Shell scripting

These are script files, for running all the commands related to the case. You can open it using any editor and see the commands executed from it. Taking as example the native bash script often present in tutorial cases Allrun and Allclean, the follwing command will execute them:

./Allrun

It will run all the command necessary to run the tutorial. While:

./Allclean

It will run all the command necessary to clean the tutorial.

Custom script

To write your shell script, start a new file with the notation:

#!/bin/bash

then followed by the command you want to execute. Elevate the file permission adding execution permission through

chmod +x shellScript.sh

For running your bash script, type:

./shellScript.sh

An example of a bash script to automate a thermal analysis is presented here:

#!/bin/bash

SLURM_NTASKS=16                                          # Processor number defined here 
source ${WM_PROJECT_DIR:?}/bin/tools/RunFunctions        # Source run functions

# Remove previous log directory for job monitoring and previous run file
./Allclean
rm -r log;
mkdir log

# Mesh generation
restore0Dir
surfaceFeatureExtract                                       > ./log/surfaceFeatureExtract.log  2>&1  && echo "surfaceFeatureExtract Executed/n"
blockMesh                                                   > ./log/blockMesh.log 2>&1  && echo "blockMesh Executed"
decomposePar -force                                         > ./log/decomposePar1.log 2>&1  && echo "decomposePar1 Executed"
mpirun -np $SLURM_NTASKS snappyHexMesh -parallel -overwrite > ./log/snappyHexMesh.log 2>&1 && echo "snappyHexMesh Executed"

# Addional mesh zones operation
reconstructParMesh -constant                                > ./log/reconstructParMesh1         2>&1 && echo "Reconstruct Case"
topoSet                                                     > ./log/topoSet  && echo "topoSet Executed"
checkMesh                                                   > ./log/checkMesh.log                   2>&1 && echo "checkMesh Executed"

decomposePar -force                                         > ./log/decomposePar2 2>&1 && echo "decomposePar2 Executed"
mpirun -np $SLURM_NTASKS $(getApplication) -parallel        > ./log/$(getApplication).log 2>&1 && echo "$(getApplication) Executed"

reconstructParMesh -constant -allRegions                    > ./log/reconstructParMesh.log 2>&1 && echo "Finished"

Parametric study

To develop a parametric study, hence you change one or more variables to get the consequent result of this boudnary conditions change. You can use the sed command to drive the dictionary changes:

sed -i '/^[[:space:]]*massFlowRate/c\ massFlowRate 1000;'  0/U

This above command substitute the row that contain the word “massFlowRate” with the follwing: “massFlowRate 1000;”. Creating a bash script to automate this practise will look similar to the following:

#!/bin/bash

SLURM_NTASKS=14
list_mass_flow_rate=(1.14E-04  2.29E-04  3.43E-04)

# Source run functions
source ${WM_PROJECT_DIR:?}/bin/tools/RunFunctions        
rm -r log;
mkdir log

# Build the mesh
surfaceFeatureExtract > ./log/surfaceFeatureExtract.log 2>&1  && echo "surfaceFeatureExtract Executed/n"
blockMesh  > ./log/blockMesh.log 2>&1  && echo "blockMesh Executed"
decomposePar -force  > ./log/decomposePar1.log 2>&1 && echo "decomposePar1 Executed"
mpirun -np $SLURM_NTASKS snappyHexMesh -parallel -overwrite > ./log/snappyHexMesh.log 2>&1 && echo "snappyHexMesh Executed"
mpirun -np $SLURM_NTASKS checkMesh -parallel > ./log/checkMesh.log 2>&1 && echo "checkMesh Executed"
reconstructParMesh -constant > ./reconstructParMesh.log 2>&1 && echo "reconstructParMesh Executed"


for flowRateValue in "${list_mass_flow_rate[@]}"
do
        rm -r process*;

        # Modify the 0/U directory with a new value of massflow rate
        sed -i "/^[[:space:]]*massFlowRate/c\ massFlowRate $flowRateValue ;"  0.orig/U  && echo "Changed 0/U with $flowRateValue kg/s"
        restore0Dir > ./log/restore0Dir.$flowRateValue.log 2>&1 && echo "restore0Dir $flowRateValue  Executed"
        decomposePar -force > ./log/decomposePar.$flowRateValue.log 2>&1 && echo "decomposePar $flowRateValue  Executed"
        mpirun -np $SLURM_NTASKS $(getApplication) -parallel   > ./log/$(getApplication).$flowRateValue.log 2>&1 && echo "$(getApplication) $flowRateValue Executed"
        reconstructPar -latestTime > ./log/reconstructParMesh.$flowRateValue.log 2>&1  && echo "reconstructPar $flowRateValue Executed"

        # Take the newly created directory and re-name it as the flow rate
        mv $(ls -1tr | tail -1) $flowRateValue
done

Find bugs

The utility shellcheck provide warnings and suggestions for bash/sh shell scripts. Run the following for instant output:

shellcheck yourscript.sh