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Discontinuous galerkin (sandialabs#403)
* EXODUS: refactor field metadata attribute output * EXODUS: Beginnings of basis read * EXODUS: basis query * EXODUS: these got lost with some branch mishaps * EXODUS: Spelling fix * EXODUS: See if can fix intel errors * EXODUS: Fix intel build * EXODUS: Move internal function to correct header * Windows fixes: make functions non-inline Making certain functions in Ioss::Utils non-inline to avoid export errors on Windows. Accessing the non-exported static variables was causing errors. This avoids that. Also added API to access current values for various streams. * eliminate warnings * IOSS: cgns - do not create assemblies from Unspecified VC * Getting kokkos build working again [ci skip] * TEST: Enable kokkos build * IOSS: Change byte-size output to debug * shellcheck recommendations * TESTING: Remove adios2 until figure out issues * EPU: Minor improvement in message (plural vs singular) * IOSS: Rename qsort to sort * IO_MODIFY: Better help output * IO_MODIFY: clean-up comment [ci skip] * Revert "EPU: Minor improvement in message (plural vs singular)" This reverts commit 6ca490c. * IOSS: Switch to using doctest from Catch2 * IOSS: cgns - remove lambdas to see if fixes stria issue * IOSS: Remove shadowed variable * Revert "Remove shadowed variable." This reverts commit 4d54381a3264dea155de65d0588cb192b37c0e1f. * Revert "IOSS: cgns - remove lambdas to see if fixes stria issue" This reverts commit 8dde87a74344b8b57f0f948e58f73e82c950e074. * IOSS: cgns - get CG_BUILD_PARALLEL define for all versions * Update readme -- replace Catch2 with doctest [ci skip] * @wortiz has signed the CLA from Pull Request sandialabs#303 * @mwestphal has signed the CLA from Pull Request sandialabs#304 * BLOT: Fix new argument mismatch warning with gcc-12 * Fix a recursive warning on assignement copy operator * IOSS: DEBUG->DbgOut, WARNING->WarnOut to avoid windows issues * IOSS: new version of clang-format * New version of clang-format * New version of clang-format * TPL: Add INSTALL_PATH to metis/parmetis installs * MODULE: Remove old unused unsupported lines [ci skip] * @gjtempl has signed the CLA from Pull Request sandialabs#305 * Updates for serial build Add SEACAS_HAVE_MPI include guards for ioss unit_tests that use MPI. These are still run for serial builds and this change allows them to compile and run. Add -DMATIO_SHARED:BOOL=${SHARED} to TPS/matio/runcmake.sh. Matio's CMake isn't respecting the CMAKE variable BUILD_SHARED_LIBS and still builds shared version when SHARED=NO. * IOSS: Handle uppercase field suffices * IOSS: Clean up uppercase suffix fix * ZELLIJ: Add offset option * KOKKOS: Use current version * TPL: Fix kokkos runcmake.sh for current version * EXODUS: Clean up * Copy top-level README to packages/seacas so available in Trilinos snapshot * CONFIG: Update name of kokkos library * EXODUS.PY: Add the get_block_id_map method This adds functionality to add being able to easily find the elements contained within EX_ELEM_BLOCK or other type without keeping track of global and internal indicies. * ZELLIJ: Better cache utilization for offset and scale * IOSS: Handle specified field ordering (via index) if present * IOSS: use reserve instead of resize since pushing back * IO_MODIFY: Add rename capability * IO_MODIFY: Clean up rename capability * CONFIG: Add gnubrew compiler option * CONFIG: Update hdf5 versions * IO_MODIFY: update help options * EXODUS: Fix problem with ex_get_block_id_map function * SUPES: Make a variable be a correct spelling * EXODUS: clang-analyzer fixes * Bring up-to-date with master * Clean up bad merge * EXODUS: Clean up bad merge * EXODUS: Clean up anothr bad merge * EPU: Bring in fix from master * EXODUS: Clean up python and varid lookup * EXODUS: Support cardinality and user-define suffices; refactor * EXODUS: Further refinement/refactoring of DG field interface * EXODUS: Refactor component separator to allow for empty value * EXODUS: Minor cleanup * EXODUS: Refactor function naems; add test of ex_field utils * EXODUS: Add missing file from last commit * EXODUS: Fix bad handling of user-defined suffices * EXODUS: Fix suffix handling in name building * CI: Fix cmake version requirement * EXODUS: More work on the basis metadata read * EXODUS: Fix null test -- use double pipe * EXODUS: refactor field metadata attribute output * EXODUS: Beginnings of basis read * EXODUS: basis query * EXODUS: these got lost with some branch mishaps * EXODUS: Spelling fix * EXODUS: See if can fix intel errors * EXODUS: Fix intel build * EXODUS: Move internal function to correct header * TEST: Enable kokkos build * EPU: Minor improvement in message (plural vs singular) * Revert "EPU: Minor improvement in message (plural vs singular)" This reverts commit 6ca490c. * IOSS: Remove shadowed variable * Revert "Remove shadowed variable." This reverts commit 4d54381a3264dea155de65d0588cb192b37c0e1f. * CONFIG: Add gnubrew compiler option * Bring up-to-date with master * EXODUS: Support cardinality and user-define suffices; refactor * EXODUS: Further refinement/refactoring of DG field interface * EXODUS: Refactor component separator to allow for empty value * EXODUS: Minor cleanup * EXODUS: Refactor function naems; add test of ex_field utils * EXODUS: Add missing file from last commit * EXODUS: Fix bad handling of user-defined suffices * EXODUS: Fix suffix handling in name building * CI: Fix cmake version requirement * EXODUS: More work on the basis metadata read * EXODUS: Fix null test -- use double pipe * EXODUS: Test field metadata read/write on nodes * CI: Fix cxx standard setting * EXODUS: Fix bad merge * EXODUS: Fix bad merge * EXODUS: Fix varid query for assembly and blob * EXODUS.PY: See if this fixes ci build issues * EXODUS: Fix ex__get_varid function * Revert "EXODUS.PY: See if this fixes ci build issues" This reverts commit 86f202d. * EXODUS: Clean up ex_attribute struct * EXODUS: realpath is gnu extension in c11/c99 * EXODUS: Provide realpath prototype * EXODUS: Add missing functions for mingw * EXODUS: Fix ex_attribute initiialization * CI: Disable nczarr in netcdf * EXODUS: Fix codacy null / 0 issue * EXODUS: Removed unused struct member * IOSS: Clean up some includes; remove the ... for ??? * EXODUS: Fix bad master merge * EXODUS: Fix intel compiler build * BLOT: Increase resolution of node/element id output * IOSS: Change meta_data to metadata * EXODUS: Use internal naming for static function * Remove ioss as required library * EXODUS: Add function name to output so know where it came from * IOSS: Add function mapping Ioss field names to exodus ex_field_type * IOSS: Output field metadata basic implemetation * IOSS: Rename function for consistency * IOSS: Add missing serialize io call * APREPRO: Make strings test more robust * IOSS: Build io_modify only if exodus enabled * IOSS: Detect if exodus enabled for exodus include * GREPOS: Intel overoptimizes unless inimap separate file * GREPOS: Fix bad merge * CONFIG: Silence CMake warning about python interpreter finding * IOSS: Fix use of c++14/17 type-traits * EXODUS: Filter out attributes Field@ * IOSS: Add mapping from exodus type to ioss field type * IOSS: Handle composite fields with different component separators * IOSS: Field - Add print method; support 2 separators for composite fields * IOSS: get_fields works after enhanced field found some fields * IOSS: Read/interpret exodus files with field metadata * IOSS: Eliminate some char **names uses -- convert to NameList * IOSS: Use more NameList and IntVector * CI: Remove cmake policy; not recognized in docker build * IOSS: CGNS - earlier versions have the CG_BUILD_HDF5 define in cgnsconfig.h * CI: Update to latest version [ci skip] * IOSS: Minor change to trigger workflows * IOSS: Propogate name_array changes to parallel * IOSS: Add serialize io calls wehre needed * IOSS: Use correct export macro * IOSS: Scalar fields do not need metadata; clutters file also * Io modify handle cgns (sandialabs#453) * IOSS: io_modify - try to get cgns structured mesh coordinate mods working * IOSS: io_modify - fix coordinate modification routines * IOSS: io_modify - try to handle block geometry modify in cgns * IOSS: io_info -- bbox works for structured mesh * IOSS: io_modify - redo geometry transformation code --------- Co-authored-by: Greg Sjaardema <gdsjaar@sandia.gov> * EXODUS: Fix element count in test writer * IOSS: Handle user-defined field metadata output * IOSS: Handle composite field multiple separators * CI: See if can fix appveyor build [ci skip] * IOSS: Put debug output in ifdef * CI: Actually trigger build... * CI: See if this affects appveyor... * CI: Change install name/location * EXODUS: Fix formatting of comment; turn off clang-format * IOSS: Initial steps in adding Basis capability * IOSS: Initial steps in adding Basis capability to field metadata query * CI: mkdir lib before plugin path in case doesnot exist [ci skip] * APREPRO: Fix some issues found in sierra input files * Testing an undefined variable against a string in a boolean (EQ, NE, LT, ...) was always returning true. . Changed such that an undefined variable in a boolean test with a string expression treats the undefined variable as the empty string. `{if (undefined_var == "Greg")}' Will parse as `{if ("" == "Greg")}' and output an undefined_variable warning. * The `exp()` function will output an ERANGE error for both underflow and overflow. We are ok with underflow not giving an error. Changed so only get math error in case of overflow. * EXPLORE: Add/Refactor qa, qainfo and info list commands * CI: Better error handling in script * EPU: Delete input files if requested * APREPRO: Fix to_string when fmt:: full precision output being used * APREPRO: Refactor last change * IOSS: heartbeat - add HEARTBEAT_FLUSH_INTERVAL property, document 0 will flush every step * EXODUS: Fix output of Curl gradient field * IOSS: Get field-metadata basis somewhat working * APREPRO: Bring branch up-to-date and fix bad merge * IOSS: Refactor function names for ComposedVariable * EXODUS: Move basis to global attribute * IOSS: Add quadrature storage type; beginnings of allowing multiple basis types * EXODUS: Redo so basis, quad stored at global level * IOSS: Modify tokenize to optionally return empty tokens * IOSS: Start of refactor for allowing multiple basis; basis at root of exodus * EXODUS: Allow more than one basis; field can specify which basis it is using * IOSS: Refactor basis struct/type * Iniitial support for quadrature storage type * EXODUS: Treat Quad@ attribute as internal * EXODUS: Add quadrature type and multiple basis/quad types to test read/write * IOSS: cleanup quadrature implementation * IOSS: Better const correctness * IOSS: VariableType -- function to return quad/basis types * IOSS: Support quadrature type in ioss<->exodus type mapping * IOSS: exodus - output basis/quadrature types * IOSS: Better suffix upper/lower detection * EXODUS: Support nesting of user-defiend fields * IOSS: Better compare output for fields * IOSS: Remove debug print * IOSS: Allow nesting on user-defined fields; refactor basis/quad output * EXODUS: Remove unused variable * EXODUS: Output from test program to stdout, not stderr * EXODUS: Add test for enhanced field metadata * EXODUS: Fix pipestatus values * EXODUS: Fix windows build * EXODUS: Remove shadowed variable * EXODUS: Fix enhanced fields for random attribute ordering * EXODUS: Test - more robust when nc4 changes attribute ordering * EXODUS: get_X_metadata functions have count argument added so call-to-call order works * EXODUS: Check for a null pointer * EXODUS: Provide internal strsep and strlcat * EXODUS: Improve portability * EXODUS: A better way to get strdup * EXODUS: Fix some compiler warnings; see if that makes test run... * EXODUS: Fix memory leak in test code * EXODUS: Deallocat struct in correct place * EXODUS: Reorder unit test and update output * IOSS: Add type and type_string to variable types * IOSS: Refactor detailed field output * IOSS: Allow detailed field output * IOSS: Minor cleanup/refactor * NEM_SLICE: Minor fix * IOSS: Clean up fmt includes/use * IOSS: Rewrite how catylyst deals with field names * IOSS: Fix up some changes for catalyst for this branch * IOSS: Fix default separator setting; do not recognize fields if property set * EXODUS: Refactor get/put basis and quad metadata * IOSS: Minor tweak to field printing * IOSS: Refactor variable type determination * EXODUS: Update nesting define; fix test dump file * IOSS: Simplify datapool - remove seldom used capabilty * IOSS: Refactor some names; add print * EXODUS: Eliminate memory leak * EXODUS: Fix spelling error * EXODUS: Fix compiler warning * EXODUS: Clean up some function name/doc * Spelling fixes [ci skip] * IOSS: Add backward compatible interfaces back --------- Co-authored-by: Utkarsh Ayachit <utkarsh.ayachit@kitware.com> Co-authored-by: Greg Sjaardema <gdsjaar@sandia.gov> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Mathieu Westphal <mathieu.westphal@kitware.com> Co-authored-by: Gary Templet <gjtempl@sandia.gov> Co-authored-by: Mario LoPrinzi <mvlopri@sandia.gov>
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