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Bioelectrics/Monodomain/CMakeLists.txt

@@ -0,0 +1,48 @@
+# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification)
+# is a mathematical modelling environment that enables the application of finite element
+# analysis techniques to a variety of complex bioengineering problems.
+# 
+# The OpenCMISS project website can be found at http://www.opencmiss.org
+# For more information see http://www.opencmiss.org/documentation
+
+# Include the OpenCMISS initalisation & macro definition file.
+include(./OpenCMISS.cmake)
+message(STATUS "C Compiler: ${CMAKE_C_COMPILER}")
+message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}")
+
+set(CMAKE_C_COMPILER mpiicc)
+set(CMAKE_Fortran_COMPILER mpiifort)
+
+# Project setup
+# -------------
+cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+
+option(USE_MPI "Use MPI" ON)
+
+project(OpenCMISS-Example VERSION 1.0 LANGUAGES C Fortran)
+enable_testing()
+
+message(STATUS "C Compiler: ${CMAKE_C_COMPILER}")
+message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}")
+message(STATUS "MPI: ${MPI}")
+message(STATUS "Instrumentation: ${OC_INSTRUMENTATION}")
+
+
+# Find OpenCMISS
+# --------------
+#
+# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. 
+# Currently available OpenCMISS package components: Iron Zinc
+# Requiring Iron will also include the iron_c bindings target if available.
+#
+# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components.
+# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include
+# paths needed!               
+#find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG)
+#find_package(MPI REQUIRED)
+
+# CMake application code
+# ----------------------
+if (CMAKE_Fortran_COMPILER)
+    add_subdirectory(Fortran)
+endif()

Bioelectrics/Monodomain/Fortran/CMakeLists.txt

@@ -0,0 +1,53 @@
+# Add example executable
+link_directories(/data/OpenCMISS/install/x86_64_linux/intel-C17.0-intel-F17.0/intel_release/lib)
+add_executable(MonodomainFortran src/FortranExample.f90)
+
+# Turn on Fortran preprocessing (#include directives)
+if (MSVC)
+    set(PROC_OPT "/fpp")
+else()
+    set(PROC_OPT "-cpp")
+endif()
+target_compile_options(MonodomainFortran PRIVATE ${PROC_OPT})
+
+# Link to opencmiss
+# -----------------
+#
+# This simply uses the opencmiss target created by OC_INIT() above.
+#
+# Alternatively, you can also directly invoke 'find_package(Iron <IRON_VERSION>)' to explicitly
+# require that version. But then you have to deal with setting up the correct MPI include directives and library paths.
+#
+# If required, add any other required link libraries (cellml, petsc ..) here, too.
+# For example, if you needed PetSC functionality, issue
+#
+#     find_package(PETSC <PETSC_VERSION> REQUIRED)
+#     target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc)
+#
+# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name.
+target_link_libraries(MonodomainFortran PRIVATE libirond.so)
+target_include_directories(MonodomainFortran
+PRIVATE /data/OpenCMISS/install/x86_64_linux/intel-C17.0-intel-F17.0/intel_release/include/opencmiss)
+target_include_directories(MonodomainFortran PRIVATE /opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/include)
+# Add a simple test that runs the executable
+add_test(NAME MonodomainFortranTest COMMAND MonodomainFortran)
+#add_opencmiss_environment(MonodomainFortranTest)
+
+###################
+# Developer notice!
+#
+# If you write Fortran code and use MPI, you need to use the following MPI directives:
+#
+# #ifndef NOMPIMOD
+#   USE MPI
+# #endif
+# [...]
+#   IMPLICIT NONE
+# [...]
+# #ifdef NOMPIMOD
+#     #include "mpif.h"
+# #endif
+#
+# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make
+# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly.
+#

Bioelectrics/Monodomain/Fortran/src/FortranExample.f90

@@ -108,7 +108,7 @@ PROGRAM MONODOMAINEXAMPLE
 
   REAL(CMISSRP) :: X,Y,DISTANCE,gNa_VALUE
 
-  INTEGER(CMISSIntg), PARAMETER :: NUMBER_OF_ELEMENTS=25
+  INTEGER(CMISSIntg), PARAMETER :: NUMBER_OF_ELEMENTS=10
   INTEGER(CMISSIntg) :: OUTPUT_FREQUENCY = 1
   REAL(CMISSRP), PARAMETER :: STIM_VALUE = 100.0_CMISSRP
   REAL(CMISSRP), PARAMETER :: STIM_STOP = 0.10_CMISSRP

Bioelectrics/Monodomain/Fortran/visualise.cmgui

@@ -0,0 +1,51 @@
+gfx read node MonodomainExample.part0.exnode;
+gfx read element MonodomainExample.part0.exelem; 
+gfx read node Time_2_1.part0.exnode
+#gfx read node Time_2_2.part0.exnode time 2
+#gfx read node Time_2_3.part0.exnode time 3
+#gfx read node Time_2_4.part0.exnode time 4
+#gfx read node Time_2_5.part0.exnode time 5
+#gfx read node Time_2_6.part0.exnode time 6
+#gfx read node Time_2_7.part0.exnode time 7
+#gfx read node Time_2_8.part0.exnode time 8
+#gfx read node Time_2_9.part0.exnode time 9
+#gfx read node Time_2_10.part0.exnode time 10
+#gfx read node Time_2_11.part0.exnode time 11
+#gfx read node Time_2_12.part0.exnode time 12
+#gfx read node Time_2_13.part0.exnode time 13
+#gfx read node Time_2_14.part0.exnode time 14
+#gfx read node Time_2_15.part0.exnode time 15
+#gfx read node Time_2_16.part0.exnode time 16
+#gfx read node Time_2_17.part0.exnode time 17
+#gfx read node Time_2_18.part0.exnode time 18
+#gfx read node Time_2_19.part0.exnode time 19
+#gfx read node Time_2_20.part0.exnode time 20
+#gfx read node Time_2_21.part0.exnode time 21
+#gfx read node Time_2_22.part0.exnode time 22
+#gfx read node Time_2_23.part0.exnode time 23
+#gfx read node Time_2_24.part0.exnode time 24
+#gfx read node Time_2_25.part0.exnode time 25
+#gfx read node Time_2_26.part0.exnode time 26
+#gfx read node Time_2_27.part0.exnode time 27
+#gfx read node Time_2_28.part0.exnode time 28
+#gfx read node Time_2_29.part0.exnode time 29
+#gfx read node Time_2_30.part0.exnode time 30
+
+#@exnodes=<./Time_*.part*.exnode>;
+#$time_index=1;
+#foreach $filename (@exnodes) {
+#    print "Reading $filename\n";
+#    gfx read node "$filename" time $time_index;
+#    $time_index++;
+#}
+gfx define faces egroup Region;
+gfx create window 1;
+gfx modify window 1 background colour 1.0 1.0 1.0;
+gfx modify window 1 view interest_point 0.5,0.5,0.0 eye_point 0.5,0.5,3.0 up_vector 0.0,1.0,0.0;
+gfx modify spectrum default clear overwrite_colour;
+gfx modify spectrum default linear reverse range -95.0 50.0 extend_above extend_below rainbow colour_range 0 1 component 1;
+gfx modify spectrum default linear reverse range -95.0 50.0 banded number_of_bands 10 band_ratio 0.05 component 1;
+gfx modify g_element Region lines material black;
+gfx modify g_element Region surfaces select_on coordinate Coordinate material default data Vm spectrum default selected_material default_selected render_shaded;
+gfx print jpg window 1 file gNa.jpg;
+gfx print postscript window 1 file gNa.ps;

Bioelectrics/Monodomain/OpenCMISS.cmake

@@ -0,0 +1,97 @@
+###########################
+# *DO NOT CHANGE THIS FILE*
+###########################
+#
+# Prepares the use of OpenCMISS by scanning at various path locations for OpenCMISS (SDK) installations.
+#
+# Search order:
+#     - OPENCMISS_INSTALL_DIR variable
+#     - OPENCMISS_INSTALL_DIR environment variable
+#     - OPENCMISS_SDK_DIR variable
+#     - OPENCMISS_SDK_DIR environment variable
+#     - [Windows only] The Registry is searched additionally for installed SDKs.
+#
+# If found
+#     - Includes the toolchain config script of the found opencmiss installation to enable toolchain selection logic (non-windows)
+
+# Convenience: The OPENCMISS_INSTALL_DIR may also be defined in the environment and various other places
+if (DEFINED OPENCMISS_INSTALL_DIR)
+    get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+        message(STATUS "Using specified installation directory '${OPENCMISS_INSTALL_DIR}'")
+    else()
+        message(WARNING "The specified OPENCMISS_INSTALL_DIR '${OPENCMISS_INSTALL_DIR}' does not exist. Skipping.")
+        unset(OPENCMISS_INSTALL_DIR)
+    endif()
+endif()
+if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_INSTALL_DIR}" STREQUAL "")
+    file(TO_CMAKE_PATH "$ENV{OPENCMISS_INSTALL_DIR}" OPENCMISS_INSTALL_DIR)
+    get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+        message(STATUS "Using environment installation directory '${OPENCMISS_INSTALL_DIR}'")
+    else()
+        message(WARNING "The environment variable OPENCMISS_INSTALL_DIR='${OPENCMISS_INSTALL_DIR}' contains an invalid path. Skipping.")
+        unset(OPENCMISS_INSTALL_DIR)
+    endif()
+endif()
+if (NOT OPENCMISS_INSTALL_DIR AND DEFINED OPENCMISS_SDK_DIR)
+    get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_SDK_DIR}")
+        message(STATUS "Using SDK installation directory: ${OPENCMISS_SDK_DIR}")
+        set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}")
+    else()
+        message(WARNING "The specified OPENCMISS_SDK_DIR '${OPENCMISS_SDK_DIR}' does not exist. Skipping.")
+    endif()
+endif()    
+if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_SDK_DIR}" STREQUAL "")
+    file(TO_CMAKE_PATH "$ENV{OPENCMISS_SDK_DIR}" OPENCMISS_SDK_DIR)
+    get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_SDK_DIR}")
+        message(STATUS "Using environment SDK installation directory: ${OPENCMISS_SDK_DIR}")
+        set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}")
+    else()
+        message(WARNING "The environment variable OPENCMISS_SDK_DIR='${OPENCMISS_SDK_DIR}' contains an invalid path. Skipping.")
+        unset(OPENCMISS_SDK_DIR)
+    endif()
+endif()
+# On windows: check the registry for installed OpenCMISS SDKs
+if(NOT OPENCMISS_INSTALL_DIR AND WIN32)
+    foreach(ROOT HKEY_CURRENT_USER HKEY_LOCAL_MACHINE)
+        foreach(PACKAGE OpenCMISSUserSDK OpenCMISSDeveloperSDK)
+            set(_REG_KEY "[${ROOT}\\Software\\Auckland Bioengineering Institute\\${PACKAGE}]")
+            get_filename_component(OPENCMISS_INSTALL_DIR "${_REG_KEY}" ABSOLUTE)
+            #message(STATUS "Trying registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}")
+            if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+                message(STATUS "Found ${PACKAGE} in Windows registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}")
+                break()
+            else()
+                unset(OPENCMISS_INSTALL_DIR)
+            endif()         
+        endforeach()
+        if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+            break()
+        endif()
+    endforeach()
+endif()
+
+if(OPENCMISS_INSTALL_DIR)
+    message(STATUS "OPENCMISS_INSTALL_DIR=${OPENCMISS_INSTALL_DIR}")
+    # Use the OpenCMISS scripts to also allow choosing a separate toolchain
+    # This file is located at the opencmiss installation rather than the local example
+    # as it avoids file replication and makes maintenance much easier
+    if (TOOLCHAIN)
+        set(_OCTC ${OPENCMISS_INSTALL_DIR}/share/cmake/Modules/OpenCMISS/OCToolchainCompilers.cmake)
+        if (EXISTS "${_OCTC}")
+            include(${_OCTC})
+        else()
+            message(WARNING "TOOLCHAIN specified but OpenCMISS config script could not be found at ${_OCTC}. Trying CMake defaults.")
+        endif()
+        unset(_OCTC)
+    endif()
+    set(OpenCMISS_DIR "${OPENCMISS_INSTALL_DIR}" CACHE PATH "Path to the found OpenCMISS (SDK) installation")    
+else()
+    message(WARNING "No OpenCMISS (SDK) installation directory detected. Using default system environment.")
+endif()
+
+message(STATUS "C Compiler: ${CMAKE_C_COMPILER}")
+message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}")

Bioelectrics/Monodomain/Python/Monodomain2DSquare.py

@@ -6,7 +6,7 @@
 sys.path.insert(1, os.path.join((os.environ['OPENCMISS_ROOT'],'cm','bindings','python')))
 
 # Intialise OpenCMISS
-from opencmiss import iron
+from opencmiss.iron import iron
 #DOC-END imports
 
 # Set problem parameters
@@ -25,10 +25,10 @@
 # Simulation parameters
 stimValue = 100.0
 stimStop = 0.1
-timeStop = 1.5
+timeStop = 4.0
 odeTimeStep = 0.00001
 pdeTimeStep = 0.001
-outputFrequency = 1
+outputFrequency = 10
 #DOC-END parameters
 
 #Setup field number handles

ClassicalField/Laplace/Laplace/C/CMakeLists.txt

@@ -0,0 +1,25 @@
+# Add example executable
+add_executable(laplace_c src/CExample.c)
+
+#
+# Link to opencmiss
+# -----------------
+#
+# This simply uses the opencmiss target created by OC_INIT() above.
+#
+# Alternatively, you can also directly invoke 'find_package(Iron <IRON_VERSION>)' to explicitly
+# require that version. But then you have to deal with setting up the correct MPI include directives and library paths.
+#
+# If required, add any other required link libraries (cellml, petsc ..) here, too.
+# For example, if you needed PetSC functionality, issue
+#
+#     find_package(PETSC <PETSC_VERSION> REQUIRED)
+#     target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc)
+#
+# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name.
+target_link_libraries(laplace_c PRIVATE opencmiss)
+target_link_libraries(laplace_c PUBLIC $<BUILD_INTERFACE:mpi>)
+
+# Add a simple test that runs the executable
+add_test(NAME Laplace_C COMMAND laplace_c)
+add_opencmiss_environment(Laplace_C)

ClassicalField/Laplace/Laplace/CMakeLists.txt

@@ -0,0 +1,55 @@
+# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification)
+# is a mathematical modelling environment that enables the application of finite element
+# analysis techniques to a variety of complex bioengineering problems.
+# 
+# The OpenCMISS project website can be found at http://www.opencmiss.org
+# For more information see http://www.opencmiss.org/documentation
+
+# Include the OpenCMISS initalisation & macro definition file.
+include(./OpenCMISS.cmake)
+
+# Project setup
+# -------------
+cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+
+option(USE_MPI "Use MPI" ON)
+
+if (USE_MPI)
+   message(STATUS "Setting compiler to MPIC")
+   if(OC_INSTRUMENTATION STREQUAL scorep)
+     set(CMAKE_Fortran_COMPILER scorep-mpif90)
+     set(CMAKE_C_COMPILER scorep-mpicc)
+   else()
+     set(CMAKE_Fortran_COMPILER mpif90)
+     set(CMAKE_C_COMPILER mpicc)
+   endif()
+endif()
+
+project(OpenCMISS-Example VERSION 1.0 LANGUAGES C Fortran)
+enable_testing()
+
+message(STATUS "C Compiler: ${CMAKE_C_COMPILER}")
+message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}")
+message(STATUS "MPI: ${MPI}")
+message(STATUS "Instrumentation: ${OC_INSTRUMENTATION}")
+
+
+# Find OpenCMISS
+# --------------
+#
+# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. 
+# Currently available OpenCMISS package components: Iron Zinc
+# Requiring Iron will also include the iron_c bindings target if available.
+#
+# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components.
+# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include
+# paths needed!               
+find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG)
+#find_package(MPI REQUIRED)
+
+# CMake application code
+# ----------------------
+if (CMAKE_Fortran_COMPILER)
+    add_subdirectory(Fortran)
+    add_subdirectory(C)
+endif()