mirror of
https://github.com/ParticulateFlow/CFDEMcoupling-PFM.git
synced 2025-12-08 06:37:44 +00:00
add a tutorial for cfdemSolverIBContinuousForcing
simulating the deformation of a red blood cell (bonded particles) in shear flow
This commit is contained in:
danielque
31
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/Allclean.sh
Executable file
31
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/Allclean.sh
Executable file
@ -0,0 +1,31 @@
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#!/bin/bash
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#------------------------------------------------------------------------------
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# Allclean script for redBloodCellShearFlow test case
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# clean up redBloodCellShearFlow
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# Achuth N. Balachandran Nair - October 2018
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#------------------------------------------------------------------------------
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#- source CFDEM env vars
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. ~/.bashrc
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#- source CFDEM functions
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source $CFDEM_PROJECT_DIR/etc/functions.sh
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#------------------------------------------------------------------------------
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#- define variables
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casePath="$(dirname "$(readlink -f ${BASH_SOURCE[0]})")"
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#------------------------------------------------------------------------------
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#- clean up case
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echo "deleting data at: $casePath"
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source $WM_PROJECT_DIR/bin/tools/CleanFunctions
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cd $casePath/CFD
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cleanTimeDirectories
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rm -rf processor* > /dev/null 2>&1
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rm -rf clockData > /dev/null 2>&1
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echo "Cleaning $casePath/DEM/post"
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rm $casePath/DEM/post/*.* > /dev/null 2>&1
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#rm -r $casePath/DEM/post/restart/*.*
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#touch $casePath/DEM/post/restart/.gitignore
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echo "done"
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30
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/Allrun.sh
Executable file
30
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/Allrun.sh
Executable file
@ -0,0 +1,30 @@
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#!/bin/bash
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#------------------------------------------------------------------------------
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# Allrun script for redBloodCellShearFlow test case
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# run redBloodCellShearFlow
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# Achuth N. Balachandran Nair - October 2018
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#------------------------------------------------------------------------------
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source $CFDEM_PROJECT_DIR/etc/functions.sh
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#- define variables
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casePath="$(dirname "$(readlink -f ${BASH_SOURCE[0]})")"
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# check if mesh was built
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if [ -f "$casePath/CFD/constant/polyMesh/points" ]; then
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echo "mesh was built before - using old mesh"
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else
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echo "mesh needs to be built"
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cd $casePath/CFD
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blockMesh
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fi
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if [ -f "$casePath/DEM/post/restart/liggghts.restart" ]; then
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echo "LIGGGHTS init was run before - using existing restart file"
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else
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#- run serial DEM
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$casePath/DEMrun.sh
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fi
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#- run parallel CFD-DEM
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bash $casePath/parCFDDEMrun.sh
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@ -0,0 +1,51 @@
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/*--------------------------------*- C++ -*----------------------------------*\
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========= |
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\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
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||||
\\ / O peration | Website: https://openfoam.org
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\\ / A nd | Version: 6
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\\/ M anipulation |
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\*---------------------------------------------------------------------------*/
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FoamFile
|
||||
{
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||||
version 2.0;
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format ascii;
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class volVectorField;
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object U;
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}
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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dimensions [0 1 -1 0 0 0 0];
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internalField uniform (0 0 0); //velocity in micrometres per second
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|
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boundaryField
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||||
{
|
||||
front
|
||||
{
|
||||
type cyclicAMI;
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||||
}
|
||||
back
|
||||
{
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||||
type cyclicAMI;
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||||
}
|
||||
top
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||||
{
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type fixedValue;
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value uniform ( 0.00225 0 0);
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}
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bottom
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{
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type fixedValue;
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value uniform (-0.00225 0 0);
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}
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left
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||||
{
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type cyclicAMI;
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||||
}
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||||
right
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{
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type cyclicAMI;
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}
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}
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// ************************************************************************* //
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@ -0,0 +1,50 @@
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/*--------------------------------*- C++ -*----------------------------------*\
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||||
========= |
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||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
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||||
\\ / A nd | Version: 6
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||||
\\/ M anipulation |
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||||
\*---------------------------------------------------------------------------*/
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||||
FoamFile
|
||||
{
|
||||
version 2.0;
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||||
format ascii;
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||||
class volVectorField;
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||||
location "0";
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object Us;
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||||
}
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||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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dimensions [0 1 -1 0 0 0 0];
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internalField uniform (0 0 0);
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boundaryField
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{
|
||||
front
|
||||
{
|
||||
type cyclicAMI;
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||||
}
|
||||
back
|
||||
{
|
||||
type cyclicAMI;
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||||
}
|
||||
top
|
||||
{
|
||||
type zeroGradient;
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||||
}
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||||
bottom
|
||||
{
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||||
type zeroGradient;
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||||
}
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||||
left
|
||||
{
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||||
type cyclicAMI;
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||||
}
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right
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{
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||||
type cyclicAMI;
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||||
}
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}
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// ************************************************************************* //
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@ -0,0 +1,49 @@
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/*--------------------------------*- C++ -*----------------------------------*\
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========= |
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\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
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||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
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||||
\\/ M anipulation |
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||||
\*---------------------------------------------------------------------------*/
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||||
FoamFile
|
||||
{
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||||
version 2.0;
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||||
format ascii;
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||||
class volScalarField;
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||||
object lambda;
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||||
}
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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dimensions [0 0 0 0 0 0 0];
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internalField uniform 100;
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boundaryField
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{
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||||
front
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||||
{
|
||||
type cyclicAMI;
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||||
}
|
||||
back
|
||||
{
|
||||
type cyclicAMI;
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||||
}
|
||||
top
|
||||
{
|
||||
type zeroGradient;
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||||
}
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||||
bottom
|
||||
{
|
||||
type zeroGradient;
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||||
}
|
||||
left
|
||||
{
|
||||
type cyclicAMI;
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||||
}
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||||
right
|
||||
{
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||||
type cyclicAMI;
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||||
}
|
||||
}
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||||
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// ************************************************************************* //
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@ -0,0 +1,49 @@
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/*--------------------------------*- C++ -*----------------------------------*\
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||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
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||||
format ascii;
|
||||
class volScalarField;
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||||
object p;
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||||
}
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||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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dimensions [0 2 -2 0 0 0 0];
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internalField uniform 0;
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boundaryField
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{
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||||
front
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||||
{
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||||
type cyclicAMI;
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||||
}
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||||
back
|
||||
{
|
||||
type cyclicAMI;
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||||
}
|
||||
top
|
||||
{
|
||||
type zeroGradient;
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||||
}
|
||||
bottom
|
||||
{
|
||||
type zeroGradient;
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||||
}
|
||||
left
|
||||
{
|
||||
type cyclicAMI;
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||||
}
|
||||
right
|
||||
{
|
||||
type cyclicAMI;
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||||
}
|
||||
}
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||||
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// ************************************************************************* //
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@ -0,0 +1,49 @@
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/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class volScalarField;
|
||||
object phiIB;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
dimensions [0 2 -1 0 0 0 0];
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||||
|
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internalField uniform 0;
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||||
|
||||
boundaryField
|
||||
{
|
||||
front
|
||||
{
|
||||
type cyclicAMI;
|
||||
}
|
||||
back
|
||||
{
|
||||
type cyclicAMI;
|
||||
}
|
||||
top
|
||||
{
|
||||
type zeroGradient;
|
||||
}
|
||||
bottom
|
||||
{
|
||||
type zeroGradient;
|
||||
}
|
||||
left
|
||||
{
|
||||
type cyclicAMI;
|
||||
}
|
||||
right
|
||||
{
|
||||
type cyclicAMI;
|
||||
}
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,49 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class volScalarField;
|
||||
object voidfraction;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
dimensions [0 0 0 0 0 0 0];
|
||||
|
||||
internalField uniform 1;
|
||||
|
||||
boundaryField
|
||||
{
|
||||
front
|
||||
{
|
||||
type cyclicAMI;
|
||||
}
|
||||
back
|
||||
{
|
||||
type cyclicAMI;
|
||||
}
|
||||
top
|
||||
{
|
||||
type zeroGradient;
|
||||
}
|
||||
bottom
|
||||
{
|
||||
type zeroGradient;
|
||||
}
|
||||
left
|
||||
{
|
||||
type cyclicAMI;
|
||||
}
|
||||
right
|
||||
{
|
||||
type cyclicAMI;
|
||||
}
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,92 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
object couplingProperties;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
// sub-models & settings
|
||||
|
||||
modelType none;
|
||||
|
||||
checkPeriodicCells;
|
||||
|
||||
couplingInterval 10;
|
||||
|
||||
depth 0;
|
||||
|
||||
voidFractionModel IB;
|
||||
|
||||
locateModel engineIB;
|
||||
|
||||
meshMotionModel noMeshMotion;
|
||||
|
||||
regionModel allRegion;
|
||||
|
||||
dataExchangeModel twoWayMPI;
|
||||
|
||||
IOModel off;
|
||||
|
||||
probeModel off;
|
||||
|
||||
averagingModel dilute;
|
||||
|
||||
clockModel off;
|
||||
|
||||
smoothingModel off;
|
||||
|
||||
forceModels
|
||||
(
|
||||
ShirgaonkarIB
|
||||
);
|
||||
|
||||
momCoupleModels
|
||||
(
|
||||
);
|
||||
|
||||
turbulenceModelType "turbulenceProperties";
|
||||
|
||||
|
||||
// sub-model properties
|
||||
|
||||
ShirgaonkarIBProps
|
||||
{
|
||||
velFieldName "U";
|
||||
pressureFieldName "p";
|
||||
densityFieldName "rho";
|
||||
solidVolFractionName "lambda";
|
||||
useTorque;
|
||||
}
|
||||
|
||||
IBProps
|
||||
{
|
||||
maxCellsPerParticle 20000;
|
||||
alphaMin 0.30;
|
||||
scaleUpVol 1.0;
|
||||
}
|
||||
|
||||
engineIBProps
|
||||
{
|
||||
engineProps
|
||||
{
|
||||
treeSearch true;
|
||||
}
|
||||
zSplit 8;
|
||||
xySplit 16;
|
||||
}
|
||||
|
||||
twoWayMPIProps
|
||||
{
|
||||
liggghtsPath "../DEM/in.liggghts_run";
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,21 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class uniformDimensionedVectorField;
|
||||
location "constant";
|
||||
object g;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
dimensions [0 1 -2 0 0 0 0];
|
||||
value (0 0 0);
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,22 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
object liggghtsCommands;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
liggghtsCommandModels
|
||||
(
|
||||
runLiggghts
|
||||
);
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,40 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
location "constant";
|
||||
object transportProperties;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
|
||||
transportModel Newtonian;
|
||||
|
||||
// Fluid properties of plasma // dextran
|
||||
nu nu [ 0 2 -1 0 0 0 0 ] 1.2; //4.9524;
|
||||
|
||||
CrossPowerLawCoeffs
|
||||
{
|
||||
nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-06;
|
||||
nuInf nuInf [ 0 2 -1 0 0 0 0 ] 1e-06;
|
||||
m m [ 0 0 1 0 0 0 0 ] 1;
|
||||
n n [ 0 0 0 0 0 0 0 ] 1;
|
||||
}
|
||||
|
||||
BirdCarreauCoeffs
|
||||
{
|
||||
nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-06;
|
||||
nuInf nuInf [ 0 2 -1 0 0 0 0 ] 1e-06;
|
||||
k k [ 0 0 1 0 0 0 0 ] 0;
|
||||
n n [ 0 0 0 0 0 0 0 ] 1;
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,20 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
location "constant";
|
||||
object turbulenceProperties;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
simulationType laminar;
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,110 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
object blockMeshDict;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
convertToMeters 1;
|
||||
|
||||
vertices
|
||||
(
|
||||
( 0.0 0.0 0.0)
|
||||
(45.0 0.0 0.0)
|
||||
(45.0 22.5 0.0)
|
||||
( 0.0 22.5 0.0)
|
||||
( 0.0 0.0 22.5)
|
||||
(45.0 0.0 22.5)
|
||||
(45.0 22.5 22.5)
|
||||
( 0.0 22.5 22.5)
|
||||
);
|
||||
|
||||
blocks
|
||||
(
|
||||
hex (0 1 2 3 4 5 6 7) (58 29 29) simpleGrading (1 1 1)
|
||||
);
|
||||
|
||||
boundary
|
||||
(
|
||||
front
|
||||
{
|
||||
type cyclicAMI;
|
||||
neighbourPatch back;
|
||||
faces
|
||||
(
|
||||
(4 5 6 7)
|
||||
);
|
||||
transform translational;
|
||||
separationVector (0 0 -22.5);
|
||||
}
|
||||
|
||||
back
|
||||
{
|
||||
type cyclicAMI;
|
||||
neighbourPatch front;
|
||||
faces
|
||||
(
|
||||
(3 2 1 0)
|
||||
);
|
||||
transform translational;
|
||||
separationVector (0 0 22.5);
|
||||
}
|
||||
|
||||
top
|
||||
{
|
||||
type wall;
|
||||
faces
|
||||
(
|
||||
(2 3 7 6)
|
||||
);
|
||||
}
|
||||
|
||||
bottom
|
||||
{
|
||||
type wall;
|
||||
faces
|
||||
(
|
||||
(0 1 5 4)
|
||||
);
|
||||
}
|
||||
|
||||
left
|
||||
{
|
||||
type cyclicAMI;
|
||||
neighbourPatch right;
|
||||
faces
|
||||
(
|
||||
(0 4 7 3)
|
||||
);
|
||||
transform translational;
|
||||
separationVector ( 45 0 0);
|
||||
}
|
||||
|
||||
right
|
||||
{
|
||||
type cyclicAMI;
|
||||
neighbourPatch left;
|
||||
faces
|
||||
(
|
||||
(1 2 6 5)
|
||||
);
|
||||
transform translational;
|
||||
separationVector (-45 0 0);
|
||||
}
|
||||
);
|
||||
|
||||
mergePatchPairs
|
||||
(
|
||||
);
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,121 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
location "system";
|
||||
object controlDict;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
application pisoFoam;
|
||||
|
||||
startFrom latestTime;
|
||||
|
||||
startTime 0;
|
||||
|
||||
stopAt endTime;
|
||||
|
||||
endTime 100000;
|
||||
|
||||
deltaT 1;
|
||||
|
||||
writeControl adjustableRunTime;
|
||||
|
||||
writeInterval 100;
|
||||
|
||||
purgeWrite 0;
|
||||
|
||||
writeFormat ascii;
|
||||
|
||||
writePrecision 6;
|
||||
|
||||
writeCompression uncompressed;
|
||||
|
||||
timeFormat general;
|
||||
|
||||
timePrecision 6;
|
||||
|
||||
runTimeModifiable yes;
|
||||
|
||||
adjustTimeStep no;
|
||||
|
||||
maxCo 1.0;
|
||||
|
||||
maxDeltaT 10;
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
DimensionedConstants
|
||||
{
|
||||
unitSet micro; // SI;
|
||||
|
||||
SICoeffs
|
||||
{
|
||||
universal
|
||||
{
|
||||
c c [ 0 1 -1 0 0 0 0 ] 2.99792e+08;
|
||||
G G [ -1 3 -2 0 0 0 0 ] 6.67429e-11;
|
||||
h h [ 1 2 -1 0 0 0 0 ] 6.62607e-34;
|
||||
}
|
||||
electromagnetic
|
||||
{
|
||||
e e [ 0 0 1 0 0 1 0 ] 1.60218e-19;
|
||||
}
|
||||
atomic
|
||||
{
|
||||
me me [ 1 0 0 0 0 0 0 ] 9.10938e-31;
|
||||
mp mp [ 1 0 0 0 0 0 0 ] 1.67262e-27;
|
||||
}
|
||||
physicoChemical
|
||||
{
|
||||
mu mu [ 1 0 0 0 0 0 0 ] 1.66054e-27;
|
||||
k k [ 1 2 -2 -1 0 0 0 ] 1.38065e-23;
|
||||
}
|
||||
standard
|
||||
{
|
||||
//- Standard pressure [Pa]
|
||||
Pstd Pstd [ 1 -1 -2 0 0 0 0 ] 100000;
|
||||
//- Standard temperature [degK]
|
||||
Tstd Tstd [ 0 0 0 1 0 0 0 ] 298.15;
|
||||
}
|
||||
}
|
||||
|
||||
microCoeffs
|
||||
{
|
||||
universal
|
||||
{
|
||||
c c [ 0 1 -1 0 0 0 0 ] 2.99792e+08;
|
||||
G G [ -1 3 -2 0 0 0 0 ] 6.67429e-20;
|
||||
h h [ 1 2 -1 0 0 0 0 ] 6.62607e-13;
|
||||
}
|
||||
electromagnetic
|
||||
{
|
||||
e e [ 0 0 1 0 0 1 0 ] 1.60218e-19;
|
||||
}
|
||||
atomic
|
||||
{
|
||||
me me [ 1 0 0 0 0 0 0 ] 9.10938e-16;
|
||||
mp mp [ 1 0 0 0 0 0 0 ] 1.67262e-12;
|
||||
}
|
||||
physicoChemical
|
||||
{
|
||||
mu mu [ 1 0 0 0 0 0 0 ] 1.66054e-12;
|
||||
k k [ 1 2 -2 -1 0 0 0 ] 1.38065e-23;
|
||||
}
|
||||
standard
|
||||
{
|
||||
//- Standard pressure [Pa]
|
||||
Pstd Pstd [ 1 -1 -2 0 0 0 0 ] 100000;
|
||||
//- Standard temperature [degK]
|
||||
Tstd Tstd [ 0 0 0 1 0 0 0 ] 298.15;
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,29 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
location "system";
|
||||
object decomposeParDict;
|
||||
}
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
numberOfSubdomains 2;
|
||||
|
||||
method simple;
|
||||
|
||||
simpleCoeffs
|
||||
{
|
||||
n (1 1 2);
|
||||
delta 0.001;
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,34 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
location "constant";
|
||||
object fvOptions;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
momentumSource
|
||||
{
|
||||
type meanVelocityForce;
|
||||
active no;
|
||||
|
||||
meanVelocityForceCoeffs
|
||||
{
|
||||
selectionMode all;
|
||||
fields (U);
|
||||
// Note: set mean velocity here
|
||||
Ubar ( 0 0 0.0004 );
|
||||
relaxation 0.9;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,75 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
location "system";
|
||||
object fvSchemes;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
ddtSchemes
|
||||
{
|
||||
default Euler;
|
||||
}
|
||||
|
||||
gradSchemes
|
||||
{
|
||||
default Gauss skewCorrected linear;
|
||||
grad(p) Gauss skewCorrected linear;
|
||||
grad(U) Gauss skewCorrected linear;
|
||||
}
|
||||
|
||||
divSchemes
|
||||
{
|
||||
default Gauss skewCorrected linear;
|
||||
div(phi,U) Gauss skewCorrected upwind;
|
||||
div(phi,k) Gauss limitedLinear 1;
|
||||
div(phi,epsilon) Gauss limitedLinear 1;
|
||||
div(phi,R) Gauss limitedLinear 1;
|
||||
div(R) Gauss linear;
|
||||
div(phi,nuTilda) Gauss limitedLinear 1;
|
||||
div((nuEff*dev(grad(U).T()))) Gauss linear;
|
||||
div(U) Gauss skewCorrected lineaUpwind;
|
||||
}
|
||||
|
||||
laplacianSchemes
|
||||
{
|
||||
default Gauss linear corrected;
|
||||
laplacian(nuEff,U) Gauss linear corrected;
|
||||
laplacian((1|A(U)),p) Gauss linear corrected;
|
||||
laplacian((voidfraction2|A(U)),p) Gauss linear corrected;
|
||||
laplacian(DkEff,k) Gauss linear corrected;
|
||||
laplacian(DepsilonEff,epsilon) Gauss linear corrected;
|
||||
laplacian(DREff,R) Gauss linear corrected;
|
||||
laplacian(DnuTildaEff,nuTilda) Gauss linear corrected;
|
||||
laplacian(phiIB) Gauss linear corrected;
|
||||
laplacian(U) Gauss linear corrected;
|
||||
}
|
||||
|
||||
interpolationSchemes
|
||||
{
|
||||
default skewCorrected linear;
|
||||
interpolate(U) skewCorrected linear;
|
||||
}
|
||||
|
||||
snGradSchemes
|
||||
{
|
||||
default corrected;
|
||||
}
|
||||
|
||||
fluxRequired
|
||||
{
|
||||
default no;
|
||||
p ;
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,118 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration | Website: https://openfoam.org
|
||||
\\ / A nd | Version: 6
|
||||
\\/ M anipulation |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class dictionary;
|
||||
location "system";
|
||||
object fvSolution;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
solvers
|
||||
{
|
||||
p
|
||||
{
|
||||
solver PCG;
|
||||
preconditioner DIC;
|
||||
tolerance 1e-06;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
pFinal
|
||||
{
|
||||
solver PCG;
|
||||
preconditioner DIC;
|
||||
tolerance 1e-06;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
U
|
||||
{
|
||||
solver PBiCG;
|
||||
preconditioner DILU;
|
||||
tolerance 1e-05;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
k
|
||||
{
|
||||
solver PBiCG;
|
||||
preconditioner DILU;
|
||||
tolerance 1e-05;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
epsilon
|
||||
{
|
||||
solver PBiCG;
|
||||
preconditioner DILU;
|
||||
tolerance 1e-05;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
R
|
||||
{
|
||||
solver PBiCG;
|
||||
preconditioner DILU;
|
||||
tolerance 1e-05;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
nuTilda
|
||||
{
|
||||
solver PBiCG;
|
||||
preconditioner DILU;
|
||||
tolerance 1e-05;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
phiIB
|
||||
{
|
||||
solver PCG;
|
||||
preconditioner DIC;
|
||||
tolerance 1e-06;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
"(U|k)Final"
|
||||
{
|
||||
$U;
|
||||
tolerance 1e-05;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
Us
|
||||
{
|
||||
$U;
|
||||
tolerance 1e-05;
|
||||
relTol 0;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
PISO
|
||||
{
|
||||
nCorrectors 2;
|
||||
nNonOrthogonalCorrectors 0;
|
||||
pRefCell 0;
|
||||
pRefValue 0;
|
||||
}
|
||||
|
||||
relaxationFactors
|
||||
{
|
||||
/*
|
||||
equations
|
||||
{
|
||||
".*" 0.9;
|
||||
}
|
||||
*/
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,10 @@
|
||||
1.58162822 1.14912017 0.00000000 1.95500000
|
||||
0.60412822 1.85931549 0.00000000 1.95500000
|
||||
-0.60412822 1.85931549 0.00000000 1.95500000
|
||||
-1.58162822 1.14912017 0.00000000 1.95500000
|
||||
-1.95500000 0.00000000 0.00000000 1.95500000
|
||||
-1.58162822 -1.14912017 0.00000000 1.95500000
|
||||
-0.60412822 -1.85931549 0.00000000 1.95500000
|
||||
0.60412822 -1.85931549 0.00000000 1.95500000
|
||||
1.58162822 -1.14912017 0.00000000 1.95500000
|
||||
1.95500000 -0.00000000 0.00000000 1.95500000
|
||||
@ -0,0 +1,113 @@
|
||||
# Insert a RBC into a box, then induce shear flow
|
||||
log ../DEM/log.liggghts
|
||||
thermo_log ../DEM/post/thermo.txt
|
||||
|
||||
# bond parameter setup
|
||||
variable rp equal 1.955 # sphere radius
|
||||
variable ro equal 1 # bond outer radius multiplier
|
||||
variable ri equal 0 # bond inner radius multiplier
|
||||
variable rb equal 2*${ro}*${rp} # bond radius
|
||||
variable lb equal 0.3090 # bond length multiplier
|
||||
variable damp equal 300 # damping coefficient
|
||||
|
||||
# material properties
|
||||
variable G equal 0.005333 # in-plane shear modulus of the membrane
|
||||
variable Y equal 0.020426 # in-plane Young's modulus of the membrane
|
||||
variable Sn equal $Y/3.91 # analogous Youngs modulus of the parallel bond
|
||||
variable St equal $G/3.91 # analogous shear modulus of the parallel bond
|
||||
variable Sben equal ${Sn}*10 # analogous bending modulus of the parallel bond
|
||||
variable Stor equal ${Sn}*10 # analogous torsional modulus of the parallel bond
|
||||
|
||||
|
||||
# atom type and style
|
||||
atom_style hybrid granular bond/gran n_bondtypes 1 bonds_per_atom 6
|
||||
atom_modify map array
|
||||
|
||||
# boundary
|
||||
boundary p f p
|
||||
|
||||
# communication
|
||||
newton off
|
||||
communicate single vel yes
|
||||
|
||||
# units
|
||||
units micro
|
||||
|
||||
#region and box creation
|
||||
region domain block 0 45 0 22.5 0 22.5 units box
|
||||
create_box 2 domain
|
||||
|
||||
# neighbors
|
||||
neighbor 1 bin
|
||||
neigh_modify exclude molecule all
|
||||
neigh_modify delay 0
|
||||
|
||||
# material properties
|
||||
fix m1 all property/global youngsModulus peratomtype 7.5e02 7.5e03
|
||||
fix m2 all property/global poissonsRatio peratomtype 0.5 0.5
|
||||
fix m3 all property/global coefficientRestitution peratomtypepair 2 1e-06 1e-03 1e-03 1e-06
|
||||
fix m4 all property/global coefficientFriction peratomtypepair 2 0.3 0.1 0.1 0.3
|
||||
|
||||
# pair style
|
||||
pair_style gran model hertz tangential history
|
||||
pair_coeff * *
|
||||
|
||||
# bond parameters
|
||||
bond_style gran
|
||||
# N ro ri lb Sn_bond St_bond s_bend s_tor damp bn bt TYPE_OF_BOND sigma_break tau_break
|
||||
bond_coeff 1 ${ro} ${ri} ${lb} ${Sn} ${St} ${Sben} ${Stor} ${damp} 2.65 0.0 1 1e50 1e50
|
||||
|
||||
|
||||
# particle template, insertion region and bond formation
|
||||
fix pts1 all particletemplate/multiplespheres 15485863 atom_type 1 &
|
||||
density constant 1098 nspheres 10 ntry 1000000 spheres file ../DEM/data/spheres.txt scale 1 &
|
||||
bonded yes/explicit &
|
||||
nbond_pairs 10 &
|
||||
1 2 &
|
||||
2 3 &
|
||||
3 4 &
|
||||
4 5 &
|
||||
5 6 &
|
||||
6 7 &
|
||||
7 8 &
|
||||
8 9 &
|
||||
9 10 &
|
||||
10 1 &
|
||||
bond_type 1
|
||||
|
||||
fix pdd1 all particledistribution/discrete 32452843 1 pts1 1.0
|
||||
|
||||
region bc1 block 0 45 0 22.5 0 22.5 units box
|
||||
|
||||
fix ins1 all insert/pack seed 32452867 distributiontemplate pdd1 &
|
||||
maxattempt 10000 insert_every once overlapcheck yes vel constant 0.0 0.0 0.0 &
|
||||
region bc1 particles_in_region 1 pos 22.5 11.25 11.25 ntry_mc 100000
|
||||
|
||||
run 1000
|
||||
|
||||
# set timestep
|
||||
timestep 0.001
|
||||
|
||||
# check timestep
|
||||
fix ts_check all check/timestep/gran 1000 0.1 0.1
|
||||
|
||||
# screen output
|
||||
thermo_style custom step atoms numbond
|
||||
thermo 10000
|
||||
thermo_modify lost ignore norm no
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
dump dmp all custom 1000 ../DEM/post/dump*.liggghts &
|
||||
id mol type x y z vx vy vz fx fy fz omegax omegay omegaz radius
|
||||
compute b1 all property/local &
|
||||
batom1x batom1y batom1z batom2x batom2y batom2z &
|
||||
batom1 batom2 btype bforceX bforceY bforceZ
|
||||
# x1 y1 z1 x2 y2 z2 id1 id2 bondtype f_bond[1] f_bond[2] f_bond[3]
|
||||
dump bnd all local 1000 ../DEM/post/bonds*.bond1 &
|
||||
c_b1[1] c_b1[2] c_b1[3] c_b1[4] c_b1[5] c_b1[6] &
|
||||
c_b1[7] c_b1[8] c_b1[9] c_b1[10] c_b1[11] c_b1[12]
|
||||
|
||||
run 100000
|
||||
|
||||
write_restart ../DEM/post/restart/liggghts.restart
|
||||
|
||||
@ -0,0 +1,130 @@
|
||||
# RBC in a box sheared by fluid
|
||||
log ../DEM/log.liggghts
|
||||
thermo_log ../DEM/post/thermo.txt
|
||||
|
||||
# bond parameter setup
|
||||
variable rp equal 1.955 # sphere radius
|
||||
variable ro equal 1 # bond outer radius multiplier
|
||||
variable ri equal 0 # bond inner radius multiplier
|
||||
variable rb equal 2*${ro}*${rp} # bond radius
|
||||
variable lb equal 0.3090 # bond length multiplier
|
||||
variable damp equal 25 # damping coefficient
|
||||
|
||||
# material properties
|
||||
variable G equal 0.005333 # in-plane shear modulus of the membrane
|
||||
variable Y equal 0.020426 # in-plane Young's modulus of the membrane
|
||||
variable Sn equal $Y/3.91 # analogous Youngs modulus of the parallel bond
|
||||
variable St equal $G/3.91 # analogous shear modulus of the parallel bond
|
||||
variable Ab equal (22/7)*${rb}${rb} # bond area
|
||||
variable Sben equal ${Sn}/${Ab} # analogous bending modulus of the parallel bond
|
||||
variable Stor equal ${St}/${Ab} # analogous torsional modulus of the parallel bond
|
||||
|
||||
# atom type and style
|
||||
atom_style hybrid granular bond/gran n_bondtypes 1 bonds_per_atom 6
|
||||
atom_modify map array
|
||||
|
||||
# boundary
|
||||
boundary p f p
|
||||
|
||||
# communication
|
||||
newton off
|
||||
communicate single vel yes
|
||||
|
||||
# units and processors
|
||||
units micro
|
||||
processors 1 1 2
|
||||
|
||||
# read the restart file
|
||||
read_restart ../DEM/post/restart/liggghts.restart
|
||||
|
||||
# neighbors
|
||||
neighbor 1.0 bin
|
||||
neigh_modify exclude molecule all
|
||||
neigh_modify delay 0
|
||||
|
||||
# material properties
|
||||
fix m1 all property/global youngsModulus peratomtype 7.5e02 7.5e04
|
||||
fix m2 all property/global poissonsRatio peratomtype 0.5 0.18
|
||||
fix m3 all property/global coefficientRestitution peratomtypepair 2 0.9 0.1 0.1 0.9
|
||||
fix m4 all property/global coefficientFriction peratomtypepair 2 0.3 0.3 0.3 0.3
|
||||
|
||||
# pair style
|
||||
pair_style gran model hertz tangential history
|
||||
pair_coeff * *
|
||||
|
||||
# bond parameters
|
||||
bond_style gran
|
||||
# N ro ri lb Sn_bond St_bond s_bend s_tor damp bn bt TYPE_OF_BOND sigma_break tau_break
|
||||
bond_coeff 1 ${ro} ${ri} ${lb} ${Sn} ${St} ${Sben} ${Stor} ${damp} 3.0 1.0 1.0 1e50 1e50
|
||||
|
||||
|
||||
# reset timestep after reading the restart file
|
||||
reset_timestep 0
|
||||
timestep 0.1
|
||||
|
||||
# cfd coupling
|
||||
fix cfd all couple/cfd couple_every 10 mpi
|
||||
fix cfd2 all couple/cfd/force
|
||||
|
||||
# apply nve integration to all constituent spheres - single sphere treatment
|
||||
fix integr all nve
|
||||
|
||||
compute unwra all property/atom xu yu zu
|
||||
|
||||
# variables for data processing
|
||||
variable x1 equal c_unwra[1][1]
|
||||
variable y1 equal c_unwra[1][2]
|
||||
variable z1 equal c_unwra[1][3]
|
||||
variable x2 equal c_unwra[2][1]
|
||||
variable y2 equal c_unwra[2][2]
|
||||
variable z2 equal c_unwra[2][3]
|
||||
variable x3 equal c_unwra[3][1]
|
||||
variable y3 equal c_unwra[3][2]
|
||||
variable z3 equal c_unwra[3][3]
|
||||
variable x4 equal c_unwra[4][1]
|
||||
variable y4 equal c_unwra[4][2]
|
||||
variable z4 equal c_unwra[4][3]
|
||||
variable x5 equal c_unwra[5][1]
|
||||
variable y5 equal c_unwra[5][2]
|
||||
variable z5 equal c_unwra[5][3]
|
||||
variable x6 equal c_unwra[6][1]
|
||||
variable y6 equal c_unwra[6][2]
|
||||
variable z6 equal c_unwra[6][3]
|
||||
variable x7 equal c_unwra[7][1]
|
||||
variable y7 equal c_unwra[7][2]
|
||||
variable z7 equal c_unwra[7][3]
|
||||
variable x8 equal c_unwra[8][1]
|
||||
variable y8 equal c_unwra[8][2]
|
||||
variable z8 equal c_unwra[8][3]
|
||||
variable x9 equal c_unwra[9][1]
|
||||
variable y9 equal c_unwra[9][2]
|
||||
variable z9 equal c_unwra[9][3]
|
||||
variable x10 equal c_unwra[10][1]
|
||||
variable y10 equal c_unwra[10][2]
|
||||
variable z10 equal c_unwra[10][3]
|
||||
variable time equal step*dt
|
||||
|
||||
fix extra1 all print 10 "${time} ${x1} ${y1} ${z1} ${x2} ${y2} ${z2} ${x3} ${y3} ${z3} ${x4} ${y4} ${z4} ${x5} ${y5} ${z5} ${x6} ${y6} ${z6} ${x7} ${y7} ${z7} ${x8} ${y8} ${z8} ${x9} ${y9} ${z9} ${x10} ${y10} ${z10}" &
|
||||
file ../DEM/post/particle_position.txt screen no
|
||||
|
||||
# check timestep
|
||||
fix ts_check all check/timestep/gran 1 0.1 0.1
|
||||
|
||||
# screen output
|
||||
thermo_style custom step atoms numbond
|
||||
thermo 1000
|
||||
thermo_modify lost ignore norm no
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
dump dmp all custom 1000 ../DEM/post/dump.liggghts &
|
||||
id mol type x y z vx vy vz fx fy fz omegax omegay omegaz radius
|
||||
compute b1 all property/local &
|
||||
batom1x batom1y batom1z batom2x batom2y batom2z &
|
||||
batom1 batom2 btype bforceX bforceY bforceZ
|
||||
# x1 y1 z1 x2 y2 z2 id1 id2 bondtype f_bond[1] f_bond[2] f_bond[3]
|
||||
dump bnd all local 1000 ../DEM/post/bonds.bond1 &
|
||||
c_b1[1] c_b1[2] c_b1[3] c_b1[4] c_b1[5] c_b1[6] &
|
||||
c_b1[7] c_b1[8] c_b1[9] c_b1[10] c_b1[11] c_b1[12]
|
||||
|
||||
run 1
|
||||
|
||||
0
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/DEM/post/restart/.gitignore
vendored
Normal file
0
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/DEM/post/restart/.gitignore
vendored
Normal file
26
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/DEMrun.sh
Executable file
26
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/DEMrun.sh
Executable file
@ -0,0 +1,26 @@
|
||||
#!/bin/bash
|
||||
#------------------------------------------------------------------------------
|
||||
# DEMrun script for redBloodCellShearFlow test case
|
||||
# init redBloodCellShearFlow
|
||||
# Achuth N. Balachandran Nair - October 2018
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
#- source CFDEM env vars
|
||||
. ~/.bashrc
|
||||
|
||||
#- include functions
|
||||
source $CFDEM_PROJECT_DIR/etc/functions.sh
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
#- define variables
|
||||
casePath="$(dirname "$(readlink -f ${BASH_SOURCE[0]})")"
|
||||
logpath="$casePath"
|
||||
headerText="run_liggghts_init_DEM"
|
||||
logfileName="log_$headerText"
|
||||
solverName="in.liggghts_init"
|
||||
debugMode="off"
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
#- call function to run DEM case
|
||||
DEMrun $logpath $logfileName $casePath $headerText $solverName $debugMode
|
||||
|
||||
@ -0,0 +1,9 @@
|
||||
## Single Red Blood Cell Dynamics in Shear Flow
|
||||
|
||||
This case uses a continuous forcing immersed boundary solver on the CFD side and
|
||||
a reduced order model of a red blood cell on the DEM side, cf.
|
||||
|
||||
Balachandran Nair, A.N., Pirker, S. and Saeedipour, M., "Resolved CFD-DEM
|
||||
simulation of blood flow with a reduced-order RBC model", Comp. Part. Mech.
|
||||
(2021)
|
||||
|
||||
@ -0,0 +1,59 @@
|
||||
#!/bin/bash
|
||||
#------------------------------------------------------------------------------
|
||||
# parCFDDEMrun script for redBloodCellShearFlow test case
|
||||
# run redBloodCellShearFlow CFD-DEM
|
||||
# Achuth N. Balachandran Nair - October 2018
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
#- source CFDEM env vars
|
||||
. ~/.bashrc
|
||||
|
||||
#- source CFDEM functions
|
||||
source $CFDEM_PROJECT_DIR/etc/functions.sh
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
#- define variables
|
||||
casePath="$(dirname "$(readlink -f ${BASH_SOURCE[0]})")"
|
||||
logpath=$casePath
|
||||
headerText="run_parallel_cfdemSolverIBContinuousForcing_redBloodCellShearFlow"
|
||||
logfileName="log_$headerText"
|
||||
solverName="cfdemSolverIBContinuousForcing"
|
||||
nrProcs="2"
|
||||
machineFileName="none" # yourMachinefileName | none
|
||||
debugMode="off" # on | off| strict
|
||||
testHarnessPath="$CFDEM_TEST_HARNESS_PATH"
|
||||
runPython="false"
|
||||
postproc="false"
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
#- call function to run a parallel CFD-DEM case
|
||||
parCFDDEMrun $logpath $logfileName $casePath $headerText $solverName $nrProcs $machineFileName $debugMode
|
||||
|
||||
if [ $runPython == "true" ]
|
||||
then
|
||||
cd $casePath
|
||||
python results.py
|
||||
fi
|
||||
|
||||
if [ $postproc == "true" ]
|
||||
then
|
||||
#- get VTK data from liggghts dump file
|
||||
cd $casePath/DEM/post
|
||||
lpp dump*
|
||||
|
||||
#- get VTK data from CFD sim
|
||||
cd $casePath/CFD
|
||||
reconstructParMesh -constant -mergeTol 1e-06
|
||||
reconstructPar -noLagrangian
|
||||
foamToVTK
|
||||
|
||||
#- start paraview
|
||||
paraview
|
||||
|
||||
#- keep terminal open (if started in new terminal)
|
||||
echo "...press enter to clean up case"
|
||||
echo "press Ctr+C to keep data"
|
||||
read
|
||||
fi
|
||||
|
||||
|
||||
31
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/post.sh
Executable file
31
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/post.sh
Executable file
@ -0,0 +1,31 @@
|
||||
#!/bin/bash
|
||||
#------------------------------------------------------------------------------
|
||||
# post script for redBloodCellShearFlow test case
|
||||
# run post-processing
|
||||
# Achuth N. Balachandran Nair - October 2018
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
#- source CFDEM env vars
|
||||
source ~/.bashrc
|
||||
|
||||
#- source CFDEM functions
|
||||
shopt -s expand_aliases
|
||||
source $CFDEM_PROJECT_DIR/etc/bashrc
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
#- define variables
|
||||
casePath="$(dirname "$(readlink -f ${BASH_SOURCE[0]})")"
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
#- get VTK data from liggghts dump file
|
||||
cd $casePath/DEM/post
|
||||
lpp dump*
|
||||
|
||||
#- get VTK data from CFD sim
|
||||
cd $casePath/CFD
|
||||
reconstructParMesh -constant -mergeTol 1e-06
|
||||
reconstructPar -noLagrangian
|
||||
|
||||
#- start paraview
|
||||
paraview
|
||||
|
||||
66
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/results.py
Executable file
66
tutorials/cfdemSolverIBContinuousForcing/redBloodCellShearFlow/results.py
Executable file
@ -0,0 +1,66 @@
|
||||
#!/usr/bin/python
|
||||
|
||||
import numpy as np
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
# Reading sphere data file
|
||||
t,x1,y1,z1,x2,y2,z2,x3,y3,z3,x4,y4,z4,x5,y5,z5,x6,y6,z6,x7,y7,z7,x8,y8,z8,x9,y9,z9,x10,y10,z10 = np.genfromtxt('DEM/post/particle_position.txt', skip_header=0,usecols = (0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30),unpack=True)
|
||||
t = t*1e-06
|
||||
|
||||
# Calculating the centre of mass of RBC
|
||||
xcm = (x1+x2+x3+x4+x5+x6+x7+x8+x9+x10)/10
|
||||
ycm = (y1+y2+y3+y4+y5+y6+y7+y8+y9+y10)/10
|
||||
zcm = (z1+z2+z3+z4+z5+z6+z7+z8+z9+z10)/10
|
||||
|
||||
# Calculating the gyration tensor
|
||||
G11 = ((x1-xcm)*(x1-xcm) + (x2-xcm)*(x2-xcm) + (x3-xcm)*(x3-xcm) + (x4-xcm)*(x4-xcm) + (x5-xcm)*(x5-xcm) + (x6-xcm)*(x6-xcm) + (x7-xcm)*(x7-xcm) + (x8-xcm)*(x8-xcm) + (x9-xcm)*(x9-xcm) + (x10-xcm)*(x10-xcm))/10
|
||||
G12 = ((x1-xcm)*(y1-ycm) + (x2-xcm)*(y2-ycm) + (x3-xcm)*(y3-ycm) + (x4-xcm)*(y4-ycm) + (x5-xcm)*(y5-ycm) + (x6-xcm)*(y6-ycm) + (x7-xcm)*(y7-ycm) + (x8-xcm)*(y8-ycm) + (x9-xcm)*(y9-ycm) + (x10-xcm)*(y10-ycm))/10
|
||||
G13 = ((x1-xcm)*(z1-zcm) + (x2-xcm)*(z2-zcm) + (x3-xcm)*(z3-zcm) + (x4-xcm)*(z4-zcm) + (x5-xcm)*(z5-zcm) + (x6-xcm)*(z6-zcm) + (x7-xcm)*(z7-zcm) + (x8-xcm)*(z8-zcm) + (x9-xcm)*(z9-zcm) + (x10-xcm)*(z10-zcm))/10
|
||||
G21 = ((y1-ycm)*(x1-xcm) + (y2-ycm)*(x2-xcm) + (y3-ycm)*(x3-xcm) + (y4-ycm)*(x4-xcm) + (y5-ycm)*(x5-xcm) + (y6-ycm)*(x6-xcm) + (y7-ycm)*(x7-xcm) + (y8-ycm)*(x8-xcm) + (y9-ycm)*(x9-xcm) + (y10-ycm)*(x10-xcm))/10
|
||||
G22 = ((y1-ycm)*(y1-ycm) + (y2-ycm)*(y2-ycm) + (y3-ycm)*(y3-ycm) + (y4-ycm)*(y4-ycm) + (y5-ycm)*(y5-ycm) + (y6-ycm)*(y6-ycm) + (y7-ycm)*(y7-ycm) + (y8-ycm)*(y8-ycm) + (y9-ycm)*(y9-ycm) + (y10-ycm)*(y10-ycm))/10
|
||||
G23 = ((y1-ycm)*(z1-zcm) + (y2-ycm)*(z2-zcm) + (y3-ycm)*(z3-zcm) + (y4-ycm)*(z4-zcm) + (y5-ycm)*(z5-zcm) + (y6-ycm)*(z6-zcm) + (y7-ycm)*(z7-zcm) + (y8-ycm)*(z8-zcm) + (y9-ycm)*(z9-zcm) + (y10-ycm)*(z10-zcm))/10
|
||||
G31 = ((z1-zcm)*(x1-xcm) + (z2-zcm)*(x2-xcm) + (z3-zcm)*(x3-xcm) + (z4-zcm)*(x4-xcm) + (z5-zcm)*(x5-xcm) + (z6-zcm)*(x6-xcm) + (z7-zcm)*(x7-xcm) + (z8-zcm)*(x8-xcm) + (z9-zcm)*(x9-xcm) + (z10-zcm)*(x10-xcm))/10
|
||||
G32 = ((z1-zcm)*(y1-ycm) + (z2-zcm)*(y2-ycm) + (z3-zcm)*(y3-ycm) + (z4-zcm)*(y4-ycm) + (z5-zcm)*(y5-ycm) + (z6-zcm)*(y6-ycm) + (z7-zcm)*(y7-ycm) + (z8-zcm)*(y8-ycm) + (z9-zcm)*(y9-ycm) + (z10-zcm)*(y10-ycm))/10
|
||||
G33 = ((z1-zcm)*(z1-zcm) + (z2-zcm)*(z2-zcm) + (z3-zcm)*(z3-zcm) + (z4-zcm)*(z4-zcm) + (z5-zcm)*(z5-zcm) + (z6-zcm)*(z6-zcm) + (z7-zcm)*(z7-zcm) + (z8-zcm)*(z8-zcm) + (z9-zcm)*(z9-zcm) + (z10-zcm)*(z10-zcm))/10
|
||||
|
||||
# Calculating the eigen values of the gyration tensor
|
||||
min_eig = []
|
||||
|
||||
for i in range(len(t)):
|
||||
G = np.matrix([ [G11[i],G12[i],G13[i]],
|
||||
[G21[i],G22[i],G23[i]],
|
||||
[G31[i],G32[i],G33[i]] ])
|
||||
|
||||
eigenvalues = np.linalg.eigvals(G)
|
||||
eig = np.min(eigenvalues)
|
||||
min_eig.append(eig)
|
||||
|
||||
plt.plot(t,min_eig,linewidth = 2)
|
||||
plt.xlabel('Time (s)')
|
||||
plt.ylabel('Min. eigen value of G')
|
||||
plt.grid()
|
||||
plt.show()
|
||||
|
||||
plt.plot(z1,y1)
|
||||
plt.plot(z2,y2)
|
||||
plt.plot(z3,y3)
|
||||
plt.plot(z4,y4)
|
||||
plt.plot(z5,y5)
|
||||
plt.plot(z6,y6)
|
||||
plt.plot(z7,y7)
|
||||
plt.plot(z8,y8)
|
||||
plt.plot(z9,y9)
|
||||
plt.plot(z10,y10)
|
||||
plt.show()
|
||||
|
||||
plt.plot(z1,x1)
|
||||
plt.plot(z2,x2)
|
||||
plt.plot(z3,x3)
|
||||
plt.plot(z4,x4)
|
||||
plt.plot(z5,x5)
|
||||
plt.plot(z6,x6)
|
||||
plt.plot(z7,x7)
|
||||
plt.plot(z8,x8)
|
||||
plt.plot(z9,x9)
|
||||
plt.plot(z10,x10)
|
||||
plt.show()
|
||||
Reference in New Issue
Block a user