Initial commit

.clang-format

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+#
+# The clang-format (Clang 6) style file used by deal.II.
+#
+
+AccessModifierOffset: -2
+
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: true
+AlignEscapedNewlines: Left
+AlignOperands: true
+AlignTrailingComments: true
+
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+
+AlwaysBreakAfterReturnType: All
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: true
+
+BinPackArguments: false
+BinPackParameters: false
+
+BraceWrapping:
+  AfterClass: true
+  AfterControlStatement: true
+  AfterEnum: true
+  AfterExternBlock: true
+  AfterFunction: true
+  AfterNamespace: true
+  AfterStruct: true
+  AfterUnion: true
+  BeforeCatch: true
+  BeforeElse: true
+  IndentBraces: true
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: false
+
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeInheritanceComma: false
+BreakBeforeTernaryOperators: false
+BreakConstructorInitializers: BeforeComma
+BreakStringLiterals: false
+
+ColumnLimit: 80
+
+CompactNamespaces: false
+
+ConstructorInitializerIndentWidth: 2
+
+ContinuationIndentWidth: 2
+
+Cpp11BracedListStyle: true
+
+DerivePointerAlignment: false
+
+FixNamespaceComments: true
+
+IncludeBlocks: Regroup
+IncludeCategories:
+# config.h must always be first:
+  - Regex:    "deal.II/base/config.h"
+    Priority: -1
+# deal.II folders in sorted order:
+  - Regex:    "deal.II/algorithms/.*\\.h"
+    Priority: 110
+  - Regex:    "deal.II/base/.*\\.h"
+    Priority: 120
+  - Regex:    "deal.II/boost_adaptors/.*\\.h"
+    Priority: 125
+  - Regex:    "deal.II/differentiation/.*\\.h"
+    Priority: 130
+  - Regex:    "deal.II/distributed/.*\\.h"
+    Priority: 140
+  - Regex:    "deal.II/dofs/.*\\.h"
+    Priority: 150
+  - Regex:    "deal.II/fe/.*\\.h"
+    Priority: 160
+  - Regex:    "deal.II/gmsh/.*\\.h"
+    Priority: 170
+  - Regex:    "deal.II/grid/.*\\.h"
+    Priority: 180
+  - Regex:    "deal.II/hp/.*\\.h"
+    Priority: 190
+  - Regex:    "deal.II/integrators/.*\\.h"
+    Priority: 200
+  - Regex:    "deal.II/lac/.*\\.h"
+    Priority: 210
+  - Regex:    "deal.II/matrix_free/.*\\.h"
+    Priority: 220
+  - Regex:    "deal.II/meshworker/.*\\.h"
+    Priority: 230
+  - Regex:    "deal.II/multigrid/.*\\.h"
+    Priority: 240
+  - Regex:    "deal.II/non_matching/.*\\.h"
+    Priority: 250
+  - Regex:    "deal.II/numerics/.*\\.h"
+    Priority: 260
+  - Regex:    "deal.II/opencascade/.*\\.h"
+    Priority: 270
+  - Regex:    "deal.II/optimization/.*\\.h"
+    Priority: 280
+  - Regex:    "deal.II/particles/.*\\.h"
+    Priority: 290
+  - Regex:    "deal.II/physics/.*\\.h"
+    Priority: 300
+  - Regex:    "deal.II/simplex/.*\\.h"
+    Priority: 310
+  - Regex:    "deal.II/sundials/.*\\.h"
+    Priority: 320
+# put boost right after deal:
+  - Regex: "<boost.*>"
+    Priority: 500
+# try to group PETSc headers:
+  - Regex: "<petsc.*\\.h>"
+    Priority: 1000
+# try to catch all third party headers and put them after deal.II but before
+# standard headers:
+  - Regex: "<.*\\.(h|hpp|hxx)>"
+    Priority: 2000
+# match all standard headers. Things like '#include <armadillo>' should be
+# surrounded by #ifdef checks (which will not be merged by clang-format) so they
+# should not be caught here
+  - Regex: "<[a-z_]+>"
+    Priority: 100000
+# make sure that "../tests.h" appears before all other local include files
+# such that replacing Assert in tests also applies to the testing header files.
+  - Regex: "\\.\\./tests\\.h"
+    Priority: 200000
+
+IndentCaseLabels: true
+IndentPPDirectives: AfterHash
+IndentWidth: 2
+
+IndentWrappedFunctionNames: false
+
+KeepEmptyLinesAtTheStartOfBlocks: false
+
+Language: Cpp
+
+MaxEmptyLinesToKeep: 3
+
+NamespaceIndentation: All
+
+PenaltyBreakBeforeFirstCallParameter: 90
+
+PointerAlignment: Right
+
+ReflowComments: true
+CommentPragmas: '( \| |\*--|<li>|@ref | @p |@param |@name |@returns |@warning |@ingroup |@author |@date |@related |@relates |@relatesalso |@deprecated |@image |@return |@brief |@attention |@copydoc |@addtogroup |@todo |@tparam |@see |@note |@skip |@skipline |@until |@line |@dontinclude |@include)'
+
+SortIncludes: true
+SortUsingDeclarations: true
+
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInContainerLiterals: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+
+Standard: Cpp11
+
+TabWidth: 2
+
+UseTab: Never

.devcontainer/Dockerfile

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+FROM heltai/dealii:vscode
+
+LABEL maintainer="[email protected]"
+
+USER $USER
+
+WORKDIR $HOME

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/vscode-remote/devcontainer.json or this file's README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.122.1/containers/docker-existing-dockerfile
+{
+	"name": "deal.II master container",
+	// Sets the run context to one level up instead of the .devcontainer folder.
+	"context": "..",
+	// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+	"dockerFile": "Dockerfile",
+	// Set *default* container specific settings.json values on container create.
+	"settings": {
+		"terminal.integrated.shell.linux": null
+	},
+	// Add the IDs of extensions you want installed when the container is created.
+	"extensions": [
+		"davydden.dealii-prm",
+		"johnpapa.vscode-peacock",
+		"alefragnani.project-manager",
+		"ms-vscode.cpptools",
+		"shan.code-settings-sync",
+		"ms-vscode.cmake-tools",
+		"xaver.clang-format",
+		"ms-azuretools.vscode-docker",
+		"davidschuldenfrei.gtest-adapter",
+		"cschleiden.vscode-github-actions"
+	],
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+	// Uncomment the next line to run commands after the container is created - for example installing curl.
+	// "postCreateCommand": "sudo apt-get update && sudo apt-get install -y gdb",
+	// Uncomment when using a ptrace-based debugger like C++, Go, and Rust
+	// "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined" ],
+	// Uncomment to use the Docker CLI from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker.
+	// "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
+	// Uncomment to connect as a non-root user. See https://aka.ms/vscode-remote/containers/non-root.
+	"remoteUser": "dealii",
+	// Make sure we add a BUILD_POSTFIX environment variable that can be used as in
+	// ${workspaceFolder}/build${env:BUILD_POSTFIX}
+	"containerEnv": {
+		"BUILD_POSTFIX": "-container",
+	},
+	"mounts": [
+		"source=vscode-extensions,target=/home/dealii/.vscode-server/extensions,type=volume",
+		// And/or for VS Code Insiders
+		"source=vscode-extensions-insiders,target=/home/dealii/.vscode-server-insiders/extensions,type=volume",
+	],
+	// Uncomment the following if you want to work on docker on a remote machine
+	// In this case, you also need  "docker.host": "ssh://name-of-machine" in your
+	// settings.
+	// "workspaceMount": "source=/home/heltai/codes/sa-pinvit,target=/workspace,type=bind,consistency=cached",
+	// "workspaceFolder": "/workspace",
+}

.github/workflows/tests.yml

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+name: GitHub CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  debug:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Build debug
+      run: |
+         .scripts/dr.sh "rm -rf build_linux_debug"
+         .scripts/dr.sh "mkdir build_linux_debug; cd build_linux_debug; cmake .. -GNinja -DCMAKE_BUILD_TYPE=Debug; ninja"
+    - name: GTest debug
+      run: |
+         .scripts/dr.sh "cd build_linux_debug; ./gtest"

.gitignore

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+compile_commands.json

.scripts/check_indentation.sh

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+#!/bin/sh
+.scripts/indent
+git diff
+git diff-files --quiet 

.scripts/dr.sh

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+#!/bin/sh
+docker run  \
+    --user $(id -u):$(id -g) \
+    --rm -t \
+    -v `pwd`:/builds/app \
+    heltai/dealii:vscode \
+    /bin/sh -c "cd /builds/app; $@"

.scripts/indent

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+#!/bin/bash
+
+if test ! -d .scripts ; then
+  echo "*** This script must be run from the top-level directory of your project."
+  exit
+fi
+
+if test ! -f .clang-format ; then
+  echo "*** No style file .clang-format found."
+  exit
+fi
+
+# collect a list of files and then indent them all
+echo "--- Indenting all header and source files"
+SRC_FILES=`find . -name "*.cc"`
+#H_FILES=`find . -name "*.h"`
+clang-format -i $SRC_FILES
+#clang-format -i $H_FILES

.vscode/settings.json

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+{
+    "cmake.buildDirectory": "${workspaceFolder}/build${env:BUILD_POSTFIX}",
+    "cmake.defaultVariants": {
+        "configOptions": {
+            "default": "dealii-app",
+            "description": "Default build option for app",
+            "choices": {
+                "dealii-app": {
+                    "short": "Build deal.II App",
+                    "long": "Options to build deal.II App",
+                }
+            }
+        }
+    },
+    "C_Cpp.default.configurationProvider": "ms-vscode.cmake-tools",
+    "files.associations": {
+        "*.inst": "cpp",
+        "*.inst.in": "cpp",
+        "*.h": "cpp"
+    }
+}

CMakeLists.txt

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+CMAKE_MINIMUM_REQUIRED(VERSION 3.15)
+
+PROJECT(gtest)
+
+FIND_PACKAGE(deal.II 9.3 REQUIRED
+HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR})
+
+DEAL_II_INITIALIZE_CACHED_VARIABLES()
+
+ADD_EXECUTABLE(step-1 source/step-1.cc)
+DEAL_II_SETUP_TARGET(step-1)
+
+ADD_EXECUTABLE(step-2 source/step-2.cc)
+DEAL_II_SETUP_TARGET(step-2)
+
+ADD_LIBRARY(step-1-lib SHARED $<TARGET_OBJECTS:step-1>)
+DEAL_II_SETUP_TARGET(step-1-lib)
+
+ADD_LIBRARY(step-2-lib SHARED $<TARGET_OBJECTS:step-2>)
+DEAL_II_SETUP_TARGET(step-2-lib)
+
+FIND_PACKAGE(GTest)
+ADD_EXECUTABLE(gtest source/gtest.cc)
+TARGET_LINK_LIBRARIES(gtest ${GTEST_LIBRARY} step-1-lib step-2-lib)   
+INCLUDE_DIRECTORIES(${GTEST_INCLUDE_DIRS})
+DEAL_II_SETUP_TARGET(gtest)
+
+ENABLE_TESTING()
+GTEST_DISCOVER_TESTS(gtest)

LICENSE

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+MIT License
+
+Copyright (c) 2021 Theory and Practice of FEM
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.