Merge pull request #2 from daavid00/development

Updating to OpenFOAM 11
cssr-tools · Feb 16, 2024 · 34b8678 · 34b8678
2 parents 6ff545e + 86844de
commit 34b8678
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diff --git a/README.md b/README.md
@@ -12,11 +12,10 @@ This repository provides a workflow to perform computational fluid dynamics (CFD
 
 ## Installation
 You will first need to install
-* OpenFOAM (https://www.openfoam.com) (tested with OpenFOAM v2206)
-* Gmsh (https://gmsh.info) (tested with Gmsh 4.11.0) 
-
-You will also need to install some python packages, see ```requirements.txt``` for a complete list. You can install all the required python packages in a virtual environment with the following commands:
+* OpenFOAM (https://www.openfoam.com) (tested with OpenFOAM-11)
+* Gmsh (https://gmsh.info) (tested with Gmsh 4.8.4) 
 
+You will also need to install some Python packages, see ```requirements.txt``` for a complete list. You can install all the required Python packages in a virtual environment with the following commands:
 ```bash
 # Clone the repo
 git clone https://github.com/daavid00/pymm.git
@@ -33,6 +32,16 @@ pip install -e .
 # For contributions/testing/linting, install the dev-requirements
 pip install -r dev-requirements.txt
 ```
+Depending on the location where OpenFOAM is installed, then before running pymm (inside the vpymm Python environment), you need to enter the OpenFoam environment:
+```bash
+# Check where openFOAM is installed
+echo $WM_PROJECT_DIR
+# The return value was /opt/openfoam11, then we activate the environment
+source /opt/openfoam11/etc/bashrc
+# Then, if everything went fine, typing 
+gmshToFoam
+# should print the argument flags for that OpenFOAM executable.
+```
 
 ## Running pymm
 You can run _pymm_ as a single command line:
@@ -48,7 +57,7 @@ See the [_documentation_](https://daavid00.github.io/pymm/introduction.html).
 The following is a list of journal papers in which _pymm_ is used:
 
 1. Liu, N., Haugen, M., Benali, B., Landa-Marbán, D., Fernø, M.A., 2023. Pore-scale spatiotemporal dynamics of microbial-induced calcium carbonate growth and distribution in porous media.  Int. J. Greenh. Gas Control 125, 103885. https://doi.org/10.1016/j.ijggc.2023.103885
-1. Liu, N., Haugen, M., Benali, B., Landa-Marbán, D., Fernø, M.A., 2023. Pore-scale kinetics of calcium dissolution and secondary precipitation during geological carbon storage. Chem. Geol., to appear.
+1. Liu, N., Haugen, M., Benali, B., Landa-Marbán, D., Fernø, M.A., 2023. Pore-scale kinetics of calcium dissolution and secondary precipitation during geological carbon storage. Chem. Geol. 641, 121782. https://doi.org/10.1016/j.chemgeo.2023.121782.
 
 ## About pymm
 The image-based Python package for computational fluid dynamics pymm is funded by [_Center for Sustainable Subsurface Resources_](https://cssr.no) [project no. 331841] and [_NORCE Norwegian Research Centre As_](https://www.norceresearch.no) [project number 101070]. 

diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1,3 @@
 porespy
+pypardiso
 mako
diff --git a/src/pymm/core/pymm.py b/src/pymm/core/pymm.py
@@ -1,4 +1,5 @@
 """Main script"""
+
 import os
 import csv
 import glob
@@ -540,8 +541,8 @@ def run_stokes(dic):
     for file in [
         "0/p",
         "0/U",
-        "constant/transportProperties",
-        "constant/turbulenceProperties",
+        "constant/physicalProperties",
+        "constant/momentumTransport",
         "system/controlDict",
         "system/fvSchemes",
         "system/fvSolution",
@@ -564,7 +565,7 @@ def run_stokes(dic):
 
     with open("constant/polyMesh/boundary", "r", encoding="utf8") as file:
         dic["boundary"] = file.readlines()
-        dic["boundary"][22] = "type      empty;"
+        dic["boundary"][20] = "type      empty;"
     mytemplate = Template(filename=f"{dic['pat']}/templates/utils/boundary.mako")
     var = {"dic": dic}
     filled_template = mytemplate.render(**var)
@@ -573,7 +574,7 @@ def run_stokes(dic):
 
     os.system(f"rm -rf {dic['cwd']}/{dic['fol']}/VTK_flowStokes")
     # Running the steady-state flow simulation
-    os.system("simpleFoam & wait")
+    os.system("foamRun -solver incompressibleFluid & wait")
     os.system("foamToVTK & wait")
     os.system(f"mkdir {dic['cwd']}/{dic['fol']}/VTK_flowStokes")
     os.system(f"cp -r VTK/* {dic['cwd']}/{dic['fol']}/VTK_flowStokes")
@@ -596,11 +597,12 @@ def run_tracer(dic):
     os.system(f"mkdir {dic['cwd']}/{dic['fol']}/OpenFOAM/tracerTransport/system")
     var = {"dic": dic}
     for file in [
-        "inlet",
         "0/T",
-        "constant/transportProperties",
-        "constant/fvOptions",
+        "constant/physicalProperties",
+        "constant/momentumTransport",
+        "constant/fvConstraints",
         "system/controlDict",
+        "system/topoSetDict",
         "system/fvSchemes",
         "system/fvSolution",
     ]:
@@ -621,15 +623,19 @@ def run_tracer(dic):
     os.system(
         f"cp {latest_folder}U {dic['cwd']}/{dic['fol']}/OpenFOAM/tracerTransport/0/"
     )
+    os.system(
+        f"cp {latest_folder}p {dic['cwd']}/{dic['fol']}/OpenFOAM/tracerTransport/0/"
+    )
     os.system(
         f"cp -r {dic['cwd']}/{dic['fol']}/OpenFOAM/flowStokes/constant/polyMesh "
         f"{dic['cwd']}/{dic['fol']}/OpenFOAM/tracerTransport/constant/"
     )
     os.chdir(f"{dic['cwd']}/{dic['fol']}/OpenFOAM/tracerTransport")
-    os.system("setSet -batch inlet & wait")
+    os.system("topoSet & wait")
 
     # Running the simulation of tracer transport
-    os.system("scalarTransportFoam & wait")
+    os.system("foamRun & wait")
+    # exit()
     os.system("foamToVTK & wait")
     os.system(f"cp -r VTK/* {dic['cwd']}/{dic['fol']}/VTK_tracerTransport")
 
@@ -650,7 +656,7 @@ def main():
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 
-# ad-wa is distributed in the hope that it will be useful,
+# pymm is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

diff --git a/src/pymm/templates/OpenFOAM/flowStokes/0/U.mako b/src/pymm/templates/OpenFOAM/flowStokes/0/U.mako
@@ -1,13 +1,12 @@
 /*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2206                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  11
+     \\/     M anipulation  |
 \*---------------------------------------------------------------------------*/
 FoamFile
 {
-    version     2.0;
     format      ascii;
     class       volVectorField;
     object      U;

diff --git a/src/pymm/templates/OpenFOAM/flowStokes/0/p.mako b/src/pymm/templates/OpenFOAM/flowStokes/0/p.mako
@@ -1,13 +1,12 @@
 /*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2206                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  11
+     \\/     M anipulation  |
 \*---------------------------------------------------------------------------*/
 FoamFile
 {
-    version     2.0;
     format      ascii;
     class       volScalarField;
     object      p;

diff --git a/src/pymm/templates/OpenFOAM/flowStokes/constant/momentumTransport.mako b/src/pymm/templates/OpenFOAM/flowStokes/constant/momentumTransport.mako
@@ -0,0 +1,20 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  11
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      momentumTransport;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+simulationType laminar;
+
+
+// ************************************************************************* //
diff --git a/src/pymm/templates/OpenFOAM/flowStokes/constant/physicalProperties.mako b/src/pymm/templates/OpenFOAM/flowStokes/constant/physicalProperties.mako
@@ -0,0 +1,21 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  11
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      physicalProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+viscosityModel  constant;
+
+nu              [0 2 -1 0 0 0 0] ${dic['nu']};
+
+// ************************************************************************* //
diff --git a/src/pymm/templates/OpenFOAM/flowStokes/constant/transportProperties.mako b/src/pymm/templates/OpenFOAM/flowStokes/constant/transportProperties.mako
diff --git a/src/pymm/templates/OpenFOAM/flowStokes/constant/turbulenceProperties.mako b/src/pymm/templates/OpenFOAM/flowStokes/constant/turbulenceProperties.mako
diff --git a/src/pymm/templates/OpenFOAM/flowStokes/system/controlDict.mako b/src/pymm/templates/OpenFOAM/flowStokes/system/controlDict.mako
@@ -1,21 +1,22 @@
 /*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  4.1                                   |
-|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
-|    \\/     M anipulation  |                                                 |
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  11
+     \\/     M anipulation  |
 \*---------------------------------------------------------------------------*/
 FoamFile
 {
-    version     2.0;
     format      ascii;
     class       dictionary;
     location    "system";
     object      controlDict;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-application     simpleFoam;
+application     foamRun;
+
+solver          incompressibleFluid;
 
 startFrom       startTime;
 

diff --git a/src/pymm/templates/OpenFOAM/flowStokes/system/fvSchemes.mako b/src/pymm/templates/OpenFOAM/flowStokes/system/fvSchemes.mako
@@ -1,13 +1,12 @@
 /*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  4.1                                   |
-|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
-|    \\/     M anipulation  |                                                 |
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  11
+     \\/     M anipulation  |
 \*---------------------------------------------------------------------------*/
 FoamFile
 {
-    version     2.0;
     format      ascii;
     class       dictionary;
     location    "system";

diff --git a/src/pymm/templates/OpenFOAM/flowStokes/system/fvSolution.mako b/src/pymm/templates/OpenFOAM/flowStokes/system/fvSolution.mako
@@ -1,13 +1,12 @@
 /*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  4.1                                   |
-|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
-|    \\/     M anipulation  |                                                 |
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  11
+     \\/     M anipulation  |
 \*---------------------------------------------------------------------------*/
 FoamFile
 {
-    version     2.0;
     format      ascii;
     class       dictionary;
     location    "system";

diff --git a/src/pymm/templates/OpenFOAM/tracerTransport/0/T.mako b/src/pymm/templates/OpenFOAM/tracerTransport/0/T.mako
@@ -1,20 +1,19 @@
 /*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2206                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  11
+     \\/     M anipulation  |
 \*---------------------------------------------------------------------------*/
 FoamFile
 {
-    version     2.0;
     format      ascii;
     class       volScalarField;
     object      T;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-dimensions      [0 0 0 0 0 0 0];
+dimensions      [0 0 0 1 0 0 0];
 
 internalField   uniform 0;
 
@@ -26,7 +25,8 @@ boundaryField
     }
     inlet
     {
-        type            zeroGradient;
+        type            fixedValue;
+        value           uniform 1;
     }
     outlet
     {

diff --git a/...M/tracerTransport/constant/fvOptions.mako → ...acerTransport/constant/fvConstraints.mako b/...M/tracerTransport/constant/fvOptions.mako → ...acerTransport/constant/fvConstraints.mako
@@ -16,16 +16,11 @@ FoamFile
 
 fixedTemperature
 {
-    type            scalarFixedValueConstraint;
-
+    type            fixedTemperatureConstraint;
+    mode            uniform;
     selectionMode   cellZone;
     cellZone        c0Zone;
-    fieldValues
-    {
-        T     1.0;
-    }
-
-
+    temperature     1.0;
 }
 
 

diff --git a/src/pymm/templates/OpenFOAM/tracerTransport/constant/momentumTransport.mako b/src/pymm/templates/OpenFOAM/tracerTransport/constant/momentumTransport.mako
@@ -0,0 +1,20 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  11
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      momentumTransport;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+simulationType laminar;
+
+
+// ************************************************************************* //