Add periodic mesh support for GMSH; format everything a bit

.clang-format

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2020 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 Language:        Cpp
 AccessModifierOffset: -4
 AlignAfterOpenBracket: Align
@@ -121,4 +125,3 @@ StatementMacros:
   - QT_REQUIRE_VERSION
 TabWidth:        8
 UseTab:          Never
-

.git-blame-ignore-revs

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2020 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 # Apply LLVM stlye for the first time
 b864952a14025d953acc5fad1198e5ba119e25d3
 # Apply mneme style

.github/workflows/cmake.yml

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 name: CMake
 
 on: [push]
@@ -8,6 +12,7 @@ jobs:
     runs-on: ubuntu-latest
 
     strategy:
+      fail-fast: false
       matrix:
         build_type: ["Release", "Debug"]
 
@@ -18,27 +23,23 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -qq g++ openmpi-bin openmpi-common libopenmpi-dev hdf5-tools libhdf5-openmpi-dev libnetcdf-dev
-  
+
       - name: Configure PUMGen
         working-directory: ${{ github.workspace }}
         run: |
           git submodule update --init --recursive
           mkdir build_${{ matrix.build_type}} && cd build_${{ matrix.build_type}}
           cmake .. -DCMAKE_PREFIX_PATH=${{ runner.workspace }}/opt -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
-  
+
       - name: Build
         working-directory: ${{ github.workspace }}/build_${{ matrix.build_type }}
         run: cmake --build .
-  
-  clang-format:
+
+  pre-commit-check:
     runs-on: ubuntu-latest
-    steps: 
+    steps:
       - uses: actions/checkout@v5
+        with:
+          submodules: recursive
 
-      - name: clang-format
-        run: |
-          sudo apt-get update
-          sudo apt-get install -qq python3 python3-pip
-          pip3 install clang-format==19.1.0
-          git submodule update --init
-          ./submodules/run-clang-format/run-clang-format.py --clang-format-executable clang-format --exclude src/third_party -r src
+      - uses: pre-commit/action@v3.0.1

.gitignore

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2017 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 # KDevelop4
 *.kdev4
 *.kdev4/

.gitmodules

@@ -1,9 +1,10 @@
+# SPDX-FileCopyrightText: 2017 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 [submodule "submodules/utils"]
 	path = submodules/utils
 	url = ../../TUM-I5/utils.git
 [submodule "submodules/tinyxml2"]
 	path = submodules/tinyxml2
 	url = ../../leethomason/tinyxml2.git
-[submodule "submodules/run-clang-format"]
-	path = submodules/run-clang-format
-	url = ../../Sarcasm/run-clang-format.git

.pre-commit-config.yaml

@@ -0,0 +1,63 @@
+# SPDX-FileCopyrightText: 2025 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-LicenseComments: Full text under /LICENSE and /LICENSES/
+#
+# SPDX-FileContributor: Author lists in /AUTHORS and /CITATION.cff
+
+---
+
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: check-merge-conflict
+        name: '[GENERIC] merge conflict check'
+    -   id: check-symlinks
+        name: '[GENERIC] symlink check'
+    -   id: destroyed-symlinks
+        name: '[GENERIC] detect broken symlinks'
+    -   id: detect-private-key
+        name: '[GENERIC] detect private keys uploaded by accident'
+    -   id: check-case-conflict
+        name: '[GENERIC] detect OS file naming case conflicts'
+    -   id: check-executables-have-shebangs
+        name: '[GENERIC] check for shebangs in executable files'
+    -   id: check-illegal-windows-names
+        name: '[GENERIC] detect illegal Windows file names'
+    -   id: check-json
+        name: '[JSON] check'
+    #-   id: check-xml
+    #    name: '[XML] check'
+
+-   repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.18.1
+    hooks:
+    -   id: markdownlint-cli2
+        name: '[MARKDOWN] lint'
+
+-   repo: https://github.com/fsfe/reuse-tool
+    rev: v5.1.1
+    hooks:
+    -   id: reuse
+        name: '[GENERIC] REUSE compatibiltiy'
+
+-   repo: https://github.com/sphinx-contrib/sphinx-lint
+    rev: 'v1.0.0'
+    hooks:
+    -   id: sphinx-lint
+        name: '[SPHINX/RST] sphinx lint'
+
+-   repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: 'v21.1.0'
+    hooks:
+    -   id: clang-format
+        name: '[C++] clang-format'
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: end-of-file-fixer
+        name: '[GENERIC] newline eof'
+    -   id: trailing-whitespace
+        name: '[GENERIC] remove trailing whitespace'

CMakeLists.txt

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2020 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 cmake_minimum_required(VERSION 3.9)
 
 cmake_policy(SET CMP0074 NEW)
@@ -38,8 +42,8 @@ add_executable(pumgen
   ${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSHLexer.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSHParser.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSH2Parser.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/src/aux/InsphereCalculator.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/src/aux/MPIConvenience.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/helper/InsphereCalculator.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/helper/MPIConvenience.cpp
   )
 
 target_include_directories(pumgen PUBLIC src
@@ -93,7 +97,7 @@ if (SIMMETRIX)
     find_package(easi 1.0.0 REQUIRED)
     target_link_libraries(pumgen PUBLIC easi::easi)
 
-    target_sources(pumgen PUBLIC 
+    target_sources(pumgen PUBLIC
       ${CMAKE_CURRENT_SOURCE_DIR}/src/input/AnalysisAttributes.cpp
       ${CMAKE_CURRENT_SOURCE_DIR}/src/input/EasiMeshSize.cpp
       ${CMAKE_CURRENT_SOURCE_DIR}/src/input/MeshAttributes.cpp

LICENSES/BSD-3-Clause.txt

@@ -0,0 +1,11 @@
+Copyright (c) <year> <owner>.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,5 +1,13 @@
+<!--
+    SPDX-FileCopyrightText: 2023 SeisSol Group
+
+    SPDX-License-Identifier: BSD-3-Clause
+-->
+
 # PUMGen
+
 A mesh converter to the PUML format, as used in SeisSol.
 
 ## Installing
-See our wiki for detailed install instructions: https://github.com/SeisSol/PUMGen/wiki
+
+See our [wiki](https://github.com/SeisSol/PUMGen/wiki) for detailed install instructions.

XmlExample/meshAttributes.xml

@@ -1,8 +1,14 @@
+<!--
+    SPDX-FileCopyrightText: 2020 SeisSol Group
+
+    SPDX-License-Identifier: BSD-3-Clause
+-->
+
 <freeSurface>1</freeSurface>
 <dynamicRupture>2</dynamicRupture>
 <absorbing>3,4</absorbing>
 <!-- see https://seissol.readthedocs.io/en/latest/fault-tagging.html for SeisSol convention regarding boundaryCondition -->
-<boundaryCondition tag="65">7</boundaryCondition> 
+<boundaryCondition tag="65">7</boundaryCondition>
 <boundaryCondition tag="67">7</boundaryCondition>
 <boundaryCondition tag="68">8,9</boundaryCondition>
 <globalMSize value="100e3"/>
@@ -27,15 +33,15 @@
 <surfaceNoMesh>1,2</surfaceNoMesh>
 <regionNoMesh>1,4</regionNoMesh>
 
-<!-- For complex geometry, finding the region in which a point lies is expensive and will 
-slow down the mesh generation significantly when using VelocityAwareMeshing. 
+<!-- For complex geometry, finding the region in which a point lies is expensive and will
+slow down the mesh generation significantly when using VelocityAwareMeshing.
 To avoid such an expensive call to the findGroup function, we can specify the group to use
 in the easi query using the (optional) argument bypassFindRegionAndUseGroup -->
 
 <VelocityAwareMeshing easiFile="easiFile.yaml" elementsPerWaveLength="2">
     <VelocityRefinementCuboid frequency="2" centerX="200" centerY="200" centerZ="-100"
                               halfSizeX="100" halfSizeY="100" halfSizeZ="100" rotationZAnticlockwiseFromX="30."/>
     <VelocityRefinementCuboid frequency="10" centerX="0" centerY="0" centerZ="0"
-                              halfSizeX="100" halfSizeY="100" halfSizeZ="100" 
+                              halfSizeX="100" halfSizeY="100" halfSizeZ="100"
                               bypassFindRegionAndUseGroup="1"/>
 </VelocityAwareMeshing>

cmake/FindAPF.cmake

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2021 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 include(FindPackageHandleStandardArgs)
 
 # simmetrixLibs = [('gmi_sim', 'gmi_sim.h'), ('apf_sim', 'apfSIM.h')]

cmake/FindNetCDF.cmake

@@ -11,6 +11,7 @@ Provides the following variables:
 # Stolen from VTK with some small modifications
 # https://github.com/Kitware/VTK/blob/master/CMake/FindNetCDF.cmake
 # (BSD 3-Clause License)
+# SPDX-License-Identifier: BSD-3-Clause
 
 #[[=========================================================================
 

cmake/FindSIMMETRIX.cmake

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2021 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 include(FindPackageHandleStandardArgs)
 
 if (SCOREC)
@@ -36,7 +40,7 @@ find_library(SIM_PARTITIONED_MESH_LIB SimPartitionedMesh ${SIM_LIB_HINT})
 find_library(SIM_PARTITIONED_MESH_MPI_LIB SimPartitionedMesh-mpi ${SIM_LIB_HINT})
 find_library(SIM_PARTITIONED_WRAPPER_LIB SimPartitionWrapper-${SIM_MPI} ${SIM_LIB_HINT})
 find_library(SIM_PS_KRNL_LIB pskernel ${SIM_LIB_HINT}/psKrnl)
-  
+
 get_filename_component(SIM_PS_KRNL_LIB_DIR ${SIM_PS_KRNL_LIB} DIRECTORY)
 
 list(APPEND SIMMETRIX_LIBRARIES