Rename svFSIplus to svMultiPhysics (#308)

* Change file name.

* Change names for high-level CMake for project name, executable, etc.

* Chane Docker files.

* Change documention files.

* Change thirdparty parametis_svfsi to parmetis_internal.

* Rename thridparty gklib_svfsi to gklib_internal.

* change thridparty metis_svfsi to metis_internal

* Rename package Booleans using svFSI.

* Add CMake comments to try to explain how all of the thirdparty works.

* Rename svFSI and svFSILS source code directories.

* Change tests Python scripts to use vMultiPhysics, change svFSIplus.xml to solver.xml, replace svFSIFile with svMultiPhysicsFile in xml files.

* Change names in workflow yaml files.

* Update README with name change.

* Fix some missed name changes.

* Remove some testing artifacts.

* Add missing slash.

* Rename some directories used by genbc.

* Rename some solver input parameter files named with the solver name.

* Change more hidden svFSIplus names.

* Modify container section.

Author: ktbolt

.github/workflows/test_macos.yml

@@ -26,22 +26,22 @@ jobs:
           cd build
           cmake ..
           make -j2
-      - name: Build svFSIplus
+      - name: Build svMultiPhysics
         run: |
           mkdir build
           cd build
           cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON ..
           make -j2
       - name: Install test dependencies
         run: |
-          conda create -n svfsiplus python=3.9
-          conda run -n svfsiplus pip install pytest pytest-cov pytest-mock numpy meshio pandas
+          conda create -n svmultiphysics python=3.9
+          conda run -n svmultiphysics pip install pytest pytest-cov pytest-mock numpy meshio pandas
       - name: Run integration tests
         run: |
           git lfs pull
           cd tests
-          conda run -n svfsiplus pytest -rPv --durations=0
+          conda run -n svmultiphysics pytest -rPv --durations=0
       - name: Run unit tests
         run: |
-          cd build/svFSIplus-build/Source/svFSI
+          cd build/svMultiPhysics-build/Source/solver
           ctest --verbose

.github/workflows/test_ubuntu.yml

@@ -13,22 +13,22 @@ jobs:
               version: ubuntu-22.04
               image: ubuntu22
       runs-on: ${{ matrix.version }}
-      container: dcodoni/lib:${{ matrix.image }}
+      container: simvascular/libraries:${{ matrix.image }}
       steps:
         - uses: actions/checkout@v3
         - name: Build svZeroDSolver
           shell: bash
           run: |
             conda init
             source /conda/etc/profile.d/conda.sh
-            conda activate svfsiplus
+            conda activate svmultiphysics
             git clone https://github.com/SimVascular/svZeroDSolver.git
             cd svZeroDSolver
             mkdir build
             cd build
             cmake ..
             make -j2
-        - name: Build svFSIplus
+        - name: Build svMultiPhysics
           run: |
             if [ -d "build" ]; then
             rm -rf "build"
@@ -38,7 +38,7 @@ jobs:
             cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON -DSV_USE_TRILINOS:BOOL=ON ..
             make -j2
             cd ..
-        - name: Build svFSIplus (PETSc)
+        - name: Build svMultiPhysics (PETSc)
           run: |
             if [ -d "build-petsc" ]; then
             rm -rf "build-petsc"
@@ -50,23 +50,23 @@ jobs:
             cd ..
         - name: Run integration tests
           run: |
-            git config --global --add safe.directory /__w/svFSIplus/svFSIplus
+            git config --global --add safe.directory /__w/svMultiPhysics/svMultiPhysics
             git lfs pull
             cd tests
-            conda run -n svfsiplus pytest -rPv --durations=0
+            conda run -n svmultiphysics pytest -rPv --durations=0
         - name: Run unit tests
           run: |  
-            cd build/svFSIplus-build/Source/svFSI
+            cd build/svMultiPhysics-build/Source/solver
             ctest --verbose
         - name: Generate code coverage
           run: |
-            cd build/svFSIplus-build
+            cd build/svMultiPhysics-build
             make coverage
         - name: Save coverage report
           uses: actions/upload-artifact@v3
           with:
             name: coverage_report
-            path: build/svFSIplus-build/coverage
+            path: build/svMultiPhysics-build/coverage
         - name: Upload coverage reports to Codecov
           uses: codecov/codecov-action@v3
           env:

CMakeLists.txt

@@ -81,7 +81,7 @@ include(SimVascularFunctionCheckCompilerFlags)
 
 # Add additional variables that can be set from the cmake gui or from the command line.
 #
-# These variables must later be add to 'ExternalProject_Add(svFSI' as -D options. 
+# These variables must later be add to 'ExternalProject_Add(svMultiPhysics' as -D options. 
 #
 set(SV_USE_TRILINOS OFF CACHE BOOL "Build with the Trilinos linear algebra package")
 #set(SV_USE_PETSC OFF CACHE BOOL "Build with the PETSc linear algebra package")
@@ -118,16 +118,17 @@ ExternalProject_Add(Externals
     ${SV_EXTERNALS_APPLE_CMAKE_ARGS}
     ${SV_EXTERNALS_ADDITIONAL_CMAKE_ARGS}
     )
+
 set(SV_EXTERNALS_TOPLEVEL_DIR "${CMAKE_BINARY_DIR}/Externals-build/sv_externals")
-#-----------------------------------------------------------------------------
 
-#-----------------------------------------------------------------------------
-# svFSIplus solver.
+# svMultiPhysics 
+#
 set(SV_ADDITIONAL_CMAKE_ARGS "" CACHE STRING "If more options want to be provided to the sv_externals build, they can be with this string")
 set(SV_APPLE_CMAKE_ARGS)
-ExternalProject_Add(svFSIplus
+
+ExternalProject_Add(svMultiPhysics
   SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Code
-  BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/svFSIplus-build
+  BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/svMultiPhysics-build
   DEPENDS Externals
   DOWNLOAD_COMMAND ""
   UPDATE_COMMAND ""

Code/CMake/LINEAR_SOLVERConfig.cmake

@@ -0,0 +1,23 @@
+
+
+set(LINEAR_SOLVER_DEFINITIONS "")
+set(LINEAR_SOLVER_NEEDED_LIBS LINEAR_SOLVER)
+
+if(IS64 AND (WIN32 OR CYGWIN))
+unset(LINEAR_SOLVER_INCLUDE_DIR)
+	set(LINEAR_SOLVER_PATH_PREFIX "LINEAR_SOLVER-2013.08.10/win/x64")
+	set(LINEAR_SOLVER_FULL_PATH "${LicensedLibs_Bin_Directory}${LINEAR_SOLVER_PATH_PREFIX}")
+	set(LINEAR_SOLVER_LIB_DIR "${LINEAR_SOLVER_FULL_PATH}" CACHE TYPE PATH)
+	set(LINEAR_SOLVER_POSSIBLE_INCLUDE_DIR "${LINEAR_SOLVER_FULL_PATH}" CACHE TYPE PATH)
+endif()
+
+find_path(LINEAR_SOLVER_INCLUDE_DIR LINEAR_SOLVER.h HINTS ${LINEAR_SOLVER_POSSIBLE_INCLUDE_DIR})
+
+GENLIBS(LINEAR_SOLVER_LIBRARY "${LINEAR_SOLVER_NEEDED_LIBS}" "LINEAR_SOLVER" "${LINEAR_SOLVER_LIB_DIR}")
+set(LINEAR_SOLVER_LIBRARY ${LINEAR_SOLVER_LINEAR_SOLVER_LIBRARY})
+
+include_directories(${LINEAR_SOLVER_INCLUDE_DIR})
+link_directories(${LINEAR_SOLVER_LIB_DIR})
+add_definitions(${LINEAR_SOLVER_DEFINITIONS})
+
+

Code/CMake/SVFSILSConfig.cmake

@@ -1,13 +1,20 @@
+
+# These names are used to create variables used to store the package library name.
+#
+#   THIRDPARTY_METIS_INTERNAL is used to create the variable 
+#   SV_LIB_THIRDPARTY_METIS_INTERNAL_NAME 
+#
+#   SV_LIB_THIRDPARTY_METIS_INTERNAL_NAME is later used to set the value 
+#   for the METIS_INTERNAL_LIBRARY_NAME variable in SimVascularThirdParty.cmake.
+# 
 set(SV_LIBS
-  THIRDPARTY_METIS_SVFSI
-  THIRDPARTY_PARMETIS_SVFSI
-  THIRDPARTY_GKLIB_SVFSI
+  THIRDPARTY_METIS_INTERNAL
+  THIRDPARTY_PARMETIS_INTERNAL
+  THIRDPARTY_GKLIB_INTERNAL
   THIRDPARTY_TETGEN
   THIRDPARTY_TINYXML
   THIRDPARTY_ZLIB
-  SVFSILS
-  SVFSI_CINTERFACE
-  SVFSILS_CINTERFACE
+  LINEAR_SOLVER
 )
 
 foreach(lib ${SV_LIBS})

Code/CMake/SimVascularInternals.cmake

@@ -155,6 +155,12 @@ endmacro()
 #-----------------------------------------------------------------------------
 # simvascular_third_party
 #
+# This adds a package defined in the Code/ThirdParty directory to the build. 
+#
+# 1) Creates an include file
+# 2) Adds the package directory to the build
+# 3) Creates the <package>_LIBRARY_NAME variable
+#
 macro(simvascular_third_party _pkg)
   string(TOLOWER "${_pkg}" _lower)
   string(TOUPPER "${_pkg}" _upper)
@@ -163,13 +169,16 @@ macro(simvascular_third_party _pkg)
     DOWNLOADABLE SYSTEM_DEFAULT
     SVEXTERN_CONFIG ADD_INSTALL
     )
+
   set(oneValueArgs VERSION)
   set(multiValueArgs PATHS HINTS COMPONENTS)
 
   cmake_parse_arguments("simvascular_third_party"
     "${options}"
     "${oneValueArgs}" "${multiValueArgs}" ${ARGN} )
+
   set(${_upper}_SUBDIR ThirdParty/${_pkg})
+
   if(simvascular_third_party_SYSTEM_DEFAULT)
     option(SV_USE_SYSTEM_${_upper} "Use system ${_pkg}" ON)
   else()
@@ -178,9 +187,15 @@ macro(simvascular_third_party _pkg)
 
   mark_as_advanced(SV_USE_SYSTEM_${_upper})
 
+  # Create a package include file and to be used in the build.
+  #
   configure_file(${SV_SOURCE_DIR}/${${_upper}_SUBDIR}/simvascular_${_lower}.h.in
     ${SV_BINARY_DIR}/${${_upper}_SUBDIR}/simvascular_${_lower}.h)
+
   include_directories(BEFORE ${SV_BINARY_DIR}/${${_upper}_SUBDIR} ${SV_SOURCE_DIR}/${${_upper}_SUBDIR})
+
+  # Add the package to the build.
+  #
   if(SV_USE_SYSTEM_${_upper})
     set(${_upper}_LIBRARIES)
     set(${_upper}_LIBRARY)
@@ -191,6 +206,7 @@ macro(simvascular_third_party _pkg)
     endif()
   endif()
 endmacro()
+
 #-----------------------------------------------------------------------------
 # print_vars - THis is a simple marco to print out a list of variables
 # with their names and value, used mostly for debugging

Code/CMake/SimVascularMacros.cmake

@@ -56,13 +56,11 @@ option(SV_USE_NOTIMER "Use notimer" ON)
 
 #-----------------------------------------------------------------------------
 # Solver Build Options (Modules)
-option(SV_USE_EIGEN_SVFSI "Use Eigen headers" ON)
-option(SV_USE_METIS_SVFSI "Use metis_svfsi Library" ON)
-option(SV_USE_GKLIB_SVFSI "Use GKlib_svfsi Library" ON)
-option(SV_USE_PARMETIS_SVFSI "Use parmetis_svfsi Library" ON)
-option(SV_USE_TETGEN "Use tetgen Library" ON)
-
-#-----------------------------------------------------------------------------
+option(SV_USE_INTERNAL_EIGEN "Use Eigen headers" ON)
+option(SV_USE_INTERNAL_METIS "Use the internal metis library" ON)
+option(SV_USE_INTERNAL_GKLIB "Use the internal GKlib library" ON)
+option(SV_USE_INTERNAL_PARMETIS "Use the internal parmetis library" ON)
+option(SV_USE_TETGEN "Use tetgen library" ON)
 
 #-----------------------------------------------------------------------------
 # Externals
@@ -78,10 +76,10 @@ option(SV_EXTERNALS_USE_TOPLEVEL_DIR "If ON, SV_EXTERNALS_TOPLEVEL_DIR will be u
 
 
 #-----------------------------------------------------------------------------
-# SVFSILS linear solver is always on 
+# The internal linear solver is always on 
 #-----------------------------------------------------------------------------
-set(USE_SVFSILS 1)
-set(SVFSILS_BUILD_TYPE "Source")
+set(USE_LINEAR_SOLVER 1)
+set(LINEAR_SOLVER_BUILD_TYPE "Source")
 
 #-----------------------------------------------------------------------------
 # WIN32

Code/CMake/SimVascularOptions.cmake

@@ -1,51 +1,40 @@
-#-----------------------------------------------------------------------------
-# GKLIB_SVFSI
-if(SV_USE_GKLIB_SVFSI)
-  set(USE_GKLIB_SVFSI ON)
-  simvascular_third_party(gklib_svfsi)
-  # require to be built here
-  set(GKLIB__SVFSI_LIBRARY ${SV_LIB_THIRDPARTY_GKLIB_SVFSI_NAME})
+
+# The Boolean SV_USE variables are set in SimVascularOptions.cmake.
+#
+# The SV_LIB_THIRDPARTY_*_INTERNAL_NAME is set in SimVascularInternals.cmake.
+#
+# The *_internal name must match the directory name in Code/ThirdParty
+#
+if(SV_USE_INTERNAL_GKLIB)
+  set(USE_INTERNAL_GKLIB ON)
+  simvascular_third_party(gklib_internal)
 endif()
 
-# METIS_SVFSI
-if(SV_USE_METIS_SVFSI)
-  set(USE_METIS_SVFSI ON)
-  simvascular_third_party(metis_svfsi)
-  # require to be built here
-  set(METIS_SVFSI_LIBRARY ${SV_LIB_THIRDPARTY_METIS_SVFSI_NAME})
+if(SV_USE_INTERNAL_METIS)
+  set(USE_INTERNAL_METIS ON)
+  simvascular_third_party(metis_internal)
 endif()
 
-#-----------------------------------------------------------------------------
-# PARMETIS_SVFSI
-if(SV_USE_PARMETIS_SVFSI)
-  set(USE_PARMETIS_SVFSI ON)
-  simvascular_third_party(parmetis_svfsi)
-  # require to be built here 
-  set(PARMETIS_SVFSI_LIBRARY ${SV_LIB_THIRDPARTY_PARMETIS_SVFSI_NAME})
+if(SV_USE_INTERNAL_PARMETIS)
+  set(USE_INTERNAL_PARMETIS ON)
+  simvascular_third_party(parmetis_internal)
 endif()
 
-#-----------------------------------------------------------------------------
 # TETGEN
 if(SV_USE_TETGEN)
   set(USE_TETGEN ON)
   simvascular_third_party(tetgen)
-  # require to be built here 
-  set(TETGEN_LIBRARY ${SV_LIB_THIRDPARTY_TETGEN_NAME})
 endif()
 
 #-----------------------------------------------------------------------------
 # EIGEN
 if(SV_USE_EIGEN)
   set(USE_EIGEN ON)
   simvascular_third_party(eigen)
-  #find_package(Eigen)
-  # require to be built here 
-  #set(TETGEN_LIBRARY ${SV_LIB_THIRDPARTY_TETGEN_NAME})
 endif()
 
 # TINYXML
 simvascular_third_party(tinyxml)
-set(TINYXML_LIBRARY ${SV_LIB_THIRDPARTY_TINYXML_NAME})
 
 
 

Code/CMake/SimVascularThirdParty.cmake

@@ -90,14 +90,14 @@ include(SimVascularDependentOptions)
 include(SimVascularInstallSetup)
 
 #set(SV_USE_TRILINOS {SV_USE_TRILINOS} PARENT_SCOPE)
-#set(SV_USE_TRILINOS OFF CACHE INTERNAL BOOL "Use Trilinos Library with svFSIplus")
+#set(SV_USE_TRILINOS OFF CACHE INTERNAL BOOL "Use Trilinos Library with svMultiPhysics")
 #set(SV_USE_TRILINOS OFF CACHE BOOL INTERNAL)
 
 #-----------------------------------------------------------------------------
 
 #-----------------------------------------------------------------------------
 # Set EXE names for the executables
-set(SV_SVFSI_EXE "svfsiplus")
+set(SV_MULTIPHYSICS_EXE "svmultiphysics")
 #-----------------------------------------------------------------------------
 
 #-----------------------------------------------------------------------------