├── .gitignore ├── .travis.yml ├── CMakeLists.txt ├── COPYRIGHT ├── LICENSE ├── README.md ├── config ├── Jali │ ├── Configure.py │ ├── __init__.py │ └── compilerOptions.py ├── SuperBuild │ ├── CMakeLists.txt │ ├── INSTALL │ ├── TPLVersions.cmake │ ├── cmake │ │ ├── BuildLibraryName.cmake │ │ ├── CheckDownload.cmake │ │ └── DefineExternalProjectArgs.cmake │ ├── doc │ │ ├── CMakeLists.txt │ │ ├── build_system_requirements.tex │ │ └── figures │ │ │ ├── Build_XXX.dia │ │ │ ├── Build_XXX.pdf │ │ │ ├── DefineINCLUDE_DIR.dia │ │ │ ├── DefineLIBRARY.dia │ │ │ ├── FindTPL.dia │ │ │ ├── LocateTPL.dia │ │ │ ├── SuperBuildCMakeList.dia │ │ │ └── SuperBuildCMakeList.pdf │ ├── include │ │ ├── Build_ExodusII.cmake │ │ ├── Build_HDF5.cmake │ │ ├── Build_HDF5Cmake.cmake │ │ ├── Build_METIS.cmake │ │ ├── Build_MSTK.cmake │ │ ├── Build_NetCDF.cmake │ │ ├── Build_NetCDF_Fortran.cmake │ │ ├── Build_OpenMPI.cmake │ │ ├── Build_SEACAS.cmake │ │ ├── Build_Trilinos.cmake │ │ ├── Build_UnitTest.cmake │ │ └── Build_zlib.cmake │ └── templates │ │ ├── Jali-tpl-config.cmake.in │ │ ├── exodusii-configure-step.cmake.in │ │ ├── exodusii-configure-step.sh.in │ │ ├── fetch-file.sh.in │ │ ├── hdf5-1.8.8-comment.patch │ │ ├── hdf5-1.8.8-disable-getpwuid.patch │ │ ├── hdf5-patch-step.cmake.in │ │ ├── hdf5-patch-step.sh.in │ │ ├── metis-build-step.cmake.in │ │ ├── metis-build-step.sh.in │ │ ├── metis-configure-step.cmake.in │ │ ├── metis-configure-step.sh.in │ │ ├── metis-install-step.cmake.in │ │ ├── metis-install-step.sh.in │ │ ├── mstk-findhdf5.patch │ │ ├── mstk-patch-step.cmake.in │ │ ├── mstk-patch-step.sh.in │ │ ├── nemesis-build.cmake.in │ │ ├── nemesis-build.sh.in │ │ ├── netcdf-cmake.patch │ │ ├── netcdf-fortran-osx.patch │ │ ├── netcdf-fortran-patch-step.cmake.in │ │ ├── netcdf-fortran-patch-step.sh.in │ │ ├── netcdf-patch-step.cmake.in │ │ ├── netcdf-patch-step.sh.in │ │ ├── trilinos-finite-value.patch │ │ ├── trilinos-ifpack-hypre2.patch │ │ ├── trilinos-patch-step.sh.in │ │ ├── unittest-cmake.patch │ │ ├── unittest-install-step.sh.in │ │ ├── unittest-patch-step.cmake.in │ │ └── unittest-patch-step.sh.in ├── cmake │ ├── BinaryManager.cmake │ ├── BuildLibraryName.cmake │ ├── CMakeParseArguments.cmake │ ├── InstallManager.cmake │ ├── JaliConfig.cmake.in │ ├── JaliConfigReport.cmake │ ├── JaliConfigVersion-install.cmake.in │ ├── LibraryManager.cmake │ ├── MakefileConfig.export.in │ ├── Modules │ │ ├── FindExodusII.cmake │ │ ├── FindMETIS.cmake │ │ ├── FindMOAB.cmake │ │ ├── FindPython.cmake │ │ ├── FindUnitTest++.cmake │ │ └── FindZoltan.cmake │ ├── SelectSearchPath.cmake │ ├── TestManager.cmake │ ├── TrilinosMacros.cmake │ └── Utils │ │ ├── BuildWhitespaceString.cmake │ │ ├── ListJoin.cmake │ │ ├── PrintVariable.cmake │ │ └── SetMacros.cmake ├── configure-examples │ ├── jali-configure-example │ └── tplbuild-configure-example ├── configure.py └── doxygen │ └── Doxyfile.in ├── examples ├── CMakeLists.txt ├── CreateMesh │ ├── CMakeLists.txt │ └── CreateMesh.cc ├── HelloJali │ ├── CMakeLists.txt │ └── HelloJali.cc ├── QueryGeometry │ ├── CMakeLists.txt │ └── QueryGeometry.cc ├── QuerySets │ ├── CMakeLists.txt │ ├── QuerySets.cc │ └── hex_3x3x3_sets.exo ├── QueryState │ ├── CMakeLists.txt │ └── QueryState.cc ├── QueryTiles │ ├── CMakeLists.txt │ └── QueryTiles.cc ├── QueryTopology │ ├── CMakeLists.txt │ └── QueryTopology.cc ├── ReadMesh │ ├── CMakeLists.txt │ ├── ReadMesh.cc │ └── quadtri.exo ├── ToyNumerics │ ├── CMakeLists.txt │ └── ToyNumerics.cc └── example-app-setup │ ├── CMakeLists.txt │ ├── README.md │ └── src │ └── main.cc ├── src ├── CMakeLists.txt ├── error_handling │ ├── CMakeLists.txt │ ├── errors.cc │ ├── errors.hh │ ├── exceptions.cc │ ├── exceptions.hh │ └── test │ │ ├── Main.cc │ │ ├── test_errors.cc │ │ └── test_exceptions.cc ├── geometry │ ├── BoxRegion.cc │ ├── BoxRegion.hh │ ├── CMakeLists.txt │ ├── Domain.cc │ ├── Domain.hh │ ├── GeometricModel.cc │ ├── GeometricModel.hh │ ├── Geometry.cc │ ├── Geometry.hh │ ├── LabeledSetRegion.cc │ ├── LabeledSetRegion.hh │ ├── LogicalRegion.cc │ ├── LogicalRegion.hh │ ├── PlaneRegion.cc │ ├── PlaneRegion.hh │ ├── Point.hh │ ├── PointRegion.cc │ ├── PointRegion.hh │ ├── PolygonRegion.cc │ ├── PolygonRegion.hh │ ├── Region.cc │ ├── Region.hh │ └── test │ │ ├── Main.cc │ │ ├── test_geometric_ops.cc │ │ └── test_points.cc ├── mesh │ ├── CMakeLists.txt │ ├── Mesh.cc │ ├── Mesh.hh │ ├── MeshDefs.hh │ ├── MeshSet.cc │ ├── MeshSet.hh │ ├── MeshTile.cc │ ├── MeshTile.hh │ ├── block_partition.cc │ ├── block_partition.hh │ ├── mesh_factory │ │ ├── CMakeLists.txt │ │ ├── MeshFactory.cc │ │ ├── MeshFactory.hh │ │ └── test │ │ │ ├── Main.cc │ │ │ ├── hex_3x3x3_ss_4P.h5m │ │ │ ├── hex_5x5x5.exo │ │ │ ├── hex_5x5x5.par.4.0 │ │ │ ├── hex_5x5x5.par.4.1 │ │ │ ├── hex_5x5x5.par.4.2 │ │ │ ├── hex_5x5x5.par.4.3 │ │ │ └── test_mesh_factory.cc │ ├── mesh_mstk │ │ ├── CMakeLists.txt │ │ ├── Mesh_MSTK.cc │ │ ├── Mesh_MSTK.hh │ │ └── test │ │ │ ├── Main.cc │ │ │ ├── colorfunc.txt │ │ │ ├── fractures.exo │ │ │ ├── hex_1x1x1_ss.exo │ │ │ ├── hex_2x2x1_ss.exo │ │ │ ├── hex_3x3x3_sets.exo │ │ │ ├── hex_3x3x3_split.par.4.0 │ │ │ ├── hex_3x3x3_split.par.4.1 │ │ │ ├── hex_3x3x3_split.par.4.2 │ │ │ ├── hex_3x3x3_split.par.4.3 │ │ │ ├── hex_5x5x5.exo │ │ │ ├── hex_5x5x5.par.4.0 │ │ │ ├── hex_5x5x5.par.4.1 │ │ │ ├── hex_5x5x5.par.4.2 │ │ │ ├── hex_5x5x5.par.4.3 │ │ │ ├── test_edges_4P.cc │ │ │ ├── test_extface_map_4P.cc │ │ │ ├── test_hex_1x1x1.cc │ │ │ ├── test_hex_2x2x1.cc │ │ │ ├── test_hex_3x3x3.cc │ │ │ ├── test_hex_3x3x3_4P.cc │ │ │ ├── test_hex_3x3x3_par_read_4P.cc │ │ │ ├── test_hex_gen_3x3x3.cc │ │ │ ├── test_hex_gen_5x5x5_par.cc │ │ │ ├── test_quad_gen_3x3.cc │ │ │ ├── test_quad_gen_5x5_par.cc │ │ │ ├── test_read_fractures.cc │ │ │ └── test_write_read_fields.cc │ ├── mesh_simple │ │ ├── CMakeLists.txt │ │ ├── Mesh_simple.cc │ │ ├── Mesh_simple.hh │ │ └── test │ │ │ ├── Main.cc │ │ │ ├── colfunc.txt │ │ │ ├── test_cell_numbering.cc │ │ │ ├── test_face_adj_cells.cc │ │ │ ├── test_geometry.cc │ │ │ ├── test_maps.cc │ │ │ ├── test_node_adj_cells.cc │ │ │ └── test_node_cell_faces.cc │ └── test │ │ ├── Main.cc │ │ ├── hex_3x3x3_sets.exo │ │ ├── test_block_partition.cc │ │ ├── test_boundary_ghosts.cc │ │ ├── test_corners.cc │ │ ├── test_entity_counts.cc │ │ ├── test_entity_iterators.cc │ │ ├── test_mesh_geometry.cc │ │ ├── test_meshsets.cc │ │ ├── test_meshtiles.cc │ │ ├── test_one_tile.cc │ │ ├── test_sides.cc │ │ └── test_wedges.cc └── statemanager │ ├── CMakeLists.txt │ ├── JaliState.cc │ ├── JaliState.h │ ├── JaliStateVector.cc │ ├── JaliStateVector.h │ └── test │ ├── Main.cc │ ├── test_jali_state.cc │ └── test_jali_state_vector.cc └── tools └── py_lib ├── CMakeLists.txt └── jali ├── __init__.py ├── command.py ├── input_tree.py ├── interface.py ├── module.py ├── mpc.py ├── mpi.py └── region.py /.gitignore: -------------------------------------------------------------------------------- 1 | build* 2 | .idea 3 | include 4 | lib 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