Sync cfd-xyz branch with master

.clang-format

@@ -0,0 +1,14 @@
+BasedOnStyle: WebKit
+BraceWrapping:
+  AfterClass: true
+  AfterControlStatement: true
+  AfterFunction: true
+  AfterNamespace: true
+  SplitEmptyFunction: false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeInheritanceComma: true
+BreakConstructorInitializers: AfterColon
+MaxEmptyLinesToKeep: 2
+SortIncludes: false
+SpaceBeforeCtorInitializerColon: false

.compileOF1812.sh

@@ -1,5 +1,5 @@
 docker pull ithacafv/openfoam1812-muq2-pytorch
 docker run -ti -d --name foam1812 -v "${PWD}":/home/ofuser/app:rw ithacafv/openfoam1812-muq2-pytorch /bin/bash
 docker exec foam1812 /bin/bash -c "cd /home/ofuser/app; ls"
-docker exec foam1812 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /root/OpenFOAM/OpenFOAM-v1812/etc/bashrc; source etc/bashrc; ./Allwmake -taumq"
+docker exec foam1812 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /root/OpenFOAM/OpenFOAM-v1812/etc/bashrc; source etc/bashrc; git submodule update --init; ./Allwmake -taumq"
 

.compileOF1906.sh

@@ -1,5 +1,5 @@
 docker pull ithacafv/openfoam1906-muq2-pytorch
 docker run -ti -d --name foam1906 -v "${PWD}":/home/ofuser/app:rw ithacafv/openfoam1906-muq2-pytorch /bin/bash
 docker exec foam1906 /bin/bash -c "cd /home/ofuser/app; ls"
-docker exec foam1906 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /root/OpenFOAM/OpenFOAM-v1906/etc/bashrc; source etc/bashrc; ./Allwmake -taumq"
+docker exec foam1906 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /root/OpenFOAM/OpenFOAM-v1906/etc/bashrc; source etc/bashrc; git submodule update --init; ./Allwmake -taumq"
 

.compileOF1912.sh

@@ -1,5 +1,5 @@
 docker pull ithacafv/openfoam1912-muq2-pytorch
 docker run -ti -d --name foam1912 -v "${PWD}":/home/ofuser/app:rw ithacafv/openfoam1912-muq2-pytorch /bin/bash
 docker exec foam1912 /bin/bash -c "cd /home/ofuser/app; ls"
-docker exec foam1912 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /usr/lib/openfoam/openfoam1912/etc/bashrc; source etc/bashrc; ./Allwmake -taumq"
+docker exec foam1912 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /usr/lib/openfoam/openfoam1912/etc/bashrc; source etc/bashrc; git submodule update --init; ./Allwmake -taumq"
 

.compileOF2006.sh

@@ -1,4 +1,4 @@
 docker pull ithacafv/openfoam2006-muq2-pytorch
 docker run -ti -d --name foam2006 -v "${PWD}":/home/ofuser/app:rw ithacafv/openfoam2006-muq2-pytorch /bin/bash
 docker exec foam2006 /bin/bash -c "cd /home/ofuser/app; ls"
-docker exec foam2006 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /usr/lib/openfoam/openfoam2006/etc/bashrc; source etc/bashrc; ./Allwmake -taumq"
+docker exec foam2006 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /usr/lib/openfoam/openfoam2006/etc/bashrc; source etc/bashrc; git submodule update --init; ./Allwmake -taumq"

.compileOF2012.sh

@@ -2,4 +2,4 @@
 docker pull ithacafv/openfoam2012-muq2-pytorch
 docker run -ti -d --name foam2012 -v "${PWD}":/home/ofuser/app:rw ithacafv/openfoam2012-muq2-pytorch /bin/bash
 docker exec foam2012 /bin/bash -c "cd /home/ofuser/app; ls"
-docker exec foam2012 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /usr/lib/openfoam/openfoam2012/etc/bashrc; source etc/bashrc; ./Allwmake -taumq"
+docker exec foam2012 /bin/bash -c "export MUQ_LIBRARIES=/home/Installations/MUQ_INSTALL; export MUQ_EXT_LIBRARIES=/home/Installations/MUQ_INSTALL/muq_external; export TORCH_LIBRARIES=/pytorch/torch; cd /home/ofuser/app; source /usr/lib/openfoam/openfoam2012/etc/bashrc; source etc/bashrc; git submodule update --init; ./Allwmake -taumq"

.compileOF2106.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 docker pull ithacafv/openfoam2106-muq2-pytorch
 docker run -ti -d --name foam2106 -v "${PWD}":/home/ofuser/app:rw ithacafv/openfoam2106-muq2-pytorch /bin/bash
-docker exec foam2106 /bin/bash -c "source /usr/lib/openfoam/openfoam2106/etc/bashrc; cd /home/ofuser/app; source etc/bashrc; ./Allwmake -taumq"
+docker exec foam2106 /bin/bash -c "source /usr/lib/openfoam/openfoam2106/etc/bashrc; cd /home/ofuser/app; source etc/bashrc; git submodule update --init; ./Allwmake -taumq"

.github/Singularity/Singularity_from_def.yml

@@ -0,0 +1,36 @@
+name: Singularity_from_Definition_file
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  singularity-from-defination-file:
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - uses: eWaterCycle/setup-singularity@v7
+        with:
+           singularity-version: 3.8.3
+
+      - name: Singularity build in detached mode
+        run: singularity build --fakeroot -d singularity_image_def.sif `pwd`/singularity/singularity-reciepe.def
+
+      - name: copying necessary files
+        run: |
+          mv singularity_image_def.sif `pwd`/tutorials/CFD/01POD/
+          mv `pwd`/singularity/Of.sh `pwd`/tutorials/CFD/01POD/
+
+      - name: Run singulairty in batch mode
+        run: |
+          cd `pwd`/tutorials/CFD/01POD/
+          singularity exec singularity_image_def.sif /bin/bash Of.sh
+
+
+
+

.github/Singularity/Singularity_from_docker.yml

@@ -0,0 +1,36 @@
+name: Singularity_from_Docker_Image
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  singularity-from-docker-image:
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - uses: eWaterCycle/setup-singularity@v7
+        with:
+           singularity-version: 3.8.3
+
+      - name: Singularity build
+        run: singularity build singularity_image.sif docker://ithacafv/ithacafv:manifest-amd64
+
+      - name: copying necessary files
+        run: |
+          mv singularity_image.sif `pwd`/tutorials/CFD/01POD/
+          mv `pwd`/singularity/Of.sh `pwd`/tutorials/CFD/01POD/
+
+      - name: Singulairty in batch mode
+        run: |
+          cd `pwd`/tutorials/CFD/01POD/
+          singularity exec singularity_image.sif /bin/bash Of.sh
+
+
+
+

.github/workflows/docker_ithaca.yml

@@ -2,7 +2,9 @@ name: Docker
 
 on:
   push:
-    branches: [ master ]
+    # Pattern matched against refs/tags
+    tags:
+      - '*'           # Push events to every tag not containing /
 
 jobs:
   docker-arm64:
@@ -61,29 +63,29 @@ jobs:
 
 
 
-  build-manifest:
-    needs: [docker-amd64, docker-arm64]
+  #build-manifest:
+    #needs: [docker-amd64, docker-arm64]
 
-    runs-on: ubuntu-latest
-    steps:
+    #runs-on: ubuntu-latest
+    #steps:
 
-      - name: Checkout
-        uses: actions/checkout@v2
+      #- name: Checkout
+        #uses: actions/checkout@v2
 
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+      #- name: Set up QEMU
+        #uses: docker/setup-qemu-action@v1
 
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+      #- name: Set up Docker Buildx
+        #uses: docker/setup-buildx-action@v1
 
-      - name: Login to DockerHub
-        uses: docker/login-action@v1
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
+      #- name: Login to DockerHub
+        #uses: docker/login-action@v1
+        #with:
+          #username: ${{ secrets.DOCKER_USERNAME }}
+          #password: ${{ secrets.DOCKER_PASSWORD }}
 
-      - name: manifest creation
-        run: docker manifest create ithacafv/ithacafv:manifest-latest --amend ithacafv/ithacafv:manifest-amd64 --amend ithacafv/ithacafv:manifest-arm64
+      #- name: manifest creation
+        #run: docker manifest create ithacafv/ithacafv:manifest-latest --amend ithacafv/ithacafv:manifest-amd64 --amend ithacafv/ithacafv:manifest-arm64
 
-      - name: push manifest
-        run: docker manifest push ithacafv/ithacafv:manifest-latest
+      #- name: push manifest
+        #run: docker manifest push ithacafv/ithacafv:manifest-latest

.github/workflows/sync.yml

@@ -0,0 +1,52 @@
+name: 'Upstream Sync'
+
+on:
+  schedule:
+    - cron: '*/60 * * * *' # every 30 minutes
+
+  workflow_dispatch:  # click the button on Github repo!
+
+jobs:
+  sync_latest_from_upstream:
+    runs-on: ubuntu-latest
+    name: Sync latest commits from upstream repo
+
+    steps:
+    # REQUIRED step
+    # Step 1: run a standard checkout action, provided by github
+    - name: Checkout target repo
+      uses: actions/checkout@v2
+      with:
+        # optional: set the branch to checkout,
+        # sync action checks out your 'target_sync_branch' anyway
+        ref:  master
+        # REQUIRED if your upstream repo is private (see wiki)
+        persist-credentials: false
+
+    # REQUIRED step
+    # Step 2: run the sync action
+    - name: Sync upstream changes
+      id: sync
+      uses: aormsby/Fork-Sync-With-Upstream-action@v3.4
+      with:
+        target_sync_branch: master
+        # REQUIRED 'target_repo_token' exactly like this!
+        target_repo_token: ${{ secrets.GITHUB_TOKEN }}
+        upstream_sync_branch: master
+        upstream_sync_repo: aormsby/Fork-Sync-With-Upstream-action
+        upstream_repo_access_token: ${{ secrets.UPSTREAM_REPO_SECRET }}
+
+        # Set test_mode true to run tests instead of the true action!!
+        test_mode: true
+
+    # Step 3: Display a sample message based on the sync output var 'has_new_commits'
+    - name: New commits found
+      if: steps.sync.outputs.has_new_commits == 'true'
+      run: echo "New commits were found to sync."
+
+    - name: No new commits
+      if: steps.sync.outputs.has_new_commits == 'false'
+      run: echo "There were no new commits."
+
+    - name: Show value of 'has_new_commits'
+      run: echo ${{ steps.sync.outputs.has_new_commits }}

.gitmodules

@@ -0,0 +1,7 @@
+[submodule "extern/pybind11"]
+	path = extern/pybind11
+	url = ../../pybind/pybind11
+	branch = stable
+[submodule "src/thirdparty/Eigen"]
+	path = src/thirdparty/Eigen
+	url = https://gitlab.com/libeigen/eigen.git