Initial GitHub commit. Previously, BitBucket

Author: pythonpal4foam

Allwclean

@@ -0,0 +1,10 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+
+# Clean solvers
+wclean applications/solvers/pythonPalIcoFoam
+
+# Clean tutorials
+(cd tutorials && ./Allclean)
+
+#------------------------------------------------------------------------------

Allwmake

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+#!/bin/bash
+cd ${0%/*} || exit 1    # run from this directory
+
+# Stop at first error
+set -e
+
+# Check if OpenFOAM/FOAM has been sourced
+if [[ -z "${WM_PROJECT}" ]]
+then
+    echo "Please source the OpenFOAM/FOAM bashrc first!"
+    exit 1
+fi
+
+# Check required environment variaables are set
+if [[ -z "${PYBIND11_INC_DIR}" ]]
+then
+    echo "Please set the PYBIND11_INC_DIR environment variable!"
+    exit 1
+fi
+if [[ -z "${PYBIND11_LIB_DIR}" ]]
+then
+    echo "Please set the PYBIND11_LIB_DIR environment variable!"
+    exit 1
+fi
+
+# Compile solvers
+echo; echo "Compiling applications"; echo
+(cd applications && ./Allwmake)
+
+echo; echo; echo "All done: check for errors above"; echo

README.md

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+# README #
+
+### What is this? ###
+
+This section contains OpenFOAM code and tutorials that show how to use Python interpreters to interact with OpenFOAM via pythonPal. pythonPal offers Python support and interoperability between the C++/Python data based on the pybind11 library [1]. The code in this repository is based on OpenFOAM-9, however, as noted below, the procedures are expected to compile with similar versions and forks of OpenFOAM.
+
+### [Manual approach] How do I get set up? ###
+
+In addition to an installation of OpenFOAM-9, a Python installation is required. The following libraries are required to run the tutorials:
+
+* Python 3.8.12
+
+* NumPy 1.18.5
+
+* pybind11 2.8.1
+
+These libraries can be installed from the supplied pythonpal-no-gpu.yml file using the conda software (https://conda.io). Once conda is installed, the Python environment is installed with:
+
+    conda env create -f pythonPal-no-gpu.yml
+
+The conda environment can be activated with:
+
+    conda activate pythonPal-no-gpu
+
+Please be aware that the examples may not work with other versions of Python libraries, although they are likely to work with similar versions, e.g. Python 3.8.*.
+
+In addition, two pybind11 environment variables must be defined, for example, as:
+
+    export PYBIND11_INC_DIR=$(python3 -m pybind11 --includes)
+    export PYBIND11_LIB_DIR=$(python3 -c 'from distutils import sysconfig; print(sysconfig.get_config_var("LIBDIR"))')
+
+Once those environment variables have been defined, the OpenFOAM code included in the current section can be compiled with the Allwmake script in the parent folder:
+
+    ./Allwmake
+
+If the Allwmake script gives the error “libpython or lpython not found” then please manually update the LD_LIBRARY_PATH environment variable with "export LD_LIBRARY_PATH=$PYBIND11_LIB_DIR:$LD_LIBRARY_PATH” and run the “./Allwmake” command again.
+
+This will install:
+
+**./applications/solvers/**:
+
+* pythonPalIcoFoam: This is a version of icoFoam that, once the simulation has converged, passes the velocity field to Python where the specific kinetic energy (k) is calculated. Then, OpenFOAM prints the k field.
+
+### How do I run the cases? ###
+
+Currently, there is only one tutorial case which solves the cavity case using pythonPalIcoFoam, as explained in the paper. To run it:
+
+    cd tutorials/pythonPalIcoFoam/cavity
+    ./Allrun
+
+### Compatible OpenFOAM versions ###
+
+pythonPal is independent of the OpenFOAM version/fork and is expected to work with all main versions. The included code compiles with the following versions and forks (it will probably work with others too): 
+
+* OpenFOAM-9
+* OpenFOAM-v2012
+* foam-extend-4.1
+
+The presented tutorial has been tested using these three versions. 
+
+If desired, the user can make the small changes required to get the cases to work with their particular version of OpenFOAM.
+
+
+### Who do I talk to? ###
+
+    Simon Rodriguez
+    simon.rodriguezluzardo@ucdconnect.ie
+    https://www.linkedin.com/in/simonrodriguezl/
+
+    Philip Cardiff
+    philip.cardiff@ucd.ie
+    https://www.linkedin.com/in/philipcardiff/
+
+
+### References ###
+
+[1]	W. Jakob, J. Rhinelander, and D. Moldovan, “pybind11 – Seamless operability between C++11 and Python.” 2017.

applications/Allwmake

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+#!/bin/bash
+cd ${0%/*} || exit 1    # run from this directory
+
+wmake all solvers

applications/solvers/pythonPalIcoFoam/Make/files

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+pythonPalIcoFoam.C
+
+EXE = $(FOAM_USER_APPBIN)/pythonPalIcoFoam

applications/solvers/pythonPalIcoFoam/Make/options

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+ifeq ($(WM_PROJECT), foam)
+    VERSION_SPECIFIC_INC = -DFOAMEXTEND
+else
+    ifneq (,$(findstring v,$(WM_PROJECT_VERSION)))
+        VERSION_SPECIFIC_INC += -DOPENFOAMESI
+    else
+        VERSION_SPECIFIC_INC += -DOPENFOAMFOUNDATION
+    endif
+endif
+
+EXE_INC = \
+    -Wno-old-style-cast \
+    $(VERSION_SPECIFIC_INC) \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    $(PYBIND11_INC_DIR) \
+    -I../../../src/pythonPal
+
+EXE_LIBS = \
+    -lfiniteVolume \
+    -lmeshTools \
+    -L$(PYBIND11_LIB_DIR) \
+    -lpython3.8

applications/solvers/pythonPalIcoFoam/createFields.esi.H

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+Info<< "Reading transportProperties\n" << endl;
+
+IOdictionary transportProperties
+(
+    IOobject
+    (
+        "transportProperties",
+        runTime.constant(),
+        mesh,
+        IOobject::MUST_READ_IF_MODIFIED,
+        IOobject::NO_WRITE
+    )
+);
+
+dimensionedScalar nu
+(
+    "nu",
+    dimViscosity,
+    transportProperties
+);
+
+Info<< "Reading field p\n" << endl;
+volScalarField p
+(
+    IOobject
+    (
+        "p",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh
+);
+
+
+Info<< "Reading field U\n" << endl;
+volVectorField U
+(
+    IOobject
+    (
+        "U",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh
+);
+
+
+volScalarField k
+(
+    IOobject
+    (
+        "k",
+        mesh.time().timeName(),
+        mesh,
+        IOobject::READ_IF_PRESENT,
+        IOobject::AUTO_WRITE
+    ),
+    mesh,
+    dimensionedScalar("k", dimensionSet(0, 2, -2, 0, 0, 0, 0), 0.0)
+);
+
+
+#include "createPhi.H"
+
+
+label pRefCell = 0;
+scalar pRefValue = 0.0;
+setRefCell(p, mesh.solutionDict().subDict("PISO"), pRefCell, pRefValue);
+mesh.setFluxRequired(p.name());

applications/solvers/pythonPalIcoFoam/createFields.foamextend.H

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+Info<< "Reading transportProperties\n" << endl;
+
+IOdictionary transportProperties
+(
+    IOobject
+    (
+        "transportProperties",
+        runTime.constant(),
+        mesh,
+        IOobject::MUST_READ_IF_MODIFIED,
+        IOobject::NO_WRITE
+    )
+);
+
+dimensionedScalar nu
+(
+        transportProperties.lookup("nu")
+);
+
+Info<< "Reading field p\n" << endl;
+volScalarField p
+(
+    IOobject
+    (
+        "p",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh
+);
+
+
+Info<< "Reading field U\n" << endl;
+volVectorField U
+(
+    IOobject
+    (
+        "U",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh
+);
+
+
+volScalarField k
+(
+    IOobject
+    (
+        "k",
+        mesh.time().timeName(),
+        mesh,
+        IOobject::READ_IF_PRESENT,
+        IOobject::AUTO_WRITE
+    ),
+    mesh,
+    dimensionedScalar("k", dimensionSet(0, 2, -2, 0, 0, 0, 0), 0.0)
+);
+
+
+#include "createPhi.H"
+
+
+label pRefCell = 0;
+scalar pRefValue = 0.0;
+setRefCell(p, piso.dict(), pRefCell, pRefValue);
+mesh.schemesDict().setFluxRequired(p.name());

applications/solvers/pythonPalIcoFoam/createFields.foundation.H

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+Info<< "Reading transportProperties\n" << endl;
+
+IOdictionary transportProperties
+(
+    IOobject
+    (
+        "transportProperties",
+        runTime.constant(),
+        mesh,
+        IOobject::MUST_READ_IF_MODIFIED,
+        IOobject::NO_WRITE
+    )
+);
+
+dimensionedScalar nu
+(
+    "nu",
+    dimViscosity,
+    transportProperties.lookup("nu")
+);
+
+Info<< "Reading field p\n" << endl;
+volScalarField p
+(
+    IOobject
+    (
+        "p",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh
+);
+
+
+Info<< "Reading field U\n" << endl;
+volVectorField U
+(
+    IOobject
+    (
+        "U",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh
+);
+
+
+volScalarField k
+(
+    IOobject
+    (
+        "k",
+        mesh.time().timeName(),
+        mesh,
+        IOobject::READ_IF_PRESENT,
+        IOobject::AUTO_WRITE
+    ),
+    mesh,
+    dimensionedScalar("k", dimensionSet(0, 2, -2, 0, 0, 0, 0), 0.0)
+);
+
+
+#include "createPhi.H"
+
+
+label pRefCell = 0;
+scalar pRefValue = 0.0;
+setRefCell(p, mesh.solutionDict().subDict("PISO"), pRefCell, pRefValue);
+mesh.setFluxRequired(p.name());

applications/solvers/pythonPalIcoFoam/pythonPalIcoFoam.C

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+#ifdef OPENFOAMFOUNDATION
+    #include "pythonPalIcoFoam.foundation.C"
+#elif OPENFOAMESI
+    #include "pythonPalIcoFoam.esi.C"
+#else
+    #include "pythonPalIcoFoam.foamextend.C"
+#endif