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Merge pull request #4 from CEED/fms-v0.2-dev
Final changes for FMS v0.2
2 parents 6b2cb5c + 52a1000 commit a66cb96

29 files changed

+1478
-1194
lines changed

‎.github/workflows/build-and-test.yaml

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# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
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# the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
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# reserved. See files LICENSE and NOTICE for details.
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#
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# This file is part of CEED, a collection of benchmarks, miniapps, software
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# libraries and APIs for efficient high-order finite element and spectral
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# element discretizations for exascale applications. For more information and
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# source code availability see http://github.com/ceed.
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#
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# The CEED research is supported by the Exascale Computing Project (17-SC-20-SC)
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# a collaborative effort of two U.S. Department of Energy organizations (Office
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# of Science and the National Nuclear Security Administration) responsible for
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# the planning and preparation of a capable exascale ecosystem, including
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# software, applications, hardware, advanced system engineering and early
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# testbed platforms, in support of the nation's exascale computing imperative.
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name: Build and test
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on:
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push:
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branches: [ master ]
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pull_request:
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branches: [ master ]
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env:
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BUILD_C_FLAGS: -Wall -Wextra -pedantic -Werror
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BUILD_CXX_FLAGS: -Wall -Wextra -pedantic -Werror
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jobs:
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build-and-test:
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runs-on: ${{matrix.os}}
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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build-type: [Debug, Release]
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name: ${{matrix.os}}-${{matrix.build-type}}
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- name: Configure
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run: |
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cmake \
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-B ${{github.workspace}}/build \
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-DCMAKE_BUILD_TYPE=${{matrix.build-type}} \
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-DFMS_ENABLE_TESTS=ON \
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-DCMAKE_C_FLAGS="$BUILD_C_FLAGS" \
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-DCMAKE_CXX_FLAGS="$BUILD_CXX_FLAGS" \
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-DCMAKE_INSTALL_PREFIX=${{github.workspace}}/install \
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-DCMAKE_VERBOSE_MAKEFILE=ON
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- name: Build
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run: |
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cmake \
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--build ${{github.workspace}}/build \
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--config ${{matrix.build-type}}
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- name: Install
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run: |
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cmake \
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--build ${{github.workspace}}/build \
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--config ${{matrix.build-type}} \
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--target install
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- name: Test
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working-directory: ${{github.workspace}}/build
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run: ctest -C ${{matrix.build-type}} --output-on-failure

‎.github/workflows/check-style.yaml

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# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
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# the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
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# reserved. See files LICENSE and NOTICE for details.
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#
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# This file is part of CEED, a collection of benchmarks, miniapps, software
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# libraries and APIs for efficient high-order finite element and spectral
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# element discretizations for exascale applications. For more information and
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# source code availability see http://github.com/ceed.
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#
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# The CEED research is supported by the Exascale Computing Project (17-SC-20-SC)
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# a collaborative effort of two U.S. Department of Energy organizations (Office
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# of Science and the National Nuclear Security Administration) responsible for
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# the planning and preparation of a capable exascale ecosystem, including
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# software, applications, hardware, advanced system engineering and early
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# testbed platforms, in support of the nation's exascale computing imperative.
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name: Check style
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on:
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push:
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branches: [ master ]
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pull_request:
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branches: [ master ]
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jobs:
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check-style:
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runs-on: ubuntu-20.04
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Get astyle
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run: sudo apt-get install astyle
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- name: Check style
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run: ./apply-style.sh

‎.gitignore

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*.out
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# IDE directories
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.vscode/
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.vscode/

‎CHANGELOG

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███████ ███ ███ ███████
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██ ████ ████ ██
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█████ ██ ████ ██ ███████
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██ ██ ██ ██ ██
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██ ██ ██ ███████
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CEED's high-order Field and Mesh Specification
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Version 0.2, released on Sep 10, 2021
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=====================================
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- Added support for writing and reading FmsDataCollections both in ASCII and
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binary format via Conduit.
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- Visualization for FMS files is available in VisIt v3.2, visit.llnl.gov.
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- Added regression and code styling.
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Version 0.1, released on Jul 8, 2018
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====================================
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- Initial release.

‎CMakeLists.txt

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# Copyright (c) 2017, Lawrence Livermore National Security, LLC. Produced at
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# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
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# the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
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# reserved. See files LICENSE and NOTICE for details.
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#
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# We use the C_STANDARD target property introduced in CMake 3.1
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cmake_minimum_required (VERSION 3.1)
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# Project name
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project(FMS VERSION 0.1 LANGUAGES C)
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# Project name and version.
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# The version is also defined in the files: fms.h and Doxyfile.
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project(FMS VERSION 0.2 LANGUAGES C)
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# Optional demo - see examples/README.md for more information
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option(FMS_ENABLE_DEMO "Enable the PUMI + MFEM demo" OFF)
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# Setup thirdparty dependencies
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# Optional conduit implementation for IO functions
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if(CONDUIT_DIR)
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find_package(Conduit 0.5.1 REQUIRED
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enable_language(CXX)
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find_package(Conduit 0.7.1 REQUIRED
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HINTS ${CONDUIT_DIR}
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NO_DEFAULT_PATH)
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set(FMS_HAVE_CONDUIT TRUE)
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endif()
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if(PUMI_DIR)
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find_package(SCOREC 2.1.0 REQUIRED
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CONFIG
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HINTS ${PUMI_DIR}
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find_package(SCOREC 2.1.0 REQUIRED
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CONFIG
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HINTS ${PUMI_DIR}
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NO_DEFAULT_PATH)
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set(FMS_HAVE_PUMI TRUE)
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message(STATUS "Demo using PUMI: ${SCOREC_DIR}")

‎Doxyfile

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# could be handy for archiving the generated documentation or if some version
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# control system is used.
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PROJECT_NUMBER = v0.1
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PROJECT_NUMBER = v0.2
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# Using the PROJECT_BRIEF tag one can provide an optional one line description
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# for a project that appears at the top of each page and should give viewer a
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# C-preprocessor directives found in the sources and include files.
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# The default value is: YES.
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ENABLE_PREPROCESSING = NO
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ENABLE_PREPROCESSING = YES
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# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
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# in the source code. If set to NO, only conditional compilation will be

‎LICENSE

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BSD 2-Clause License
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Copyright (c) 2017 Lawrence Livermore National Security, LLC.
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Copyright (c) 2021 Lawrence Livermore National Security, LLC.
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All rights reserved.
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Redistribution and use in source and binary forms, with or without

‎README.md

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# FMS: CEED's high-order Field and Mesh Specification
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███████ ███ ███ ███████
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██ ████ ████ ██
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█████ ██ ████ ██ ███████
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██ ██ ██ ██ ██
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██ ██ ██ ███████
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CEED's high-order Field and Mesh Specification
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29

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[![License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
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[![Documentation](https://codedocs.xyz/CEED/FMS.svg)](https://codedocs.xyz/CEED/FMS/)
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[![Build and Test (GH Actions)](https://github.com/CEED/FMS/actions/workflows/build-and-test.yaml/badge.svg?branch=master)](https://github.com/CEED/FMS/actions?query=workflow%3Abuild-and-test)
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[![Build and Test (GH Actions)](https://github.com/CEED/FMS/actions/workflows/check-style.yaml/badge.svg?branch=master)](https://github.com/CEED/FMS/actions?query=workflow%3Acheck-style)
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## High-Order Data Description
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elements, such as Nedelec and Raviart-Thomas elements. See the [FMS
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documentation](doc/fms.md) for more details.
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Initial support for the FMS file formats is available in
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[VisIt](https://visit.llnl.gov/) version 3.2.
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![High-order mesh and solution](doc/triple-pt-2x2.png)
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The following diagram illustrates the current and planned components of FMS.
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## Building
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You can get started with the default build configuration using the command line listed below. Checkout the [build documentation](doc/build.md) for more info.
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You can get started with the default build configuration using the command line
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listed below. Checkout the [build documentation](doc/build.md) for more info.
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```console
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mkdir build
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The following copyright applies to each file in the CEED software suite, unless
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otherwise stated in the file:
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> Copyright (c) 2017, Lawrence Livermore National Security, LLC. Produced at the
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> Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at the
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> Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights reserved.
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See files LICENSE and NOTICE for details.

‎apply-style.sh

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#!/bin/bash
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# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
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# the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
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# reserved. See files LICENSE and NOTICE for details.
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#
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# This file is part of CEED, a collection of benchmarks, miniapps, software
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# libraries and APIs for efficient high-order finite element and spectral
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# element discretizations for exascale applications. For more information and
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# source code availability see http://github.com/ceed.
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#
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# The CEED research is supported by the Exascale Computing Project (17-SC-20-SC)
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# a collaborative effort of two U.S. Department of Energy organizations (Office
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# of Science and the National Nuclear Security Administration) responsible for
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# the planning and preparation of a capable exascale ecosystem, including
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# software, applications, hardware, advanced system engineering and early
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# testbed platforms, in support of the nation's exascale computing imperative.
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function main()
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{
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cd $(dirname "$0")
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fms_astyle_file="fms.astylerc"
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if [[ ! -r "${fms_astyle_file}" ]]; then
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echo "FMS's astyle format file not found: '${fms_astyle_file}'. Stop."
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exit 21
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fi
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find_astyle
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local old_IFS="${IFS}"
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IFS=$'\n'
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format_files=($(git ls-files "*.[ch]" "*.[ch]pp"))
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if [[ "$?" -ne 0 ]]; then
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echo "Error getting list of C/C++ source files from Git. Stop."
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exit 22
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fi
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IFS="${old_IFS}"
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if ${astyle_bin} --options="${fms_astyle_file}" "${format_files[@]}" | \
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grep "Formatted"; then
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printf "\nPlease make sure the changes are committed.\n\n"
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return 1
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else
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printf "All source files are properly formatted.\n"
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fi
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return 0
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} # end of function 'main'
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function find_astyle()
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{
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astyle_req_version="Artistic Style Version 3.1"
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astyle_bin_list=("${ASTYLE_BIN:-astyle}" astyle-3.1)
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for astyle_bin in "${astyle_bin_list[@]}"; do
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if ! command -v "${astyle_bin}" > /dev/null 2>&1; then
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continue
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fi
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astyle_version="$("${astyle_bin}" --version)"
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if [[ "${astyle_version}" != "${astyle_req_version}" ]]; then
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continue
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fi
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return 0
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done
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echo "Required astyle version not found: '${astyle_req_version}'."
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printf "Astyle commands tried:"
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printf " '%s'" "${astyle_bin_list[@]}"
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printf ".\n"
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exit 23
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} # end of function 'find_astyle'
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# Invoke the 'main' function
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main "$@"

‎doc/build.md

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cmake -DFMS_DIR=*fms/install/prefix* ..
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make
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./main
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```
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```

‎doc/components.png

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‎examples/CMakeLists.txt

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# Copyright (c) 2020, Lawrence Livermore National Security, LLC. Produced at
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# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
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# the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
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# reserved. See files LICENSE and NOTICE for details.
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#

‎examples/demo_pumi_mfem/CMakeLists.txt

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# Copyright (c) 2020, Lawrence Livermore National Security, LLC. Produced at
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# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
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# the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
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# reserved. See files LICENSE and NOTICE for details.
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#

‎examples/demo_pumi_mfem/demo_pumi_mfem.cpp

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}
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// Edges
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FmsInt nvtxs = 2;
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const FmsInt nvtxs = 2;
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FmsInt num_edges = 0;
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int edge[nvtxs];
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itr = pumi_mesh->begin(1);
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pumi_mesh->end(itr);
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159159
// Define Face based on edge Id's
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FmsInt nedges = 3;
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const FmsInt nedges = 3;
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int face[nedges];
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int num_triangles = 0;
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itr = pumi_mesh->begin(2);
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pumi_mesh->end(itr);
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// Define Elem based on face Id's
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FmsInt nfaces = 4;
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const FmsInt nfaces = 4;
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FmsEntityReordering EntReord;
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int tetOrd[4] = {0,1,3,2}; // PUMI order for tet element faces
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EntReord[FMS_TETRAHEDRON] = &tetOrd[0];

‎examples/include-fms/main.cpp

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auto a = FmsMeshConstruct(&m);
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printf("Hello %d\n", a);
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return a;
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}
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}

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