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Discontinuous galerkin#403

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gsjaardema merged 248 commits intomastersandialabs/seacas:masterfrom discontinuous-galerkinsandialabs/seacas:discontinuous-galerkinCopy head branch name to clipboardMay 30, 2024

+4,475-1,088

Commits

Commits on Apr 6, 2022

• EXODUS: refactor field metadata attribute output

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• EXODUS: Beginnings of basis read

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Commits on Apr 7, 2022

• EXODUS: basis query

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• Merge branch 'master' into discontinuous-galerkin

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• EXODUS: these got lost with some branch mishaps

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Commits on Apr 8, 2022

• EXODUS: Spelling fix

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• EXODUS: See if can fix intel errors

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• EXODUS: Fix intel build

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Commits on Apr 11, 2022

• EXODUS: Move internal function to correct header

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Commits on Jun 2, 2022

• Windows fixes: make functions non-inline

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• eliminate warnings

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• IOSS: cgns - do not create assemblies from Unspecified VC

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• Getting kokkos build working again [ci skip]

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• TEST: Enable kokkos build

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• IOSS: Change byte-size output to debug

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• shellcheck recommendations

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• TESTING: Remove adios2 until figure out issues

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• EPU: Minor improvement in message (plural vs singular)

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• IOSS: Rename qsort to sort

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• IO_MODIFY: Better help output

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• IO_MODIFY: clean-up comment [ci skip]

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• Revert "EPU: Minor improvement in message (plural vs singular)"

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• IOSS: Switch to using doctest from Catch2

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• IOSS: cgns - remove lambdas to see if fixes stria issue

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• IOSS: Remove shadowed variable

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• Revert "Remove shadowed variable."

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• Revert "IOSS: cgns - remove lambdas to see if fixes stria issue"

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• IOSS: cgns - get CG_BUILD_PARALLEL define for all versions

  

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• Update readme -- replace Catch2 with doctest [ci skip]

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• @wortiz has signed the CLA from Pull Request #303

  

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• @mwestphal has signed the CLA from Pull Request #304

  

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• BLOT: Fix new argument mismatch warning with gcc-12

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• Fix a recursive warning on assignement copy operator

  

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• IOSS: DEBUG->DbgOut, WARNING->WarnOut to avoid windows issues

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• IOSS: new version of clang-format

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• New version of clang-format

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• New version of clang-format

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• TPL: Add INSTALL_PATH to metis/parmetis installs

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• MODULE: Remove old unused unsupported lines [ci skip]

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• @gjtempl has signed the CLA from Pull Request #305

  

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• Updates for serial build

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• IOSS: Handle uppercase field suffices

  

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• IOSS: Clean up uppercase suffix fix

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• ZELLIJ: Add offset option

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• KOKKOS: Use current version

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• TPL: Fix kokkos runcmake.sh for current version

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• EXODUS: Clean up

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• Copy top-level README to packages/seacas so available in Trilinos snapshot

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• CONFIG: Update name of kokkos library

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• EXODUS.PY: Add the get_block_id_map method

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• ZELLIJ: Better cache utilization for offset and scale

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• IOSS: Handle specified field ordering (via index) if present

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• IOSS: use reserve instead of resize since pushing back

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• IO_MODIFY: Add rename capability

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• IO_MODIFY: Clean up rename capability

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• CONFIG: Add gnubrew compiler option

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• CONFIG: Update hdf5 versions

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• IO_MODIFY: update help options

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• EXODUS: Fix problem with ex_get_block_id_map function

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• SUPES: Make a variable be a correct spelling

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• EXODUS: clang-analyzer fixes

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Commits on Sep 20, 2023

• Merge branch 'master' into discontinuous-galerkin

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• Bring up-to-date with master

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• Clean up bad merge

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• EXODUS: Clean up bad merge

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• EXODUS: Clean up anothr bad merge

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• EPU: Bring in fix from master

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Commits on Sep 21, 2023

• EXODUS: Clean up python and varid lookup

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• EXODUS: Support cardinality and user-define suffices; refactor

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Commits on Sep 25, 2023

• EXODUS: Further refinement/refactoring of DG field interface

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Commits on Sep 27, 2023

• EXODUS: Refactor component separator to allow for empty value

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• EXODUS: Minor cleanup

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Commits on Sep 28, 2023

• EXODUS: Refactor function naems; add test of ex_field utils

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• EXODUS: Add missing file from last commit

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• EXODUS: Fix bad handling of user-defined suffices

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Commits on Oct 11, 2023

• EXODUS: Fix suffix handling in name building

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Commits on Oct 24, 2023

• CI: Fix cmake version requirement

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Commits on Oct 26, 2023

• EXODUS: More work on the basis metadata read

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• EXODUS: Fix null test -- use double pipe

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• Merge branch 'master' into discontinuous-galerkin

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• EXODUS: refactor field metadata attribute output

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• EXODUS: Beginnings of basis read

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• EXODUS: basis query

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• EXODUS: these got lost with some branch mishaps

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• EXODUS: Spelling fix

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• EXODUS: See if can fix intel errors

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• EXODUS: Fix intel build

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• EXODUS: Move internal function to correct header

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• TEST: Enable kokkos build

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• EPU: Minor improvement in message (plural vs singular)

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• Revert "EPU: Minor improvement in message (plural vs singular)"

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• IOSS: Remove shadowed variable

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• Revert "Remove shadowed variable."

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• CONFIG: Add gnubrew compiler option

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• Bring up-to-date with master

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• EXODUS: Support cardinality and user-define suffices; refactor

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• EXODUS: Further refinement/refactoring of DG field interface

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• EXODUS: Refactor component separator to allow for empty value

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• EXODUS: Minor cleanup

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• EXODUS: Refactor function naems; add test of ex_field utils

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• EXODUS: Add missing file from last commit

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• EXODUS: Fix bad handling of user-defined suffices

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• EXODUS: Fix suffix handling in name building

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• CI: Fix cmake version requirement

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• EXODUS: More work on the basis metadata read

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• EXODUS: Fix null test -- use double pipe

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• EXODUS: Test field metadata read/write on nodes

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• CI: Fix cxx standard setting

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• EXODUS: Fix bad merge

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• Merge branch 'discontinuous-galerkin' of https://github.com/sandialabs/seacas into discontinuous-galerkin

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• EXODUS: Fix bad merge

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Commits on Oct 27, 2023

• EXODUS: Fix varid query for assembly and blob

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• EXODUS.PY: See if this fixes ci build issues

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• EXODUS: Fix ex__get_varid function

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Commits on Oct 30, 2023

• Revert "EXODUS.PY: See if this fixes ci build issues"

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• EXODUS: Clean up ex_attribute struct

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• EXODUS: realpath is gnu extension in c11/c99

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• EXODUS: Provide realpath prototype

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• EXODUS: Add missing functions for mingw

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• EXODUS: Fix ex_attribute initiialization

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• CI: Disable nczarr in netcdf

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• EXODUS: Fix codacy null / 0 issue

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• EXODUS: Removed unused struct member

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• IOSS: Clean up some includes; remove the ... for ???

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Commits on Mar 25, 2024

• Merge branch 'master' into discontinuous-galerkin

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• EXODUS: Fix bad master merge

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• EXODUS: Fix intel compiler build

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Commits on Mar 26, 2024

• BLOT: Increase resolution of node/element id output

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• IOSS: Change meta_data to metadata

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• EXODUS: Use internal naming for static function

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• Remove ioss as required library

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Commits on Mar 27, 2024

• EXODUS: Add function name to output so know where it came from

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• IOSS: Add function mapping Ioss field names to exodus ex_field_type

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• IOSS: Output field metadata basic implemetation

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• IOSS: Rename function for consistency

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• IOSS: Add missing serialize io call

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Commits on Mar 29, 2024

• APREPRO: Make strings test more robust

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Commits on Apr 1, 2024

• IOSS: Build io_modify only if exodus enabled

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• IOSS: Detect if exodus enabled for exodus include

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Commits on Apr 9, 2024

• GREPOS: Intel overoptimizes unless inimap separate file

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Commits on Apr 10, 2024

• Merge branch 'master' into discontinuous-galerkin

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• GREPOS: Fix bad merge

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• CONFIG: Silence CMake warning about python interpreter finding

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• IOSS: Fix use of c++14/17 type-traits

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Commits on Apr 11, 2024

• EXODUS: Filter out attributes Field@

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• IOSS: Add mapping from exodus type to ioss field type

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• IOSS: Handle composite fields with different component separators

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• IOSS: Field - Add print method; support 2 separators for composite fields

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• IOSS: get_fields works after enhanced field found some fields

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• IOSS: Read/interpret exodus files with field metadata

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Commits on Apr 12, 2024

• IOSS: Eliminate some char **names uses -- convert to NameList

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• IOSS: Use more NameList and IntVector

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• CI: Remove cmake policy; not recognized in docker build

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• IOSS: CGNS - earlier versions have the CG_BUILD_HDF5 define in cgnsconfig.h

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• CI: Update to latest version [ci skip]

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• IOSS: Minor change to trigger workflows

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• Merge branch 'discontinuous-galerkin' of https://github.com/SandiaLabs/seacas into discontinuous-galerkin

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• IOSS: Propogate name_array changes to parallel

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• IOSS: Add serialize io calls wehre needed

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• IOSS: Use correct export macro

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Commits on Apr 15, 2024

• IOSS: Scalar fields do not need metadata; clutters file also

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• Io modify handle cgns (#453)

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• EXODUS: Fix element count in test writer

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• IOSS: Handle user-defined field metadata output

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• IOSS: Handle composite field multiple separators

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Commits on Apr 16, 2024

• CI: See if can fix appveyor build [ci skip]

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• IOSS: Put debug output in ifdef

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• EXODUS: Fix formatting of comment; turn off clang-format

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• IOSS: Initial steps in adding Basis capability

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• IOSS: Initial steps in adding Basis capability to field metadata query

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Commits on Apr 18, 2024

• CI: mkdir lib before plugin path in case doesnot exist [ci skip]

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• APREPRO: Fix some issues found in sierra input files

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• EXPLORE: Add/Refactor qa, qainfo and info list commands

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• CI: Better error handling in script

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• EPU: Delete input files if requested

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• APREPRO: Fix to_string when fmt:: full precision output being used

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• IOSS: heartbeat - add HEARTBEAT_FLUSH_INTERVAL property, document 0 will flush every step

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• EXODUS: Fix output of Curl gradient field

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• IOSS: Get field-metadata basis somewhat working

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• IOSS: Refactor function names for ComposedVariable

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Commits on Apr 25, 2024

• EXODUS: Move basis to global attribute

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• IOSS: Add quadrature storage type; beginnings of allowing multiple basis types

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• EXODUS: Redo so basis, quad stored at global level

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• IOSS: Modify tokenize to optionally return empty tokens

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• IOSS: Start of refactor for allowing multiple basis; basis at root of exodus

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Commits on Apr 29, 2024

• EXODUS: Allow more than one basis; field can specify which basis it is using

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Commits on Apr 30, 2024

• IOSS: Refactor basis struct/type

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• Iniitial support for quadrature storage type

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• EXODUS: Treat Quad@ attribute as internal

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• EXODUS: Add quadrature type and multiple basis/quad types to test read/write

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• IOSS: cleanup quadrature implementation

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• IOSS: Better const correctness

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• IOSS: VariableType -- function to return quad/basis types

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• IOSS: Support quadrature type in ioss<->exodus type mapping

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• IOSS: exodus - output basis/quadrature types

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• IOSS: Better suffix upper/lower detection

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• EXODUS: Support nesting of user-defiend fields

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• IOSS: Better compare output for fields

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• IOSS: Remove debug print

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• IOSS: Allow nesting on user-defined fields; refactor basis/quad output

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• EXODUS: Remove unused variable

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• EXODUS: Output from test program to stdout, not stderr

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• EXODUS: Add test for enhanced field metadata

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• EXODUS: Fix pipestatus values

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• EXODUS: Fix windows build

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• EXODUS: Remove shadowed variable

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Commits on May 14, 2024

• EXODUS: Fix enhanced fields for random attribute ordering

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• EXODUS: Test - more robust when nc4 changes attribute ordering

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• EXODUS: get_X_metadata functions have count argument added so call-to-call order works

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• EXODUS: Check for a null pointer

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• EXODUS: Provide internal strsep and strlcat

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Commits on May 15, 2024

• EXODUS: Improve portability

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• EXODUS: A better way to get strdup

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• EXODUS: Fix some compiler warnings; see if that makes test run...

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• EXODUS: Fix memory leak in test code

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• EXODUS: Deallocat struct in correct place

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• EXODUS: Reorder unit test and update output

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Commits on May 20, 2024

• IOSS: Add type and type_string to variable types

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• IOSS: Refactor detailed field output

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• IOSS: Allow detailed field output

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• IOSS: Minor cleanup/refactor

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• NEM_SLICE: Minor fix

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Commits on May 21, 2024

• IOSS: Clean up fmt includes/use

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• IOSS: Rewrite how catylyst deals with field names

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Commits on May 22, 2024

• IOSS: Fix up some changes for catalyst for this branch

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• IOSS: Fix default separator setting; do not recognize fields if property set

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Commits on May 23, 2024

• EXODUS: Refactor get/put basis and quad metadata

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• IOSS: Minor tweak to field printing

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• IOSS: Refactor variable type determination

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• EXODUS: Update nesting define; fix test dump file

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Commits on May 28, 2024

• IOSS: Simplify datapool - remove seldom used capabilty

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• IOSS: Refactor some names; add print

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• EXODUS: Eliminate memory leak

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• EXODUS: Fix spelling error

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• EXODUS: Fix compiler warning

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• EXODUS: Clean up some function name/doc

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• Spelling fixes [ci skip]

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Commits on May 30, 2024

• IOSS: Add backward compatible interfaces back

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