Added isogeometric module

.clang-format

@@ -0,0 +1,227 @@
+---
+Language: Cpp
+Standard: Auto
+BasedOnStyle: ''
+DisableFormat: false
+# do not indent modifiers, i.e., public,protected,private,...
+AccessModifierOffset: -1
+# maximum number of columns per line
+ColumnLimit : 120
+
+AlignAfterOpenBracket: AlwaysBreak
+AlignArrayOfStructures: Left
+
+# do not align consecutive assignments
+AlignConsecutiveAssignments: None
+
+# align macros definition
+AlignConsecutiveMacros: AcrossEmptyLinesAndComments
+
+# do not align consecutive declarations
+AlignConsecutiveDeclarations: None
+
+# aligning backslashes in escaped newlines
+AlignEscapedNewlines: Right
+
+# align operands of expressions that need to split over multiple lines
+AlignOperands: Align
+
+# align trailing comments, stop to align if there are more than 1 empty line
+AlignTrailingComments: true
+
+# do not put each argument of a function call on a separate line
+AllowAllArgumentsOnNextLine: true
+
+# do not put each parameter of a function declaration on a separate line
+AllowAllParametersOfDeclarationOnNextLine: true
+
+# contract on a single lines the following
+AllowShortBlocksOnASingleLine: Always
+AllowShortEnumsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: WithoutElse
+AllowShortLambdasOnASingleLine: All
+AllowShortLoopsOnASingleLine: true
+
+# do not contract switch case statments
+AllowShortCaseLabelsOnASingleLine: false
+
+AlwaysBreakAfterReturnType: None
+# go to newline after template declaration only if it cannot fit one line
+AlwaysBreakTemplateDeclarations: MultiLine
+
+AttributeMacros: ['__capability']
+
+# put function call's arguments and function declaration's parameters all on the same line
+BinPackArguments: true
+BinPackParameters: true
+
+# add one space on each side of : in a bit field
+BitFieldColonSpacing: Both
+
+# control of individual brace wrapping cases
+BreakBeforeBraces: Custom # brace breaking style
+BraceWrapping:
+   AfterCaseLabel:        false
+   AfterClass:            false
+   AfterControlStatement: Never
+   AfterEnum:             false
+   AfterFunction:         false
+   AfterNamespace:        false
+   AfterStruct:           false
+   AfterUnion:            false
+   AfterExternBlock:      false
+   BeforeCatch:           false
+   BeforeElse:            false
+   BeforeLambdaBody:      false
+   BeforeWhile:           false
+   IndentBraces:          false
+
+# other breaking rules
+BreakBeforeBinaryOperators: None
+BreakBeforeConceptDeclarations: Always
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: AfterColon
+BreakBeforeTernaryOperators: false
+BreakConstructorInitializers: AfterColon
+BreakStringLiterals: true
+
+# a regular expression that describes comments with special meaning, which should not be split into lines or otherwise changed.
+CommentPragmas:  '^ fdaPDE pragma:'
+
+QualifierAlignment: Leave
+
+# put each namespace on its line
+CompactNamespaces: false
+# number of characters to use for indentation of constructor initializer lists as well as inheritance lists.
+ConstructorInitializerIndentWidth: 4
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+# if constructor initializers do not fit current line, try to fit them on the next line
+PackConstructorInitializers: NextLine
+
+# indent with for all continuations
+ContinuationIndentWidth: 2
+
+# use c++11 braced list style: No spaces inside the braced list, no line break before the closing brace, indentation with the continuation indent
+Cpp11BracedListStyle: true
+
+# never put an empty line after and before public, protected, private
+EmptyLineAfterAccessModifier: Never
+EmptyLineBeforeAccessModifier: Never
+
+# add a namespace foo at closing namespace brace
+FixNamespaceComments: true
+
+# put first system includes starting with <, then internal includes
+IncludeBlocks:   Regroup
+IncludeCategories:
+   - Regex:           '^<.*\.h>'
+     Priority:        1
+     CaseSensitive:   false
+   - Regex:           '^<.*'
+     Priority:        2
+     CaseSensitive:   false
+   - Regex:           '.*'
+     Priority:        3
+     CaseSensitive:   false
+SortIncludes: CaseSensitive
+SortUsingDeclarations: true
+
+# indentation rules
+IndentAccessModifiers: false
+IndentCaseLabels: false
+IndentCaseBlocks: false
+IndentGotoLabels: true
+IndentPPDirectives: AfterHash
+IndentExternBlock: AfterExternBlock
+IndentRequiresClause: true
+IndentWrappedFunctionNames: false
+
+# indentation with
+IndentWidth: 4  
+TabWidth: 4
+
+# always insert braces after control statments
+InsertBraces: false
+InsertTrailingCommas: None
+
+# remove empty lines at start of new block
+KeepEmptyLinesAtTheStartOfBlocks: false
+
+# align lambda body relative to the lambda signature
+LambdaBodyIndentation: Signature
+
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+
+# do not keep more than one empty line
+MaxEmptyLinesToKeep: 1
+
+# indent namespaces, but only the inner block is indented
+NamespaceIndentation: None
+
+# align pointer * to left, i.e., int* a instead of int *a. references follows same style
+PointerAlignment: Left
+ReferenceAlignment: Pointer
+
+# do not format comments
+ReflowComments: true
+RemoveBracesLLVM: false
+
+RequiresClausePosition: OwnLine
+
+SeparateDefinitionBlocks: Leave
+ShortNamespaceLines: 1
+
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+
+# insert a space after template keyword
+SpaceAfterTemplateKeyword: true
+# insert a space before assignment operator
+SpaceBeforeAssignmentOperators: true
+# no space before a case colon
+SpaceBeforeCaseColon: false
+# insert a space before braced list
+SpaceBeforeCpp11BracedList: true
+# insert a space after colon constructor initializer list
+SpaceBeforeCtorInitializerColon: true
+# insert a space after colon inheritance list
+SpaceBeforeInheritanceColon: true
+
+# other spacing definition
+SpaceBeforeParens: Custom
+SpaceBeforeParensOptions:
+   AfterControlStatements: true
+   AfterFunctionDefinitionName: false
+   AfterFunctionDeclarationName: false
+   AfterIfMacros:   true
+   AfterOverloadedOperator: false
+   AfterRequiresInClause: false
+   AfterRequiresInExpression: false
+   BeforeNonEmptyParentheses: false
+
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: true
+SpaceInEmptyParentheses: false
+
+SpacesBeforeTrailingComments: 3
+# never put spaces in template parameter lists
+SpacesInAngles: Never
+# never put spaces in conditional statments
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: false
+SpacesInCStyleCastParentheses: false
+# one space is forced after // start of comment, but more are possible
+SpacesInLineCommentPrefix:
+   Minimum:         1
+   Maximum:         -1
+
+# no spaces after and before round or square brakets
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+
+# never use tab, always replace them with spaces
+UseTab: Never

.github/workflows/Dockerfile

@@ -0,0 +1,21 @@
+# define base OS environment
+FROM alpine:latest
+
+# install base dependencies for compiling and testing fdaPDE
+
+# base system dependencies
+RUN apk --no-cache add --update \
+    g++ \
+    clang \
+    libstdc++ \
+    cmake \
+    git \
+    make
+
+# c++ library dependencies
+RUN apk add --update \
+    eigen-dev
+
+# test dependencies
+RUN apk add --update \
+    gtest-dev

.github/workflows/test-linux-clang.yml

@@ -0,0 +1,29 @@
+name: test-linux-clang
+on:
+  push:
+     branches: [ stable, develop ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container:
+      image: alepalu/fdapde-docker-linux:latest
+    steps:
+    - name: checkout repository
+      uses: actions/checkout@v2
+      with:
+        submodules: 'recursive'
+    - name: run_tests
+      run: |
+        cd test/
+        export Eigen3_DIR=/usr/share/cmake/Modules # reguired to let eigen3 work with CMake in alpine
+        chmod +x run_tests.sh
+        ./run_tests.sh --compiler clang
+        echo "TEST_RESULT=$(echo $?)" >> $GITHUB_ENV
+    - name: check_tests_passed
+      run: |
+        if [ "$TEST_RESULT" -eq "0" ]; then
+           exit 0
+        else
+           exit 1
+        fi

.github/workflows/test-linux-gcc.yml

@@ -0,0 +1,29 @@
+name: test-linux-gcc
+on:
+  push:
+     branches: [ stable, develop ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container:
+      image: alepalu/fdapde-docker-linux:latest
+    steps:
+    - name: checkout repository
+      uses: actions/checkout@v2
+      with:
+        submodules: 'recursive'
+    - name: run_tests
+      run: |
+        cd test/
+        export Eigen3_DIR=/usr/share/cmake/Modules # reguired to let eigen3 work with CMake in alpine
+        chmod +x run_tests.sh
+        ./run_tests.sh --compiler gcc
+        echo "TEST_RESULT=$(echo $?)" >> $GITHUB_ENV
+    - name: check_tests_passed
+      run: |
+        if [ "$TEST_RESULT" -eq "0" ]; then
+           exit 0
+        else
+           exit 1
+        fi

.github/workflows/test-macos-clang.yml

@@ -0,0 +1,29 @@
+name: test-macos-clang
+on:
+  push:
+     branches: [ stable, develop ]
+
+jobs:
+  build:
+    runs-on: macos-13
+    steps:
+    - name: checkout repository
+      uses: actions/checkout@v2
+      with:
+        submodules: 'recursive'
+    - name: install_eigen
+      run: |
+        brew install eigen
+    - name: run_tests
+      run: |
+        cd test/
+        chmod +x run_tests.sh
+        ./run_tests.sh --compiler clang
+        echo "TEST_RESULT=$(echo $?)" >> $GITHUB_ENV
+    - name: check_tests_passed
+      run: |
+        if [ "$TEST_RESULT" -eq "0" ]; then
+           exit 0
+        else
+           exit 1
+        fi

.gitignore

@@ -0,0 +1,48 @@
+
+*.json
+*.cmake
+*Makefile
+*.Rhistory
+*.tar.gz
+*.RData
+*.o
+*.so
+test/fdapde_test
+test/.cache
+test/build/
+build/
+.DS_Store
+.bash_history
+.idea/
+cmake-build-debug-docker/
+cmake-build-default/
+
+cmake-build-debug/
+experiments/test_RSVD/performances.csv
+.vscode
+**/results/
+
+
+#plots
+*.pdf
+*.png
+*.txt
+*.eps
+!CMakeLists.txt
+
+!simulations/sphere_diff/plot_mesh.png
+!simulations/sphere_diff/plot_solution.png
+
+!simulations/torus_diff/plot_mesh.png
+!simulations/torus_diff/plot_solution.png
+
+#help files
+*.csv
+*.mtx
+
+#docs files
+*.puml
+.Rproj.user
+
+#some test directories
+test_massimo/