sachetto changes --> update_monodomain_library has been added!

CMakeLists.txt

@@ -3,10 +3,10 @@ IF(EXISTS "/etc/manjaro-release")
     set(CMAKE_CXX_COMPILER "/opt/cuda/bin/g++")
 ENDIF(EXISTS "/etc/manjaro-release")
 
-IF(EXISTS "/etc/debconf.conf")
-    set(CMAKE_C_COMPILER "/usr/bin/gcc-6")
-    set(CMAKE_CXX_COMPILER "/usr/bin/g++-6")
-ENDIF(EXISTS "/etc/debconf.conf")
+#IF(EXISTS "/etc/debconf.conf")
+#    set(CMAKE_C_COMPILER "/usr/bin/gcc-6")
+#    set(CMAKE_CXX_COMPILER "/usr/bin/g++-6")
+#ENDIF(EXISTS "/etc/debconf.conf")
 
 
 cmake_minimum_required(VERSION 3.0.1)
@@ -41,11 +41,11 @@ SET( CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/shared_libs )
 
 IF(MSVC)
 	SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} /w" )
-	ADD_SUBDIRECTORY(src/getopt)
-	ADD_SUBDIRECTORY(src/dlfcn-win32)
-	SET(OPT_DEPS getopt)
 ELSE()
 	SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fno-strict-aliasing -Wall -Wno-unused-function")
+    IF(CMAKE_BUILD_TYPE MATCHES DEBUG)
+        SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fno-omit-frame-pointer" )
+    ENDIF(CMAKE_BUILD_TYPE MATCHES DEBUG)
 ENDIF()
 
 FIND_PACKAGE(OpenMP)
@@ -78,42 +78,43 @@ IF (CUDA_FOUND)
        ENDIF()
     ENDIF()
 
-    ADD_SUBDIRECTORY(src/gpu_utils)
-    SET(OPT_DEPS gpu_utils)
+
 ENDIF(CUDA_FOUND)
 
 SET(OpenGL_GL_PREFERENCE "GLVND")
-
 FIND_PACKAGE(OpenGL)
 
-IF(OPENGL_FOUND AND OPENMP_FOUND)
-    IF(MSVC)
-        #SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -I \"${GLUT_INCLUDE_DIR}\" -DCOMPILE_OPENGL")
-        SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DCOMPILE_OPENGL")
-    ELSE()
-        #SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -I \"${OPENGL_INCLUDE_DIR}\" -I \"${GLUT_INCLUDE_DIR}\" -DCOMPILE_OPENGL")
-        SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DCOMPILE_OPENGL")
-    ENDIF()
-
-    set(BUILD_EXAMPLES OFF CACHE BOOL "" FORCE) # don't build the supplied examples
-    set(BUILD_GAMES    OFF CACHE BOOL "" FORCE) # or games
-
-    #    # build raylib
-    ADD_SUBDIRECTORY(src/raylib/src)
-
-    ADD_SUBDIRECTORY(src/draw)
-
-    SET(OPT_DEPS ${OPT_DEPS} draw raylib)
+IF(NOT MSVC AND OPENGL_FOUND AND OPENMP_FOUND)
+    SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DCOMPILE_OPENGL")
 ENDIF()
 
 ADD_SUBDIRECTORY(src/utils)
 ADD_SUBDIRECTORY(src/alg)
 ADD_SUBDIRECTORY(src/monodomain)
-ADD_SUBDIRECTORY(src/hash)
 ADD_SUBDIRECTORY(src/ini_parser)
 ADD_SUBDIRECTORY(src/string)
 ADD_SUBDIRECTORY(src/config)
 ADD_SUBDIRECTORY(src/graph)
+ADD_SUBDIRECTORY(src/vtk_utils)
+
+IF(NOT MSVC AND OPENGL_FOUND AND OPENMP_FOUND)
+    set(BUILD_EXAMPLES OFF CACHE BOOL "" FORCE)
+    set(BUILD_GAMES    OFF CACHE BOOL "" FORCE)
+    ADD_SUBDIRECTORY(src/raylib/src)
+    ADD_SUBDIRECTORY(src/draw)
+    SET(OPT_DEPS ${OPT_DEPS} draw raylib)
+ENDIF()
+
+IF(MSVC)
+    ADD_SUBDIRECTORY(src/getopt)
+    ADD_SUBDIRECTORY(src/dlfcn-win32)
+    SET(OPT_DEPS ${OPT_DEPS} getopt)
+ENDIF()
+
+IF (CUDA_FOUND)
+    ADD_SUBDIRECTORY(src/gpu_utils)
+    SET(OPT_DEPS ${OPT_DEPS} gpu_utils)
+ENDIF()
 
 #SET(COMPILE_GUI FALSE)
 #
@@ -131,21 +132,21 @@ ADD_SUBDIRECTORY(src/graph)
 #ENDIF()
 
 ADD_EXECUTABLE(MonoAlg3D src/main.c)
-ADD_DEPENDENCIES(MonoAlg3D utils alg solvers hashes ini_parser string graph config ${OPT_DEPS})
+ADD_DEPENDENCIES(MonoAlg3D utils alg solvers ini_parser string graph config ${OPT_DEPS})
 
 FIND_PACKAGE(MPI)
 IF(MPI_C_FOUND)
     INCLUDE_DIRECTORIES(${MPI_C_INCLUDE_PATH})
     ADD_EXECUTABLE(MonoAlg3D_batch src/main_batch.c)
-    ADD_DEPENDENCIES(MonoAlg3D_batch utils alg solvers hashes ini_parser string graph config ${OPT_DEPS})
-    TARGET_LINK_LIBRARIES(MonoAlg3D_batch alg solvers utils hashes ini_parser string graph config ${OPT_DEPS} ${CUDA_LIBRARIES} ${MPI_C_LIBRARIES}  dl m)
+    ADD_DEPENDENCIES(MonoAlg3D_batch utils alg solvers ini_parser string graph config ${OPT_DEPS})
+    TARGET_LINK_LIBRARIES(MonoAlg3D_batch alg solvers utils ini_parser string graph config ${OPT_DEPS} ${CUDA_LIBRARIES} ${MPI_C_LIBRARIES}  dl m)
 ENDIF(MPI_C_FOUND)
 
 IF(MSVC)
-    TARGET_LINK_LIBRARIES(MonoAlg3D alg solvers utils hashes ini_parser string graph config ${OPT_DEPS} ${CUDA_LIBRARIES} dl)
+    TARGET_LINK_LIBRARIES(MonoAlg3D alg solvers utils ini_parser string graph config ${OPT_DEPS} ${CUDA_LIBRARIES} dl)
     SET( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/shared_libs )
 ELSE()
-    TARGET_LINK_LIBRARIES(MonoAlg3D alg solvers utils hashes ini_parser string graph config ${OPT_DEPS} ${CUDA_LIBRARIES} dl m)
+    TARGET_LINK_LIBRARIES(MonoAlg3D alg solvers utils ini_parser string graph config ${OPT_DEPS} ${CUDA_LIBRARIES} dl m)
 ENDIF()
 
 ADD_SUBDIRECTORY(src/models_library)
@@ -161,7 +162,9 @@ ADD_SUBDIRECTORY(src/linear_system_solver_library)
 ADD_SUBDIRECTORY(src/save_mesh_library)
 ADD_SUBDIRECTORY(src/save_state_library)
 ADD_SUBDIRECTORY(src/restore_state_library)
+ADD_SUBDIRECTORY(src/update_monodomain_library)
 
 SET( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests_bin )
 
 ADD_SUBDIRECTORY(src/tests)
+

README.md

@@ -191,7 +191,7 @@ $ bin/MonoAlg3D -c example_configs/cuboid_ohara.ini
 The output will be saved in the VTK format. In order to see the results you can use Paraview (https://www.paraview.org/). You can also set the output to plain text, by changing the option ```vtk_output``` to false in the configuration file. The text format is defined as following:
 
 - Each line represents a Volume
-- Each volume is represented by its center point (X, Y, and Z), the value of halt of its side length and the calculated V
+- Each volume is represented by its center point (X, Y, and Z), the value of half of its side length and the calculated V
 
 Example file:
 

ToDo

@@ -1,5 +1,5 @@
 Sachetto
-- Rewrite the GUI using raygui https://github.com/raysan5/raygui
+- Rewrite the flags parsing using: https://github.com/kgabis/kgflags/blob/master/examples/full_api.c
 - Correct the domain version that sets the two scars and the fibrosis from file (maybe the error is on extra-data)
 - Compare the mesh with the mesh from the scientific reports paper
 - Use a sparse matrix format and take the matrix out of the alg mesh (http://people.sc.fsu.edu/~jburkardt/c_src/csparse/csparse.html)

clean_project.sh

@@ -1,3 +1,15 @@
 #!/bin/bash
-cd build; rm -r *; cd ..
-cd bin; rm *
+
+BUILD_DIR="build"
+
+if [[ "$#" -eq 1 ]]; then
+    BUILD_DIR=$1
+fi
+
+if [[ ! -d "${BUILD_DIR}" ]]; then
+  echo "Directory ${BUILD_DIR} does not exist"
+  exit
+fi
+
+rm -fr ${BUILD_DIR}/*
+rm -fr bin/*

example_configs/gold_simulation_no_adapt.ini

@@ -9,7 +9,7 @@ use_adaptivity=false
 [save_result]
 ;/////mandatory/////////
 print_rate=50
-output_dir=./tests_bin/gold_simulation_no_adapt_gpu
+output_dir=./outputs/gold_simulation_no_adapt_gpu
 function=save_as_text_or_binary
 ;function=save_as_vtu
 ;binary=false
@@ -49,4 +49,4 @@ start = 10.0
 duration = 2.0
 current = -38.0
 x_limit = 500.0
-function=stim_if_x_less_than
+function=stim_if_x_less_than

example_configs/mouse_mesh_config_example.ini

@@ -1,7 +1,7 @@
 [main]
 num_threads=4
 dt_pde=0.02
-simulation_time=0.3
+simulation_time=100.0
 abort_on_no_activity=false
 use_adaptivity=true
 start_adapting_at=1.2

example_configs/plain_mesh_ddm_2d.ini

@@ -15,6 +15,8 @@ save_pvd=true
 ;//////////////////
 file_prefix=V
 
+[update_monodomain]
+function=update_monodomain_ddm
 
 [assembly_matrix]
 sigma_x=0.00176

example_configs/plain_mesh_no_fibrosis_example.ini

@@ -1,7 +1,7 @@
 [main]
-num_threads=2
+num_threads=4
 dt_pde=0.02
-simulation_time=100.0
+simulation_time=200.0
 abort_on_no_activity=false
 use_adaptivity=false
 

example_configs/plain_mesh_with_fibrosis.ini

@@ -9,7 +9,9 @@ use_adaptivity=false
 ;/////mandatory/////////
 print_rate=50
 output_dir=./outputs/atpi_2_Ko_8_acidosis_single_cell
-function=save_as_text_or_binary
+;function=save_as_text_or_binary
+function=save_as_vtu
+save_pvd=true
 ;//////////////////
 file_prefix=V
 
@@ -32,7 +34,7 @@ start_dx=100.0
 start_dy=100.0
 start_dz=100.0
 side_length=10000.0
-;seed=1505958974
+seed=1505958974
 phi=0.36
 function=initialize_grid_with_plain_fibrotic_mesh
 
@@ -50,10 +52,10 @@ x_limit = 500.0
 function=stim_if_x_less_than
 
 [extra_data]
-atpi=2.0
-Ko=8.0
+atpi=4.0
+;Ko=8.0
 ;These paremeters below are for acidosis
-;Ki_multiplicator=1.0
-Ki_multiplicator=0.863259669
+Ki_multiplicator=1.0
+;Ki_multiplicator=0.863259669
 acidosis=true
 function=set_extra_data_for_fibrosis_plain

example_configs/plain_mesh_with_fibrosis_and_border_zone_inside_circle_example.ini

@@ -9,8 +9,8 @@ use_adaptivity=false
 /////mandatory/////////
 print_rate=50
 output_dir=./outputs/plain_and_circle
-function=save_as_vtu
-save_pvd=true
+function=save_as_vtk
+;save_pvd=true
 //////////////////
 file_prefix=V
 
@@ -36,8 +36,8 @@ function=initialize_grid_with_plain_and_sphere_fibrotic_mesh
 ;this are optional
 num_layers=1
 side_length=40000
-seed=1508201274
-phi=0.62
+;seed=1508201274
+phi=0.55
 plain_center=20050.0
 sphere_radius=14000.0
 border_zone_radius=16000.0

example_configs/valgring_run.ini

@@ -1,7 +1,7 @@
 [main]
 num_threads=1
 dt_pde=0.02
-simulation_time=3.0
+simulation_time=2.0
 abort_on_no_activity=false
 vm_threshold=-86.0
 use_adaptivity=true

recompile_project.sh

@@ -1,2 +1,21 @@
 #!/bin/bash
-cd build; cmake ..; make
+
+BUILD_DIR="build"
+BUILD_TYPE="Release"
+
+if [[ "$#" -eq 1 ]]; then
+    BUILD_DIR=$1
+fi
+
+if [[ "$#" -eq 2 ]]; then
+    BUILD_DIR=$1
+    BUILD_TYPE=$2
+fi
+
+
+if [[ ! -d "${BUILD_DIR}" ]]; then
+  echo "Directory ${BUILD_DIR} does not exist. Creating."
+  mkdir ${BUILD_DIR}
+fi
+
+cd ${BUILD_DIR}; cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} ..; make

scripts/animations/convert_png_to_mp4.sh

@@ -12,4 +12,4 @@ OUTPUT_VIDEO_FILENAME="video/ddm_3d"
 RESOLUTION="1020x720"
 
 # Execute the converting command using FFMPEG
-ffmpeg -r $FRAME_RATE -f image2 -s $RESOLUTION -start_number 1 -i $FILENAME.%04d.png -vframes $END_FRAME -vcodec libx264 -crf 25  -pix_fmt yuv420p $OUTPUT_VIDEO_FILENAME.mp4
+ffmpeg -r ${FRAME_RATE} -f image2 -s ${RESOLUTION} -start_number 1 -i ${FILENAME}.%04d.png -vframes ${END_FRAME} -vcodec libx264 -crf 25  -pix_fmt yuv420p ${OUTPUT_VIDEO_FILENAME}.mp4

scripts/calc_APD.py

@@ -1,15 +1,16 @@
 from sys import argv
 
+
 def forwarddiff(y, h):
     n = len(y)
     res = []
-    i = 1
 
-    for i in range(1,n):
-        res.append((y[i] - y[i-1]) / h);
+    for i in range(1, n):
+        res.append((y[i] - y[i-1]) / h)
 
     return res
 
+
 def slope_start(data, start=0, epsilon=0.0001, h=1.0):
 
     d = data[start:]
@@ -19,6 +20,7 @@ def slope_start(data, start=0, epsilon=0.0001, h=1.0):
         if abs(d[i] - d[i-1]/h) > epsilon:
             return i+start
 
+
 def slope_end(data, start=0, epsilon=0.0001, h=1.0):
 
     d = data[start:]
@@ -29,7 +31,6 @@ def slope_end(data, start=0, epsilon=0.0001, h=1.0):
             return i+start
 
 
-
 def max_index(data, start, end):
 
     d = data[start:(start+end)]
@@ -40,13 +41,15 @@ def max_index(data, start, end):
 
     return max_index
 
+
 def index_activation(data, start=0):
     d = data[start:]
 
     for i, v in enumerate(d):
-        if d[i+start] < 0.0 and d[i+start+1] > 0.0:
+        if d[i + start] < 0.0 < d[i + start + 1]:
             return i+start
 
+
 ap_file_name = argv[1]
 num_aps = int(argv[2])
 ms_each_step = float(argv[3])

scripts/getAps.sh

@@ -1,10 +1,11 @@
+#!/usr/bin/env bash
 AP_DIR=$1
 AP_PREFIX=$2
 AP_LINE=$3
 AP_OUT=$4
 CELL_ID=$5
 
-if [ "$#" -ne 5 ]; then
+if [[ "$#" -ne 5 ]]; then
     echo "-------------------------------------------------------------------"
     echo "Usage:> $0 <AP_DIR> <AP_PREFIX> <AP_LINE> <AP_OUT> <CELL_ID>"
     echo "-------------------------------------------------------------------"
@@ -24,5 +25,5 @@ if [ "$#" -ne 5 ]; then
     exit 1
 fi
 
-for i in `ls -1v ${AP_DIR}/${AP_PREFIX}*`; do sed -n "${AP_LINE}p" $i | awk -v "col=${CELL_ID}" -F ' ' '{print $col}'  ; done > output/${AP_OUT}.txt
+for i in `ls -1v ${AP_DIR}/${AP_PREFIX}*`; do sed -n "${AP_LINE}p" ${i} | awk -v "col=${CELL_ID}" -F ' ' '{print $col}'  ; done > output/${AP_OUT}.txt