Solver/two phase semi implicit

.circleci/config.yml

@@ -16,6 +16,8 @@ jobs:
             export MODULEPATH=$MODULEPATH:/usr/share/modulefiles
             module load mpi/openmpi-x86_64
             export CXX_COMPILER=mpicxx
+            export PETSC_ARCH=arch-linux2-c-opt
+            export PETSC_DIR=/home/cbgeo/petsc/
             cmake -GNinja -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_EXPORT_COMPILE_COMMANDS=On -DKAHIP_ROOT=/home/cbgeo/KaHIP/ -DPARTIO_ROOT=/home/cbgeo/partio/ ..
             ninja -j2
             ctest -VV
@@ -32,6 +34,8 @@ jobs:
             mkdir -p build
             [ "$(ls -A build)" ] && rm -rf build/*
             cd build
+            export PETSC_ARCH=arch-linux2-c-opt
+            export PETSC_DIR=/home/cbgeo/petsc/
             scan-build cmake -GNinja -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_EXPORT_COMPILE_COMMANDS=On -DKAHIP_ROOT=/home/cbgeo/KaHIP/ -DPARTIO_ROOT=/home/cbgeo/partio/ ..
             scan-build -k -V ninja -j2
             ctest -VV
@@ -64,6 +68,8 @@ jobs:
             mkdir -p build
             [ "$(ls -A build)" ] && rm -rf build/*
             cd build
+            export PETSC_ARCH=arch-linux2-c-opt
+            export PETSC_DIR=/home/cbgeo/petsc/
             cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_EXPORT_COMPILE_COMMANDS=On -DENABLE_COVERAGE=On -DKAHIP_ROOT=/home/cbgeo/KaHIP/ -DPARTIO_ROOT=/home/cbgeo/partio/ ..
             make mpmtest_coverage -j2
             ./mpmtest_coverage
@@ -140,4 +146,4 @@ workflows:
                 filters:
                     branches:
                         only:
-                          - develop
+                          - master

.gitignore

@@ -77,3 +77,4 @@ configure.scan
 *missing
 *stamp-h1
 benchmarks/
+bin/

CMakeLists.txt

@@ -41,6 +41,9 @@ option(MPM_BUILD_TESTING "enable testing for mpm" ON)
 # Halo exchange
 option(HALO_EXCHANGE "Enable halo exchange" OFF)
 
+# PETSC
+option(USE_PETSC "Use PETSC solver library" OFF)
+
 # CMake Modules
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
@@ -71,6 +74,7 @@ if (HDF5_FOUND)
   include_directories(${HDF5_INCLUDE_DIRS})
   link_libraries(${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_CXX_HL_LIBRARIES})
   add_definitions(${HDF5_DEFINITIONS})
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-invalid-offsetof")
 endif()
 
 # OpenMP
@@ -97,6 +101,15 @@ if (MKL_FOUND)
   endif()
 endif()
 
+# PETSc
+if (USE_PETSC)
+  find_package(PETSc COMPONENTS C)
+endif()
+if (PETSC_FOUND)
+  include_directories(${PETSC_INC})
+  link_libraries(${PETSC_LIB})
+  add_definitions("-DUSE_PETSC")
+endif()
 
 # KaHIP
 if (MPI_FOUND)
@@ -131,19 +144,22 @@ endif()
 # Include directories
 include_directories(BEFORE
   ${mpm_SOURCE_DIR}/include/
+  ${mpm_SOURCE_DIR}/include/contacts/
   ${mpm_SOURCE_DIR}/include/containers/
   ${mpm_SOURCE_DIR}/include/elements/
   ${mpm_SOURCE_DIR}/include/elements/2d
   ${mpm_SOURCE_DIR}/include/elements/3d
   ${mpm_SOURCE_DIR}/include/functions/
   ${mpm_SOURCE_DIR}/include/generators/
   ${mpm_SOURCE_DIR}/include/io/
-  ${mpm_SOURCE_DIR}/include/contacts/
+  ${mpm_SOURCE_DIR}/include/linear_solvers/
   ${mpm_SOURCE_DIR}/include/loads_bcs/
   ${mpm_SOURCE_DIR}/include/materials/
   ${mpm_SOURCE_DIR}/include/particles/
+  ${mpm_SOURCE_DIR}/include/particles/pod_particles
   ${mpm_SOURCE_DIR}/include/solvers/
   ${mpm_SOURCE_DIR}/include/solvers/mpm_scheme/
+  ${mpm_SOURCE_DIR}/include/utilities/
   ${mpm_SOURCE_DIR}/external/
   ${mpm_SOURCE_DIR}/tests/include/
 )
@@ -157,12 +173,14 @@ SET(mpm_src
   ${mpm_SOURCE_DIR}/src/functions/linear_function.cc
   ${mpm_SOURCE_DIR}/src/functions/sin_function.cc
   ${mpm_SOURCE_DIR}/src/geometry.cc
-  ${mpm_SOURCE_DIR}/src/hdf5_particle.cc
+  ${mpm_SOURCE_DIR}/src/pod_particle.cc
+  ${mpm_SOURCE_DIR}/src/pod_particle_twophase.cc
   ${mpm_SOURCE_DIR}/src/io/io.cc
   ${mpm_SOURCE_DIR}/src/io/io_mesh.cc
   ${mpm_SOURCE_DIR}/src/io/logger.cc
   ${mpm_SOURCE_DIR}/src/io/partio_writer.cc
   ${mpm_SOURCE_DIR}/src/io/vtk_writer.cc
+  ${mpm_SOURCE_DIR}/src/linear_solver.cc
   ${mpm_SOURCE_DIR}/src/material.cc
   ${mpm_SOURCE_DIR}/src/mpm.cc
   ${mpm_SOURCE_DIR}/src/nodal_properties.cc
@@ -200,41 +218,55 @@ if(MPM_BUILD_TESTING)
     ${mpm_SOURCE_DIR}/tests/elements/triangle_quadrature_test.cc
     ${mpm_SOURCE_DIR}/tests/functions/linear_function_test.cc
     ${mpm_SOURCE_DIR}/tests/functions/sin_function_test.cc
+    ${mpm_SOURCE_DIR}/tests/functions/radial_basis_function_test.cc
     ${mpm_SOURCE_DIR}/tests/graph_test.cc
     ${mpm_SOURCE_DIR}/tests/interface_test.cc
     ${mpm_SOURCE_DIR}/tests/io/io_mesh_ascii_test.cc
     ${mpm_SOURCE_DIR}/tests/io/io_test.cc
     ${mpm_SOURCE_DIR}/tests/io/vtk_writer_test.cc
     ${mpm_SOURCE_DIR}/tests/io/write_mesh_particles.cc
     ${mpm_SOURCE_DIR}/tests/io/write_mesh_particles_unitcell.cc
+    ${mpm_SOURCE_DIR}/tests/linear_solver_test.cc
     ${mpm_SOURCE_DIR}/tests/materials/bingham_test.cc
     ${mpm_SOURCE_DIR}/tests/materials/linear_elastic_test.cc
     ${mpm_SOURCE_DIR}/tests/materials/modified_cam_clay_test.cc
     ${mpm_SOURCE_DIR}/tests/materials/mohr_coulomb_test.cc
     ${mpm_SOURCE_DIR}/tests/materials/newtonian_test.cc
     ${mpm_SOURCE_DIR}/tests/materials/norsand_test.cc
     ${mpm_SOURCE_DIR}/tests/materials/material_utility_test.cc
+    ${mpm_SOURCE_DIR}/tests/mesh_free_surface_test.cc
     ${mpm_SOURCE_DIR}/tests/mesh_neighbours_test.cc
     ${mpm_SOURCE_DIR}/tests/mesh_test_2d.cc
     ${mpm_SOURCE_DIR}/tests/mesh_test_3d.cc
     ${mpm_SOURCE_DIR}/tests/mpi_transfer_particle_test.cc
+    ${mpm_SOURCE_DIR}/tests/nodes/nodal_properties_test.cc
+    ${mpm_SOURCE_DIR}/tests/nodes/node_map_test.cc
+    ${mpm_SOURCE_DIR}/tests/nodes/node_test.cc
+    ${mpm_SOURCE_DIR}/tests/nodes/node_twophase_test.cc
+    ${mpm_SOURCE_DIR}/tests/nodes/node_vector_test.cc
+    ${mpm_SOURCE_DIR}/tests/particles/particle_cell_crossing_test.cc
+    ${mpm_SOURCE_DIR}/tests/particles/particle_test.cc
+    ${mpm_SOURCE_DIR}/tests/particles/particle_twophase_test.cc
+    ${mpm_SOURCE_DIR}/tests/particles/particle_traction_test.cc
+    ${mpm_SOURCE_DIR}/tests/particles/particle_vector_test.cc
+    ${mpm_SOURCE_DIR}/tests/particles/particle_serialize_deserialize_test.cc
+    ${mpm_SOURCE_DIR}/tests/particles/particle_serialize_deserialize_twophase_test.cc
+    ${mpm_SOURCE_DIR}/tests/point_in_cell_test.cc
     ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_musl_test.cc
     ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_musl_unitcell_test.cc
     ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_usf_test.cc
     ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_usf_unitcell_test.cc
     ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_usl_test.cc
     ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_usl_unitcell_test.cc
+    ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_twophase_usf_test.cc
+    ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_twophase_usf_unitcell_test.cc
+    ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_twophase_usl_test.cc
+    ${mpm_SOURCE_DIR}/tests/solvers/mpm_explicit_twophase_usl_unitcell_test.cc
+    ${mpm_SOURCE_DIR}/tests/solvers/mpm_semi_implicit_navierstokes_test.cc
+    ${mpm_SOURCE_DIR}/tests/solvers/mpm_semi_implicit_navierstokes_unitcell_test.cc
+    ${mpm_SOURCE_DIR}/tests/solvers/mpm_semi_implicit_twophase_test.cc
+    ${mpm_SOURCE_DIR}/tests/solvers/mpm_semi_implicit_twophase_unitcell_test.cc
     ${mpm_SOURCE_DIR}/tests/solvers/mpm_scheme_test.cc
-    ${mpm_SOURCE_DIR}/tests/nodal_properties_test.cc
-    ${mpm_SOURCE_DIR}/tests/node_map_test.cc
-    ${mpm_SOURCE_DIR}/tests/node_test.cc
-    ${mpm_SOURCE_DIR}/tests/node_vector_test.cc
-    ${mpm_SOURCE_DIR}/tests/particle_cell_crossing_test.cc
-    ${mpm_SOURCE_DIR}/tests/particle_serialize_deserialize_test.cc
-    ${mpm_SOURCE_DIR}/tests/particle_test.cc
-    ${mpm_SOURCE_DIR}/tests/particle_traction_test.cc
-    ${mpm_SOURCE_DIR}/tests/particle_vector_test.cc
-    ${mpm_SOURCE_DIR}/tests/point_in_cell_test.cc
   )
   add_executable(mpmtest ${mpm_src} ${test_src})
   add_test(NAME mpmtest COMMAND $<TARGET_FILE:mpmtest>)

cmake/FindPETSc.cmake

@@ -0,0 +1,154 @@
+#################################################################
+# Try to find PETSc                                             #
+#                                                               #
+# Once done this will define:                                   #
+#  PETSC_FOUND         - system has PETSc                       #
+#  PETSC_DIR           - PETSc directory                        #
+#  PETSC_ARCH          - PETSc architecture                     #
+#  PETSC_INC           - PETSc include directory                #
+#  PETSC_LIB           - PETSc library (static or dynamic)      #
+#  PETSC_VARIABLES     - Content of PETSc 'petscvariables' file #
+#                                                               #
+#  PETSC_MUMPS         - Was PETSc compiled with MUMPS?         #
+#  PETSC_MUMPS_INC     - PETSc MUMPS include file               #
+#  PETSC_MUMPS_LIB     - PETSc MUMPS libraries                  #
+#                                                               #
+#  PETSC_SCALAPACK     - Was PETSc compiled with ScaLAPACK?     #
+#  PETSC_SCALAPACK_LIB - PETSc ScaLAPACK libraries              #
+#                                                               #
+#  PETSC_PARMETIS      - Was PETSc compiled with ParMETIS?      #
+#  PETSC_PARMETIS_LIB  - PETSc ParMETIS libraries               #
+#                                                               #
+#  PETSC_METIS         - Was PETSc compiled with Metis?         #
+#  PETSC_METIS_LIB     - PETSc METIS libraries                  #
+#                                                               #
+#  PETSC_MPIUNI        - Was PETSc compiled with MPIUNI?        #
+#  PETSC_MPIUNI_INC    - MPIUNI include file                    #
+#                                                               #
+# Usage:                                                        #
+#  find_package(PETSc)                                          #
+#                                                               #
+# Setting these changes the behavior of the search              #
+#  PETSC_DIR           - PETSc directory                        #
+#  PETSC_ARCH          - PETSc architecture                     #
+#################################################################
+
+## Try to set PETSC_DIR and PETSC_ARCH ##
+#########################################
+if(NOT DEFINED PETSC_DIR)
+  set(PETSC_DIR $ENV{PETSC_DIR})
+endif()
+if(NOT DEFINED PETSC_ARCH)
+  set(PETSC_ARCH $ENV{PETSC_ARCH})
+endif()
+
+## Includes ##
+##############
+if(EXISTS "${PETSC_DIR}/include" AND
+   EXISTS "${PETSC_DIR}/${PETSC_ARCH}/include")
+  set(PETSC_INC "${PETSC_DIR}/include" "${PETSC_DIR}/${PETSC_ARCH}/include")
+else()
+  message(SEND_ERROR "PETSc includes not found")
+endif()
+
+## Library ##
+#############
+if(EXISTS "${PETSC_DIR}/${PETSC_ARCH}/lib/libpetsc.so")
+  set(PETSC_LIB "${PETSC_DIR}/${PETSC_ARCH}/lib/libpetsc.so")
+elseif(EXISTS "${PETSC_DIR}/${PETSC_ARCH}/lib/libpetsc.a")
+  set(PETSC_LIB "${PETSC_DIR}/${PETSC_ARCH}/lib/libpetsc.a")
+else()
+  message(SEND_ERROR "PETSc library not found")
+endif()
+
+## PETSc variables ##
+#####################
+if(EXISTS ${PETSC_DIR}/${PETSC_ARCH}/conf/petscvariables)
+  file(STRINGS ${PETSC_DIR}/${PETSC_ARCH}/conf/petscvariables
+    PETSC_VARIABLES NEWLINE_CONSUME)
+elseif(EXISTS ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/petscvariables)
+  file(STRINGS ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/petscvariables
+    PETSC_VARIABLES NEWLINE_CONSUME)
+else()
+  message(SEND_ERROR "PETSc variables not found")
+endif()
+
+## MUMPS ##
+###########
+if(EXISTS ${PETSC_DIR}/${PETSC_ARCH}/lib/libmumps_common.a)
+  set(PETSC_MUMPS TRUE)
+  set(PETSC_MUMPS_INC ${PETSC_INC})
+  set(PETSC_MUMPS_LIB
+    ${PETSC_DIR}/${PETSC_ARCH}/lib/libcmumps.a
+    ${PETSC_DIR}/${PETSC_ARCH}/lib/libdmumps.a
+    ${PETSC_DIR}/${PETSC_ARCH}/lib/libsmumps.a
+    ${PETSC_DIR}/${PETSC_ARCH}/lib/libzmumps.a
+    ${PETSC_DIR}/${PETSC_ARCH}/lib/libmumps_common.a
+    ${PETSC_DIR}/${PETSC_ARCH}/lib/libpord.a)
+
+  if(EXISTS ${PETSC_DIR}/${PETSC_ARCH}/lib/libmpiseq.a)
+    set(PETSC_MUMPS_SEQ ${PETSC_DIR}/${PETSC_ARCH}/lib/libmpiseq.a)
+  else()
+    set(PETSC_MUMPS_SEQ "")
+  endif()
+
+else()
+  set(PETSC_MUMPS FALSE)
+  set(PETSC_MUMPS_INC "")
+  set(PETSC_MUMPS_LIB "")
+  set(PETSC_MUMPS_SEQ "")
+endif()
+
+## ScaLAPACK ##
+###############
+if(EXISTS ${PETSC_DIR}/${PETSC_ARCH}/lib/libscalapack.a)
+  set(PETSC_SCALAPACK TRUE)
+  set(PETSC_SCALAPACK_LIB ${PETSC_DIR}/${PETSC_ARCH}/lib/libscalapack.a)
+else()
+  set(PETSC_SCALAPACK FALSE)
+  set(PETSC_SCALAPACK_LIB "")
+endif()
+
+## ParMETIS ##
+##############
+if(EXISTS ${PETSC_DIR}/${PETSC_ARCH}/lib/libparmetis.so)
+  set(PETSC_PARMETIS TRUE)
+  set(PETSC_PARMETIS_LIB ${PETSC_DIR}/${PETSC_ARCH}/lib/libparmetis.so)
+else()
+  set(PETSC_PARMETIS FALSE)
+  set(PETSC_PARMETIS_LIB "")
+endif()
+
+## METIS ##
+############
+if(EXISTS ${PETSC_DIR}/${PETSC_ARCH}/lib/libmetis.so)
+  set(PETSC_METIS TRUE)
+  set(PETSC_METIS_LIB ${PETSC_DIR}/${PETSC_ARCH}/lib/libmetis.so)
+else()
+  set(PETSC_METIS FALSE)
+  set(PETSC_METIS_LIB "")
+endif()
+
+## MPI Uni ##
+#############
+string(REGEX MATCH "MPI_IS_MPIUNI = [^\n\r]*" PETSC_MPIUNI ${PETSC_VARIABLES})
+if(PETSC_MPIUNI)
+  string(REPLACE "MPI_IS_MPIUNI = " "" PETSC_MPIUNI ${PETSC_MPIUNI})
+  string(STRIP ${PETSC_MPIUNI} PETSC_MPIUNI)
+  string(COMPARE EQUAL ${PETSC_MPIUNI} "1" PETSC_MPIUNI)
+
+  string(REGEX MATCH "MPI_INCLUDE = -I[^\n\r]*"
+    PETSC_MPIUNI_INC ${PETSC_VARIABLES})
+  string(REPLACE "MPI_INCLUDE = -I" "" PETSC_MPIUNI_INC ${PETSC_MPIUNI_INC})
+  string(STRIP ${PETSC_MPIUNI_INC} PETSC_MPIUNI_INC)
+else()
+  set(PETSC_MPIUNI     FALSE)
+  set(PETSC_MPIUNI_INC "")
+endif()
+
+## CMake check and done ##
+##########################
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(PETSc
+  "PETSc could not be found: be sure to set PETSC_DIR and PETSC_ARCH in your environment variables"
+  PETSC_LIB PETSC_INC PETSC_DIR PETSC_ARCH)

cmake/git_watcher.cmake

@@ -311,4 +311,4 @@ function(Main)
 endfunction()
 
 # And off we go...
-Main()
+Main()