Merge branch 'main' into git_lfs_warning_26

.github/codecov.yml

@@ -0,0 +1,9 @@
+# configuration for code coverage testing with codecov
+coverage:
+ status:
+ project:
+ default:
+ informational: true
+ patch:
+ default:
+ informational: true

.github/workflows/test.yml

@@ -38,7 +38,7 @@ jobs:
  run: |
  git lfs pull
  cd tests
- conda run -n svfsiplus pytest -v --durations=0
+ conda run -n svfsiplus pytest -rPv --durations=0
  - name: Generate code coverage
  if: startsWith(matrix.os, 'ubuntu-22.04')
  run: |

CMakeLists.txt

@@ -82,9 +82,12 @@ include(SimVascularFunctionCheckCompilerFlags)
 #
 # These variables must later be add to 'ExternalProject_Add(svFSI' as -D options. 
 #
-set(SV_USE_TRILINOS OFF CACHE BOOL "Use Trilinos Library with svFSI")
+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")
+set(SV_PETSC_DIR "" CACHE STRING "Path to a local install of the PETSc linear algebra package")
 set(ENABLE_COVERAGE OFF CACHE BOOL "Enable code coverage")
 set(ENABLE_ARRAY_INDEX_CHECKING OFF CACHE BOOL "Enable Array index checking")
+set(SV_LOCAL_VTK_PATH "" CACHE STRING "Path to a local build of VTK.")
 
 #-----------------------------------------------------------------------------
 # RPATH handling
@@ -117,7 +120,7 @@ set(SV_EXTERNALS_TOPLEVEL_DIR "${CMAKE_BINARY_DIR}/Externals-build/sv_externals"
 #-----------------------------------------------------------------------------
 
 #-----------------------------------------------------------------------------
-# svSolver!
+# svFSIplus solver.
 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(svFSI
@@ -141,8 +144,11 @@ ExternalProject_Add(svFSI
  -DSV_EXTERNALS_USE_TOPLEVEL_DIR:BOOL=ON
  -DSV_EXTERNALS_TOPLEVEL_DIR:PATH=${SV_EXTERNALS_TOPLEVEL_DIR}
  -DSV_USE_TRILINOS:BOOL=${SV_USE_TRILINOS}
+ #-DSV_USE_PETSC:BOOL=${SV_USE_PETSC}
+ -DSV_PETSC_DIR:STRING=${SV_PETSC_DIR}
  -DENABLE_COVERAGE:BOOL=${ENABLE_COVERAGE}
  -DENABLE_ARRAY_INDEX_CHECKING:BOOL=${ENABLE_ARRAY_INDEX_CHECKING}
+ -DSV_LOCAL_VTK_PATH:STRING=${SV_LOCAL_VTK_PATH}
  ${SV_APPLE_CMAKE_ARGS}
  ${SV_ADDITIONAL_CMAKE_ARGS}
  )

Code/Source/svFSI/CMakeLists.txt

@@ -49,20 +49,56 @@ if(SV_USE_TRILINOS)
  MESSAGE(WARNING "Trilinos_FOUND is true but Trilinos_LIBRARIES is empty. This suggests that FIND_PACKAGE(Trilinos) failed quietly. Proceed with caution.")
  endif()
 
- MESSAGE("Setting WITH_TRILINOS to true\n")
- set(WITH_TRILINOS 1)
+ set(USE_TRILINOS 1)
  ELSE()
  MESSAGE(WARNING "Could not find Trilinos. Compiling svFSI without Trilinos.")
  ENDIF()
 
 endif()
 
 # add trilinos flags and defines
-if(WITH_TRILINOS)
+if(USE_TRILINOS)
  ADD_DEFINITIONS(-DWITH_TRILINOS)
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
 endif()
 
+# Build with the PETSc linear algebra package.
+#
+if(NOT "${SV_PETSC_DIR}" STREQUAL "")
+
+ if(NOT EXISTS ${SV_PETSC_DIR})
+ message(ERROR "The PETSc directory ${SV_PETSC_DIR} could not be found.")
+ endif()
+
+ if(NOT EXISTS "${SV_PETSC_DIR}/include")
+ message(ERROR "The PETSc include directory ${SV_PETSC_DIR}/include could not be found.")
+ endif()
+
+ if(NOT EXISTS "${SV_PETSC_DIR}/lib")
+ message(ERROR "The PETSc library directory ${SV_PETSC_DIR}/lib could not be found.")
+ endif()
+
+ set(PETSC_INCLUDE_DIRS "${SV_PETSC_DIR}/include;${SV_PETSC_DIR}/../include")
+ set(PETSC_LIBRARY_DIRS "-L${SV_PETSC_DIR}/lib -lpetsc")
+ message("\nBuilding with the PETSc package; the include and libraries directories are: ")
+ message(" PETSC_LIBRARY_DIRS = ${PETSC_LIBRARY_DIRS}")
+ message(" PETSC_INCLUDE_DIRS = ${PETSC_INCLUDE_DIRS}")
+
+ # Set PETSc include directory.
+ include_directories(${PETSC_INCLUDE_DIRS})
+
+ # Set C++ directive to use PETSc in svFSIplus code.
+ ADD_DEFINITIONS(-DWITH_PETSC)
+ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pedantic -std=c99")
+
+ set(USE_PETSC 1)
+
+else()
+
+ set(USE_PETSC 0)
+
+endif()
+
 if(ENABLE_ARRAY_INDEX_CHECKING)
  ADD_DEFINITIONS(-DENABLE_ARRAY_INDEX_CHECKING)
 endif()
@@ -71,11 +107,15 @@ endif()
 find_package(BLAS REQUIRED)
 find_package(LAPACK REQUIRED)
 
-# Including VTK produces warnings when compiling Fortran code.
+# Include VTK either from a local build using SV_LOCAL_VTK_PATH
+# or from a default installed version.
 #
-# -iframe is valid for C/C++/ObjC/ObjC++ but not for Fortran
-#
-find_package(VTK REQUIRED)
+if("${SV_LOCAL_VTK_PATH}" STREQUAL "")
+ find_package(VTK REQUIRED ) 
+else()
+ find_package(VTK PATHS ${SV_LOCAL_VTK_PATH} NO_DEFAULT_PATH REQUIRED) 
+endif()
+
 include(${VTK_USE_FILE})
 
 set(lib ${SV_LIB_SVFSI_NAME})
@@ -151,7 +191,12 @@ set(CSRCS
  SPLIT.c
 )
 
-if(WITH_TRILINOS)
+ # Set PETSc interace code.
+ if(USE_PETSC)
+ #set(CSRCS ${CSRCS} petsc_linear_solver.c)
+ endif()
+
+if(USE_TRILINOS)
  set(CSRCS ${CSRCS} trilinos_linear_solver.cpp)
 
  # trilinos directories and libraries
@@ -168,9 +213,6 @@ simvascular_add_executable(${SV_SVFSI_EXE}
  INSTALL_COMP CoreExecutables
  INSTALL_DESTINATION ${SV_INSTALL_RUNTIME_DIR})
 
-message("##### TINY ${TINYXML_LIBRARY_NAME}")
-message("##### TET ${TETGEN_LIBRARY_NAME}")
-
 target_link_libraries(${SV_SVFSI_EXE}
  ${GLOBAL_LIBRARIES}
  ${INTELRUNTIME_LIBRARIES}
@@ -190,10 +232,14 @@ if(SV_MPI_EXTRA_LIBRARY)
  target_link_libraries(${SV_SVFSI_EXE} ${SV_MPI_EXTRA_LIBRARY})
 endif()
 
-if(WITH_TRILINOS)
+if(USE_TRILINOS)
  target_link_libraries(${SV_SVFSI_EXE} ${Trilinos_LIBRARIES} ${Trilinos_TPL_LIBRARIES})
 endif()
 
+if(USE_PETSC)
+ target_link_libraries(${SV_SVFSI_EXE} ${PETSC_LIBRARY_DIRS})
+endif()
+
 # coverage
 if(ENABLE_COVERAGE)
  # set compiler flags

Code/Source/svFSI/mat_models_carray.h

@@ -943,7 +943,7 @@ void get_pk2cc(const ComMod& com_mod, const CepMod& cep_mod, const dmnType& lDmn
  for (int j = 0; j < N; j++) {
  for (int k = 0; k < N; k++) {
  for (int l = 0; l < N; l++) {
- CCb[i][j][k][l] += g1 * Hss_prod[i][j][k][l];
+ CCb[i][j][k][l] += g2 * Hss_prod[i][j][k][l];
  }
  }
  }

Code/Source/svFSI/nn.cpp

@@ -575,19 +575,22 @@ void gnnb(const ComMod& com_mod, const faceType& lFa, const int e, const int g,
  for (int a = 0; a < eNoNb; a++) {
  int Ac = lFa.IEN(a,e);
  int b = 0;
+ bool found_node = false;
 
  for (int ib = 0; ib < eNoN; ib++) {
  b = ib;
  if (setIt[ib]) {
  int Bc = msh.IEN(ib,Ec);
  if (Bc == Ac) {
+ found_node = true;
  break;
  }
  }
  }
 
- if (b > eNoN) {
- throw std::runtime_error("could not find matching face nodes");
+ if (!found_node) {
+ throw std::runtime_error("[svFSIplus::gnnb] The '" + lFa.name + "' face node " + std::to_string(Ac) + 
+ " could not be matched to a node in the '" + msh.name + "' volume mesh.");
  }
 
  ptr(a) = b;

Code/Source/svFSI/trilinos_linear_solver.cpp

@@ -347,9 +347,8 @@ void trilinos_doassem_(int &numNodesPerElement, const int *eqN,
  //converts eqN in local proc values to global values
  std::vector<int> localToGlobal(numNodesPerElement);
 
- //subtract 1 since eqN is 1 based and C is 0 based indexing
  for (int i = 0; i < numNodesPerElement; ++i)
- localToGlobal[i] = localToGlobalUnsorted[eqN[i] - 1];
+ localToGlobal[i] = localToGlobalUnsorted[eqN[i]];
 
  //loop over local nodes on the element
  for (int a = 0; a < numNodesPerElement; ++a)

Code/ThirdParty/metis_svfsi/simvascular_metis_svfsi/METISLib/.gitignore

@@ -0,0 +1 @@
+temp/