Beam embedding feature

.clang-format

@@ -0,0 +1,114 @@
+---
+Language:        Cpp
+AccessModifierOffset: -4
+AlignAfterOpenBracket: DontAlign
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Right
+AlignOperands:   false
+AlignTrailingComments: false
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: false
+BinPackArguments: true
+BinPackParameters: true
+BreakBeforeBraces: Custom
+BraceWrapping:   
+  AfterClass:      true
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   true
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: All
+BreakBeforeInheritanceComma: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: AfterColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     0
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: false
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:   
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Preserve
+IncludeCategories: 
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|isl|json)/)'
+    Priority:        3
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '(Test)?$'
+IndentCaseLabels: false
+IndentPPDirectives: None
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 4
+ObjCSpaceAfterProperty: true
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Right
+RawStringFormats: 
+  - Delimiters:       [pb]
+    Language:        TextProto
+    BasedOnStyle:    google
+ReflowComments:  true
+SortIncludes:    false
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: true
+SpacesInSquareBrackets: false
+Standard:        Cpp03
+TabWidth:        8
+UseTab:          Never
+...
+

.github/workflows/build.yml

@@ -0,0 +1,46 @@
+name: Build
+
+on: [push, pull_request]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally
+    # well on Windows or Mac.  You can convert this to a matrix build if you need
+    # cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Create Build Environment
+      # Some projects don't allow in-source building, so create a separate build directory
+      # We'll use this as our working directory for all subsequent commands
+      run: cmake -E make_directory ${{github.workspace}}/build
+
+    - name: Configure CMake
+      # Use a bash shell so we can use the same syntax for environment variable
+      # access regardless of the host operating system
+      shell: bash
+      working-directory: ${{github.workspace}}/build
+      # Note the current convention is to use the -S and -B options here to specify source 
+      # and build directories, but this is only available with CMake 3.13 and higher.  
+      # The CMake binaries on the Github Actions machines are (as of this writing) 3.12
+      run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$BUILD_TYPE
+
+    - name: Build
+      working-directory: ${{github.workspace}}/build
+      shell: bash
+      # Execute the build.  You can specify a specific target with "--target <NAME>"
+      run: cmake --build . --config $BUILD_TYPE
+
+    - name: Test
+      working-directory: ${{github.workspace}}/build
+      shell: bash
+      # Execute tests defined by the CMake configuration.  
+      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+      run: ctest -C $BUILD_TYPE --rerun-failed --output-on-failure

.gitignore

@@ -9,14 +9,21 @@ targets/
 release/
 debug/
 
+# ignore any files under build directories
+build/
+_build/
+
 # test results
 *.out
 *.vtu
 *.pvd
 *.out.*
+*.out-*
 t3d.bmf*
 perf.data*
 *.orig
+*.vtk
+*_out.*
 
 # documentation aux-files.
 *.aux
@@ -48,3 +55,8 @@ tests/sm/crack0Step0.vtk
 tests/sm/crack1Step0.vtk
 tests/sm/crack2Step0.vtk
 tests/sm/t3d.bmf
+/.vs/oofem/v17/Browse.VC.db
+*.db-shm
+*.db-wal
+*.opendb
+/.vs/oofem/v17/DocumentLayout.backup.json

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "extern/pybind11"]
+	path = extern/pybind11
+	url = https://github.com/pybind/pybind11.git
+	branch = stable

.travis.yml

@@ -1,16 +1,33 @@
 language: cpp
+os: linux
+dist: focal
+#sudo: required
+before_install:
+   - PYCMD=$(which python3)
+   - echo $PYCMD
+   - sudo -H $PYCMD -m pip install --upgrade pip
+   #- sudo -H $PYCMD -m pip install --upgrade pytest
+   - git clone https://github.com/pybind/pybind11.git; cd pybind11; git checkout stable; cd ..
+install:
+   - echo $PYCMD
+   - cd pybind11; mkdir build; cd build; cmake .. -DPYTHON_EXECUTABLE=$PYCMD; sudo make install; cd ../..
 script:
-   - CXX=g++-4.8 cmake -DUSE_PYTHON_BINDINGS=ON -DENABLE_COVERAGE:BOOL=TRUE .
-   - make
+   - echo $PYCMD
+   - cmake -DPYTHON_EXECUTABLE=$PYCMD -DUSE_PYBIND_BINDINGS=ON -DUSE_PYTHON_EXTENSION=ON -DENABLE_COVERAGE:BOOL=TRUE .
+   - make -j 2
    - make test
-   - bash <(curl -s https://codecov.io/bash)
+   #Comment out various unrelated messages
+   #- bash <(curl -s https://codecov.io/bash)
 
-sudo: false
 addons:
    apt:
       sources:
          - ubuntu-toolchain-r-test
       packages:
-         - libboost-python-dev
-         - g++-4.8
+         #- g++-9
          - binutils-gold
+         - python3
+         - python3-pip
+         - python3-dev
+         - python3-setuptools
+         - python3-pytest

.vs/CMakeWorkspaceSettings.json

@@ -0,0 +1,2 @@
+{
+}

.vs/ProjectSettings.json

@@ -0,0 +1,3 @@
+{
+  "CurrentProjectSetting": "x64-Debug"
+}

.vs/VSWorkspaceState.json

@@ -0,0 +1,12 @@
+{
+  "OutputFoldersPerTargetSystem": {
+    "Local Machine": [
+      "..\\oofem_Build2",
+      "..\\oofem_Build"
+    ]
+  },
+  "ExpandedNodes": [
+    ""
+  ],
+  "PreviewInSolutionExplorer": false
+}

.vs/oofem/v17/DocumentLayout.json

@@ -0,0 +1,90 @@
+{
+  "Version": 1,
+  "WorkspaceRootPath": "C:\\Users\\CMourlas001\\source\\repos\\oofem\\",
+  "Documents": [
+    {
+      "AbsoluteMoniker": "D:0:0:{A2FE74E1-B743-11D0-AE1A-00A0C90FFFC3}|\u003CMiscFiles\u003E|C:\\Users\\CMourlas001\\source\\repos\\oofem\\src\\oofemlib\\hangingnode.C||{D0E1A5C6-B359-4E41-9B60-3365922C2A22}",
+      "RelativeMoniker": "D:0:0:{A2FE74E1-B743-11D0-AE1A-00A0C90FFFC3}|\u003CMiscFiles\u003E|solutionrelative:src\\oofemlib\\hangingnode.C||{D0E1A5C6-B359-4E41-9B60-3365922C2A22}"
+    },
+    {
+      "AbsoluteMoniker": "D:0:0:{A2FE74E1-B743-11D0-AE1A-00A0C90FFFC3}|\u003CMiscFiles\u003E|C:\\Users\\CMourlas001\\source\\repos\\oofem\\src\\main\\main.C||{D0E1A5C6-B359-4E41-9B60-3365922C2A22}",
+      "RelativeMoniker": "D:0:0:{A2FE74E1-B743-11D0-AE1A-00A0C90FFFC3}|\u003CMiscFiles\u003E|solutionrelative:src\\main\\main.C||{D0E1A5C6-B359-4E41-9B60-3365922C2A22}"
+    },
+    {
+      "AbsoluteMoniker": "D:0:0:{A2FE74E1-B743-11D0-AE1A-00A0C90FFFC3}|\u003CMiscFiles\u003E|C:\\Users\\CMourlas001\\source\\repos\\oofem\\CMakeLists.txt||{8B382828-6202-11D1-8870-0000F87579D2}",
+      "RelativeMoniker": "D:0:0:{A2FE74E1-B743-11D0-AE1A-00A0C90FFFC3}|\u003CMiscFiles\u003E|solutionrelative:CMakeLists.txt||{8B382828-6202-11D1-8870-0000F87579D2}"
+    },
+    {
+      "AbsoluteMoniker": "D:0:0:{A2FE74E1-B743-11D0-AE1A-00A0C90FFFC3}|\u003CMiscFiles\u003E|C:\\Users\\CMourlas001\\source\\repos\\oofem\\src\\oofemlib\\vtkxmlexportmodule.C||{D0E1A5C6-B359-4E41-9B60-3365922C2A22}",
+      "RelativeMoniker": "D:0:0:{A2FE74E1-B743-11D0-AE1A-00A0C90FFFC3}|\u003CMiscFiles\u003E|solutionrelative:src\\oofemlib\\vtkxmlexportmodule.C||{D0E1A5C6-B359-4E41-9B60-3365922C2A22}"
+    }
+  ],
+  "DocumentGroupContainers": [
+    {
+      "Orientation": 0,
+      "VerticalTabListWidth": 256,
+      "DocumentGroups": [
+        {
+          "DockedWidth": 200,
+          "SelectedChildIndex": 3,
+          "Children": [
+            {
+              "$type": "Bookmark",
+              "Name": "ST:0:0:{1c4feeaa-4718-4aa9-859d-94ce25d182ba}"
+            },
+            {
+              "$type": "Document",
+              "DocumentIndex": 1,
+              "Title": "main.C",
+              "DocumentMoniker": "C:\\Users\\CMourlas001\\source\\repos\\oofem\\src\\main\\main.C",
+              "RelativeDocumentMoniker": "src\\main\\main.C",
+              "ToolTip": "C:\\Users\\CMourlas001\\source\\repos\\oofem\\src\\main\\main.C",
+              "RelativeToolTip": "src\\main\\main.C",
+              "ViewState": "AgIAAJAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==",
+              "Icon": "ae27a6b0-e345-4288-96df-5eaf394ee369.000423|",
+              "WhenOpened": "2025-04-07T12:57:46.717Z",
+              "EditorCaption": ""
+            },
+            {
+              "$type": "Document",
+              "DocumentIndex": 3,
+              "Title": "vtkxmlexportmodule.C",
+              "DocumentMoniker": "C:\\Users\\CMourlas001\\source\\repos\\oofem\\src\\oofemlib\\vtkxmlexportmodule.C",
+              "RelativeDocumentMoniker": "src\\oofemlib\\vtkxmlexportmodule.C",
+              "ToolTip": "C:\\Users\\CMourlas001\\source\\repos\\oofem\\src\\oofemlib\\vtkxmlexportmodule.C",
+              "RelativeToolTip": "src\\oofemlib\\vtkxmlexportmodule.C",
+              "ViewState": "AgIAAFoAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==",
+              "Icon": "ae27a6b0-e345-4288-96df-5eaf394ee369.000423|",
+              "WhenOpened": "2025-04-07T12:51:33.388Z"
+            },
+            {
+              "$type": "Document",
+              "DocumentIndex": 0,
+              "Title": "hangingnode.C",
+              "DocumentMoniker": "C:\\Users\\CMourlas001\\source\\repos\\oofem\\src\\oofemlib\\hangingnode.C",
+              "RelativeDocumentMoniker": "src\\oofemlib\\hangingnode.C",
+              "ToolTip": "C:\\Users\\CMourlas001\\source\\repos\\oofem\\src\\oofemlib\\hangingnode.C",
+              "RelativeToolTip": "src\\oofemlib\\hangingnode.C",
+              "ViewState": "AgIAAB4AAAAAAAAAAAAAAJMAAAAHAAAAAAAAAA==",
+              "Icon": "ae27a6b0-e345-4288-96df-5eaf394ee369.000423|",
+              "WhenOpened": "2025-04-07T11:28:23.575Z",
+              "EditorCaption": ""
+            },
+            {
+              "$type": "Document",
+              "DocumentIndex": 2,
+              "Title": "CMakeLists.txt",
+              "DocumentMoniker": "C:\\Users\\CMourlas001\\source\\repos\\oofem\\CMakeLists.txt",
+              "RelativeDocumentMoniker": "CMakeLists.txt",
+              "ToolTip": "C:\\Users\\CMourlas001\\source\\repos\\oofem\\CMakeLists.txt",
+              "RelativeToolTip": "CMakeLists.txt",
+              "ViewState": "AgIAABUAAAAAAAAAAAAAAH4AAAASAAAAAAAAAA==",
+              "Icon": "ae27a6b0-e345-4288-96df-5eaf394ee369.003109|",
+              "WhenOpened": "2024-10-09T22:21:10.591Z"
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}

.vs/tasks.vs.json

@@ -0,0 +1,10 @@
+{
+  "version": "0.2.1",
+  "tasks": [
+    {
+      "taskLabel": "task-oofem",
+      "appliesTo": "/",
+      "type": "launch"
+    }
+  ]
+}