Merge pull request #5 from JulianJohannes/main

Second Merge
tmaric · May 20, 2023 · c5c5e5b · c5c5e5b
2 parents bb5cd0c + aecce77
commit c5c5e5b
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,53 @@
+name: Documentation
+on: [push]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container: tmaric/openfoam-v2206_ubuntu-focal
+    defaults:
+        run:
+            shell: bash
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: Update system
+        run: apt update -y && apt upgrade -y
+      - name: Install Latex and graphviz
+        run: |
+          apt install -y texlive texlive-latex-base \
+            texlive-fonts-recommended texlive-science texlive-xetex \
+            dvipng ghostscript cm-super \
+            graphviz
+      - name: Install doxygen and Build doc # version 1.9
+        run: |
+          wget https://www.doxygen.nl/files/doxygen-1.9.6.linux.bin.tar.gz
+          tar -xzf doxygen-1.9.6.linux.bin.tar.gz
+          export PATH="$(realpath doxygen-1.9.6/bin):$PATH"
+          ls /opt/OpenFOAM && . /opt/OpenFOAM/OpenFOAM-v2206/etc/bashrc && true
+          cd doc/Doxygen/
+          ./update-macros.sh
+          ./Allwmake
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: doc/Doxygen/html
+  deploy:  
+    # Add a dependency to the build job
+    needs: build
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    # Specify runner + deployment step
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2 # or the latest "vX.X.X" version tag for this action
diff --git a/.gitignore b/.gitignore
@@ -117,6 +117,14 @@ processor*/
 # python
 __pycache__
 
+# Doxygen generated
+doc/Doxygen/html
+doc/Doxygen/latex
+doc/Doxygen/man
+doc/Doxygen/DTAGS
+doc/Doxygen/Doxygen.warnings
+
+# by JR
 cases/tmp_save_calculated_cases/
 cases/3D*_[0-9][0-9][0-9][0-9][0-9]_3D*/
 cases/**/*.csv

diff --git a/cases/2Dcontactline-periodic.parameter b/cases/2Dcontactline-periodic.parameter
@@ -34,6 +34,19 @@ values
 		quad
 	);
 
+	NEIGHBOURS
+	(
+		5
+		10
+	);
+
+	NARROWBAND
+	(
+		signChange
+		neighbours
+		distance
+	);
+
 	BC
 	(
 		zeroGradient
@@ -54,6 +67,7 @@ values
 		SuperBee
 		UMIST
 		vanAlbada 
+    upwind
 	);
 
 	TANH_LIMIT

diff --git a/cases/2Dcontactline-periodic/Allrun_perturbed_parallel.sh b/cases/2Dcontactline-periodic/Allrun_perturbed_parallel.sh
@@ -11,6 +11,7 @@ rm -rf 0 && cp -r 0.org 0
 find 0/ -name "*.template" -delete && \
 touch "$(basename ${PWD}).foam" && \
 set -o errexit
+cp system/fvSchemes.non-orthogonal system/fvSchemes
 blockMesh 
 
 leiaPerturbMesh 

diff --git a/cases/2Dcontactline-periodic/Allrun_perturbed_serial.sh b/cases/2Dcontactline-periodic/Allrun_perturbed_serial.sh
@@ -4,6 +4,7 @@ set -o verbose
 rm -rf 0 && cp -r 0.org 0  
 touch "$(basename ${PWD}).foam" && \
 set -o errexit
+cp system/fvSchemes.non-orthogonal system/fvSchemes
 blockMesh 
 
 leiaPerturbMesh 

diff --git a/cases/2Dcontactline-periodic/system/aliasDict b/cases/2Dcontactline-periodic/system/aliasDict
@@ -9,4 +9,5 @@
 
 // ## Convection schemes
 
-LinearUpwind			linearUpwind grad(U);
+LinearUpwind      linearUpwind grad(U);
+Gamma1            Gamma 1;
diff --git a/cases/2Dcontactline-periodic/system/blockMeshDict b/cases/2Dcontactline-periodic/system/blockMeshDict
@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-n_cells	200;
+n_cells  200;
 
 scale   (1 1 0.5);
 

diff --git a/cases/2Dcontactline-periodic/system/controlDict b/cases/2Dcontactline-periodic/system/controlDict
@@ -25,15 +25,15 @@ stopAt          endTime;
 
 endTime         0.8; 
 
-Umax						1.2;
+Umax            1.2;
 
-CFL							0.5;
+CFL              0.5;
 
 // safty factor which is necessary to ensure maxCFL for some reason
-CFLsafty				1.0;
+CFLsafty        1.0;
 
 // dummy float value. Will be replaced by Allrun
-deltaX					0.0;
+deltaX          1.0;
 
 deltaT          #eval "$CFL * $CFLsafty * $deltaX / $Umax";
 

diff --git a/cases/2Dcontactline-periodic/system/controlDict.template b/cases/2Dcontactline-periodic/system/controlDict.template
@@ -25,15 +25,15 @@ stopAt          endTime;
 
 endTime         0.8;
 
-Umax						1.2;
+Umax            1.2;
 
-CFL							@!CFL!@;
+CFL              @!CFL!@;
 
 // safty factor which is necessary to ensure maxCFL for some reason
-CFLsafty				1.0;
+CFLsafty        1.0;
 
 // dummy float value. Will be replaced by Allrun
-deltaX					0.0;
+deltaX          1.0;
 
 deltaT          #eval "$CFL * $CFLsafty * $deltaX / $Umax";
 

diff --git a/cases/2Dcontactline-periodic/system/fvSchemes.non-orthogonal.template b/cases/2Dcontactline-periodic/system/fvSchemes.non-orthogonal.template
@@ -0,0 +1,57 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2012                                 |
+|   \\  /    A nd           | Website:  www.openfoam.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "aliasDict"
+
+ddtSchemes
+{
+    default         CrankNicolson 1; 
+}
+
+gradSchemes
+{
+    default         Gauss linear;
+    grad(p)         Gauss linear;
+}
+
+divSchemes
+{
+    default         none;
+    div(phi,psi)    Gauss @!DIV!@;
+}
+
+laplacianSchemes
+{
+    default         Gauss linear corrected;
+}
+
+interpolationSchemes
+{
+    default         linear;
+}
+
+snGradSchemes
+{
+    default         corrected;
+}
+
+fluxRequired
+{
+    p;
+}
+
+// ************************************************************************* //
diff --git a/cases/2Dcontactline-periodic/system/fvSolution b/cases/2Dcontactline-periodic/system/fvSolution
@@ -46,20 +46,20 @@ velocityModel
 {
     type periodic2D; 
     oscillation on;
-		tau 				0.4;
+    tau         0.4;
 }
 
 levelSet
 {
-		narrowBand	
-		{
-			type	signChange;
-		}
-		
-		profile
-		{
-			type	signedDistance;
-		}
+    narrowBand  
+    {
+      type  signChange;
+    }
+    
+    profile
+    {
+      type  signedDistance;
+    }
 
 
     implicitSurface 
@@ -79,11 +79,11 @@ levelSet
         type noRedistancing;
     }
 
-		SDPLSSource
-		{
+    SDPLSSource
+    {
         type noSource;
         discretization none;
-		}
+    }
 }
 
 

diff --git a/cases/2Dcontactline-periodic/system/fvSolution.template b/cases/2Dcontactline-periodic/system/fvSolution.template
@@ -46,21 +46,21 @@ velocityModel
 {
     type periodic2D; 
     oscillation on;
-		tau 				0.4;
+    tau         0.4;
 }
 
 levelSet
 {
-		narrowBand	
-		{
-			type	signChange;
-		}
-		
-		profile
-		{
-			type	@!PROFILE!@;
-			limit	@!TANH_LIMIT!@;
-		}
+    narrowBand  
+    {
+      type  signChange;
+    }
+    
+    profile
+    {
+      type  @!PROFILE!@;
+      limit  @!TANH_LIMIT!@;
+    }
 
 
     implicitSurface 
@@ -80,16 +80,16 @@ levelSet
         type noRedistancing;
     }
 
-		SDPLSSource
-		{
+    SDPLSSource
+    {
         type @!SDPLS_SOURCE!@;
         discretization @!SOURCE_SCHEME!@;
-				mollifier
-				{
-					type 	@!MOLLIFIER!@;
-					w1		0.05;
-				}
-		}
+        mollifier
+        {
+          type   @!MOLLIFIER!@;
+          w1    0.05;
+        }
+    }
 }
 
 

diff --git a/cases/2Dcontactline-vortex-oscillate/Allrun_perturbed_parallel.sh b/cases/2Dcontactline-vortex-oscillate/Allrun_perturbed_parallel.sh
@@ -11,6 +11,7 @@ rm -rf 0 && cp -r 0.org 0
 find 0/ -name "*.template" -delete && \
 touch "$(basename ${PWD}).foam" && \
 set -o errexit
+cp system/fvSchemes.non-orthogonal system/fvSchemes
 blockMesh 
 
 leiaPerturbMesh 

diff --git a/cases/2Dcontactline-vortex-oscillate/Allrun_perturbed_serial.sh b/cases/2Dcontactline-vortex-oscillate/Allrun_perturbed_serial.sh
@@ -4,6 +4,7 @@ set -o verbose
 rm -rf 0 && cp -r 0.org 0  
 touch "$(basename ${PWD}).foam" && \
 set -o errexit
+cp system/fvSchemes.non-orthogonal system/fvSchemes
 blockMesh 
 
 leiaPerturbMesh 

diff --git a/cases/2Dcontactline-vortex-oscillate/system/aliasDict b/cases/2Dcontactline-vortex-oscillate/system/aliasDict
@@ -9,4 +9,5 @@
 
 // ## Convection schemes
 
-LinearUpwind			linearUpwind grad(U);
+LinearUpwind      linearUpwind grad(U);
+Gamma1            Gamma 1;
diff --git a/cases/2Dcontactline-vortex-oscillate/system/blockMeshDict b/cases/2Dcontactline-vortex-oscillate/system/blockMeshDict
@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-n_cells	200;
+n_cells  200;
 
 scale   (1 1 0.5);
 

diff --git a/cases/2Dcontactline-vortex-oscillate/system/controlDict b/cases/2Dcontactline-vortex-oscillate/system/controlDict
@@ -25,15 +25,15 @@ stopAt          endTime;
 
 endTime         1.0; 
 
-Umax						0.2;
+Umax            0.2;
 
-CFL							0.5;
+CFL              0.5;
 
 // safty factor which is necessary to ensure maxCFL for some reason
-CFLsafty				1.0;
+CFLsafty        1.0;
 
 // dummy float value. Will be replaced by Allrun
-deltaX					0.0;
+deltaX          1.0;
 
 deltaT          #eval "$CFL * $CFLsafty * $deltaX / $Umax";