Restructure runscripts and related resources

elastic-tube-3d/fluid-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh, 0.orig/ is copied to 0/

elastic-tube-3d/fluid-openfoam/run.sh

@@ -1,41 +1,7 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    		    		# Run from this directory
-. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
+#!/bin/sh
+set -e -u
 
-# Fluid participant
-
-# Run this script in one terminal and the execute the coupled_elasto_dynamics bindary 
-# in another terminal.
-# These scripts present how the two participants would be started manually.
-
-# Run this script with "-parallel" for parallel simulations
-
-# The script "Allclean" cleans-up the result and log files.
-
-# 1 for true, 0 for false
-parallel=0
-if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-
-rm -rfv 0/
-cp -r 0.orig/ 0/
 cp -r constant/polyMesh.orig constant/polyMesh
-checkMesh
 touch fluid-openfoam.foam
 
-# Run
-solver=$(getApplication)
-procs=$(getNumberOfProcessors)
-if [ $parallel -eq 1 ]; then
-    decomposePar -force
-    mpirun -np $procs $solver -parallel
-    reconstructPar
-else
-    $solver
-fi
-
-# Workaround for issue #26 (OF-adapter, relevant for OF .com versions) 
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"

elastic-tube-3d/fluid-openfoam/system/controlDict

@@ -40,7 +40,7 @@ timeFormat general;
 
 timePrecision 8;
 
-runTimeModifiable yes;
+runTimeModifiable false;
 
 adjustTimeStep no;
 

elastic-tube-3d/solid-calculix/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_calculix .
+clean_calculix .

elastic-tube-3d/solid-calculix/run.sh

@@ -1,13 +1,6 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    # Run from this directory
+#!/bin/sh
+set -e -u
 
-# This script prepares and runs the CalculiX solver
-
-# =============== Participant: Solid ===========================
-Solver="ccx_preCICE"
-
-    # Run and get the process id
-    echo "Starting the CalculiX..."
-    export OMP_NUM_THREADS=1
-    export CCX_NPROC_EQUATION_SOLVER=1
-    ${Solver} -i tube -precice-participant Calculix 
+export OMP_NUM_THREADS=1
+export CCX_NPROC_EQUATION_SOLVER=1
+ccx_preCICE -i tube -precice-participant Calculix

flow-over-heated-plate-nearest-projection/fluid-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

flow-over-heated-plate-nearest-projection/fluid-openfoam/run.sh

@@ -1,40 +1,7 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    		    		# Run from this directory
-. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
+#!/bin/sh
+set -e -u
 
-# Fluid participant
-
-# Run this script in one terminal in order to start this participant.
-# Run this script with "-parallel" for parallel simulations
-
-# 1 for true, 0 for false
-parallel=0
-if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-
-rm -rfv 0/
-cp -r 0.orig/ 0/
 blockMesh
-checkMesh
 touch fluid-openfoam.foam
 
-# Run
-solver=$(getApplication)
-procs=$(getNumberOfProcessors)
-
-if [ $parallel -eq 1 ]; then
-    decomposePar -force
-    mpirun -np $procs $solver -parallel
-    reconstructPar
-else
-    $solver
-fi
-
-# Workaround for issue #26
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
-
-echo ""
-echo "### NOTE ### Make sure to use the correct solver for your OpenFOAM version! (pimpleFoam for OpenFOAM v1806, OpenFOAM 6, or newer, vs pimpleDyMFoam for older) You may change this in your Fluid/system/controlDict file, if needed."
+../../tools/run-openfoam.sh "$@"

flow-over-heated-plate-nearest-projection/solid-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

flow-over-heated-plate-nearest-projection/solid-openfoam/run.sh

@@ -1,40 +1,7 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    		    		# Run from this directory
-. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
+#!/bin/sh
+set -e -u
 
-# Fluid participant
-
-# Run this script in one terminal in order to start this participant.
-# Run this script with "-parallel" for parallel simulations
-
-# 1 for true, 0 for false
-parallel=0
-if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-
-rm -rfv 0/
-cp -r 0.orig/ 0/
 blockMesh
-checkMesh
 touch solid-openfoam.foam
 
-# Run
-solver=$(getApplication)
-procs=$(getNumberOfProcessors)
-
-if [ $parallel -eq 1 ]; then
-    decomposePar -force
-    mpirun -np $procs $solver -parallel
-    reconstructPar
-else
-    $solver
-fi
-
-# Workaround for issue #26
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
-
-echo ""
-echo "### NOTE ### Make sure to use the correct solver for your OpenFOAM version! (pimpleFoam for OpenFOAM v1806, OpenFOAM 6, or newer, vs pimpleDyMFoam for older) You may change this in your Fluid/system/controlDict file, if needed."
+../../tools/run-openfoam.sh "$@"

flow-over-heated-plate-steady-state/fluid-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

flow-over-heated-plate-steady-state/fluid-openfoam/run.sh

@@ -1,41 +1,7 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    		    		# Run from this directory
-. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
+#!/bin/sh
+set -e -u
 
-# Fluid participant
-
-# Run this script in one terminal and the execute the coupled_elasto_dynamics bindary 
-# in another terminal.
-# These scripts present how the two participants would be started manually.
-
-# Run this script with "-parallel" for parallel simulations
-
-# The script "Allclean" cleans-up the result and log files.
-
-# 1 for true, 0 for false
-parallel=0
-if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-
-rm -rfv 0/
-cp -r 0.orig/ 0/
 blockMesh
-checkMesh
 touch fluid-openfoam.foam
 
-# Run
-solver=$(getApplication)
-procs=$(getNumberOfProcessors)
-if [ $parallel -eq 1 ]; then
-    decomposePar -force
-    mpirun -np $procs $solver -parallel
-    reconstructPar
-else
-    $solver
-fi
-
-# Workaround for issue #26 (OF-adapter, relevant for OF .com versions) 
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"

flow-over-heated-plate-steady-state/solid-codeaster/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_codeaster .
+clean_codeaster .

flow-over-heated-plate-steady-state/solid-codeaster/run.sh

@@ -1,4 +1,10 @@
-#!/bin/bash
-    export TUTORIAL_ROOT=${PWD}
-    export PRECICE_PARTICIPANT=Solid
-    as_run --run solid.export
+#!/bin/sh
+set -e -u
+
+echo "Warning: this case requires a manual preparation step for code_aster."
+echo "See the tutorial and code_aster adapter documentation pages for more:"
+echo "https://www.precice.org/adapter-code_aster.html\n"
+
+export TUTORIAL_ROOT=${PWD}
+export PRECICE_PARTICIPANT=Solid
+as_run --run solid.export

flow-over-heated-plate/fluid-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

flow-over-heated-plate/fluid-openfoam/run.sh

@@ -1,34 +1,7 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    		    		# Run from this directory
-. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
-# Fluid participant
-# Run this script in one terminal and the "runSolid" script in another terminal.
-# These scripts present how the two participants would be started manually.
-# Alternatively, you may execute the "Allrun" script in one terminal.
-# Run this script with "-parallel" for parallel simulations
-# The script "Allclean" cleans-up the result and log files.
-# 1 for true, 0 for false
+#!/bin/sh
+set -e -u
 
-parallel=0
-if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-rm -rfv 0/
-cp -r 0.orig/ 0/
 blockMesh
-checkMesh
 touch fluid-openfoam.foam
 
-solver=$(getApplication)
-procs=$(getNumberOfProcessors)
-if [ $parallel -eq 1 ]; then
-    decomposePar -force
-    mpirun -np $procs $solver -parallel
-    reconstructPar
-else
-    $solver
-fi
-
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"

flow-over-heated-plate/solid-fenics/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_fenics .
+clean_fenics .

flow-over-heated-plate/solid-fenics/run.sh

@@ -1,11 +1,4 @@
-#!/bin/bash
-
-# Solid participant
-
-# Run this script in one terminal and the "runFluid" script in another terminal.
-# These scripts present how the two participants would be started manually.
-# Alternatively, you may execute the "Allrun" script in one terminal.
-
-# The script "Allclean" cleans-up the result and log files.
+#!/bin/sh
+set -e -u
 
 python3 solid.py

flow-over-heated-plate/solid-nutils/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_nutils .
+clean_nutils .

flow-over-heated-plate/solid-nutils/run.sh

@@ -1,7 +1,5 @@
 #!/bin/bash
+set -e -u
 
-# Solid participant
-
-# Run
 python3 solid.py
 

flow-over-heated-plate/solid-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

flow-over-heated-plate/solid-openfoam/run.sh

@@ -1,34 +1,7 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    		    		# Run from this directory
-. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
-# Fluid participant
-# Run this script in one terminal and the "runSolid" script in another terminal.
-# These scripts present how the two participants would be started manually.
-# Alternatively, you may execute the "Allrun" script in one terminal.
-# Run this script with "-parallel" for parallel simulations
-# The script "Allclean" cleans-up the result and log files.
-# 1 for true, 0 for false
+#!/bin/sh
+set -e -u
 
-parallel=0
-if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-rm -rfv 0/
-cp -r 0.orig/ 0/
 blockMesh
-checkMesh
 touch solid-openfoam.foam
 
-solver=$(getApplication)
-procs=$(getNumberOfProcessors)
-if [ $parallel -eq 1 ]; then
-    decomposePar -force
-    mpirun -np $procs $solver -parallel
-    reconstructPar
-else
-    $solver
-fi
-
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"

heat-exchanger/README.md

@@ -9,7 +9,7 @@ summary: Tutorial for a shell-and-tube heat exchanger, using OpenFOAM and Calcul
 
 This tutorial describes how to run a conjugate heat transfer simulation with two separate OpenFOAM solvers and CalculiX. The files for this tutorial are located in this repository (directory CHT/heat_exchanger).
 
-This tutorial is based on [a case](https://www.simscale.com/projects/cheunglucia/heat_exchanger_-_cht_simulation/) prepared with [SimScale](https://www.simscale.com/) by [Lucia Cheung Yau](https://github.com/ludcila) for her [Master's Thesis](https://www5.in.tum.de/pub/Cheung2016_Thesis.pdf). It works with OpenFOAM 5.0 and CalculiX 2.12, but newer minor versions should work as well.
+This tutorial is based on [a case](https://www.simscale.com/projects/cheunglucia/heat_exchanger_-_cht_simulation/) prepared with [SimScale](https://www.simscale.com/) by [Lucia Cheung Yau](https://github.com/ludcila) for her [Master's Thesis](https://www5.in.tum.de/pub/Cheung2016_Thesis.pdf).
 
 {% include note.html content="Since the already prepared case contains mesh files of approx. 50MB in size, we host these files outside of the repository and you can download and extract them automatically in the appropriate locations by running the Download_meshes script. We plan to integrate the preparation part in this tutorial in the future." %}
 
@@ -32,7 +32,7 @@ We define the participants `Inner-Fluid`, `Solid`, and `Outer-Fluid` and two int
 
 ## Running the Simulation
 
-Before starting the simulation for the first time you need to download the mesh files and copy them into the appropriate location. The shell script `./Download_meshes` will handle these things automatically. Afterwards, the simulation setup is ready to run.
+Before starting the simulation for the first time you need to download the mesh files and copy them into the appropriate location. The shell script `./download-meshes.sh` will handle these things automatically. Afterwards, the simulation setup is ready to run.
 
 In order to run the coupled simulation, you can simply step into the participant directories and execute`./run.sh` for run (or `./run.sh -parallel`) for a parallel run. The simulation will need approximately one hour on a modern laptop to end (t=500). Before repeating the simulation, you can use the `clean.sh` script to clean-up any previous results and log files.
 

heat-exchanger/Download_meshes → heat-exchanger/download-meshes.sh

@@ -1,5 +1,4 @@
 #!/bin/sh
-cd ${0%/*} || exit 1    # Run from this directory
 
 echo "This tutorial is based on a case prepared with SimScale."
 echo "Since the mesh files are several MB large, we don't store them in the Git repository."
@@ -14,8 +13,10 @@ sed -i 's/Solid/\./g' solid-calculix/solid.inp
 
 echo "Downloading and extracting the Inner-Fluid mesh..."
 wget -nv -O - https://syncandshare.lrz.de/dl/fiNsYGC1DKzgio4jS5NhsXg7/polyMesh.org.tar.gz | tar -xzv -C fluid-inner-openfoam/constant
+mv fluid-inner-openfoam/constant/polyMesh.org fluid-inner-openfoam/constant/polyMesh
 
 echo "Downloading and extracting the Outer-Fluid mesh..."
 wget -nv -O - https://syncandshare.lrz.de/dl/fiEZRQ8rcVWRkoyZvANim1R1/polyMesh.org.tar.gz | tar -xzv -C fluid-outer-openfoam/constant
+mv fluid-outer-openfoam/constant/polyMesh.org fluid-outer-openfoam/constant/polyMesh
 
 echo "Completed."

heat-exchanger/fluid-inner-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

heat-exchanger/fluid-inner-openfoam/constant/.gitignore

@@ -0,0 +1 @@
+polyMesh/

heat-exchanger/fluid-inner-openfoam/run.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+set -e -u
+
+touch fluid-inner-openfoam.foam
+
+../../tools/run-openfoam.sh "$@"

heat-exchanger/fluid-inner-openfoam/system/controlDict

@@ -4,15 +4,15 @@ FoamFile {
     object controlDict;
     format ascii;
 }
-application chtMultiRegionSimpleFoam;
+application buoyantSimpleFoam;
 startFrom startTime;
 stopAt endTime;
 writeFormat ascii;
 writePrecision 12;
 writeCompression on;
 timeFormat general;
 timePrecision 12;
-runTimeModifiable yes;
+runTimeModifiable false;
 deltaT 1;
 startTime 0.0;
 writeInterval 50;

heat-exchanger/fluid-outer-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

heat-exchanger/fluid-outer-openfoam/constant/.gitignore

@@ -0,0 +1 @@
+polyMesh/

heat-exchanger/fluid-outer-openfoam/run.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+set -e -u
+
+touch fluid-outer-openfoam.foam
+
+../../tools/run-openfoam.sh "$@"

heat-exchanger/fluid-outer-openfoam/system/controlDict

@@ -4,15 +4,15 @@ FoamFile {
     object controlDict;
     format ascii;
 }
-application chtMultiRegionSimpleFoam;
+application buoyantSimpleFoam;
 startFrom startTime;
 stopAt endTime;
 writeFormat ascii;
 writePrecision 12;
 writeCompression on;
 timeFormat general;
 timePrecision 12;
-runTimeModifiable yes;
+runTimeModifiable false;
 deltaT 1;
 startTime 0.0;
 writeInterval 50;

heat-exchanger/precice-config.xml

@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8" ?>
+<?xml version="1.0" ?>
 <precice-configuration>
   <log>
     <sink

heat-exchanger/solid-calculix/.gitignore

@@ -0,0 +1,10 @@
+# Files distributed separately, downloaded via download-meshes.sh
+adiabatic.dfl
+all.msh
+inner-interface.flm
+inner-interface.nam
+inner-interface.sur
+outer-interface.flm
+outer-interface.nam
+outer-interface.sur
+solid.inp

heat-exchanger/solid-calculix/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_calculix .
+clean_calculix .

heat-exchanger/solid-calculix/run.sh

@@ -1,21 +1,11 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    # Run from this directory
-
-# This script prepares and runs all the participants in one terminal,
-# forwarding the solvers' output to log files.
-# You need to first download the mesh files separately using the Download_meshes script.
-# The script "Allclean" cleans-up the result and log files.
+#!/bin/sh
+set -e -u
 
 if [ ! -f all.msh ]; then
     echo "Mesh files not found. Use the Download_meshes script to download them."
     exit
 fi
 
-Participant="Solid"
-Solver="ccx_preCICE"
-
-# Run and get the process id
-echo "Starting the ${Participant} participant..."
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
-${Solver} -i solid -precice-participant ${Participant}
+ccx_preCICE -i solid -precice-participant Solid

multiple-perpendicular-flaps/fluid-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

multiple-perpendicular-flaps/fluid-openfoam/run.sh

@@ -1,43 +1,7 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    		    # Run from this directory
-. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
+#!/bin/sh
+set -e -u
 
-# Fluid participant
-
-# Run this script in one terminal and the execute the runSolid1 and runSolid2 in separate terminals.
-# These scripts present how the three participants would be started manually.
-
-# Run this script with "-parallel" for parallel simulations
-
-# The script "Allclean" cleans-up the result and log files.
-
-# 1 for true, 0 for false
-parallel=0
-if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-
-rm -rfv 0/
-cp -r 0.orig/ 0/
-blockMesh 
-checkMesh
+blockMesh
 touch fluid-openfoam.foam
 
-# Run
-solver=$(getApplication)
-procs=$(getNumberOfProcessors)
-if [ $parallel -eq 1 ]; then
-    decomposePar -force
-    mpirun -np $procs $solver -parallel
-    reconstructPar
-else
-    $solver
-fi
-
-# Workaround for issue #26 (OF-adapter, relevant for OF .com versions) 
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
-
-echo ""
-echo "### NOTE ### Make sure to use the correct solver for your OpenFOAM version! (pimpleFoam for OpenFOAM v1806, OpenFOAM 6, or newer, vs pimpleDyMFoam for older) You may change this in your Fluid/system/controlDict file, if needed."
+../../tools/run-openfoam.sh "$@"

multiple-perpendicular-flaps/solid-left-dealii/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_dealii .
+clean_dealii .

multiple-perpendicular-flaps/solid-right-dealii/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_dealii .
+clean_dealii .

partitioned-elastic-beam/dirichlet-calculix/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_calculix .
+clean_calculix .

partitioned-elastic-beam/dirichlet-calculix/run.sh

@@ -1,13 +1,6 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    # Run from this directory
+#!/bin/sh
+set -e -u
 
-# This script prepares and runs the CalculiX solver
-
-# =============== Participant: Solid ===========================
-Solver="ccx_preCICE"
-
-    # Run and get the process id
-    echo "Starting the CalculiX..."
-    export OMP_NUM_THREADS=1
-    export CCX_NPROC_EQUATION_SOLVER=1
-    ${Solver} -i beam1 -precice-participant Calculix1 
+export OMP_NUM_THREADS=1
+export CCX_NPROC_EQUATION_SOLVER=1
+ccx_preCICE -i beam1 -precice-participant Calculix1

partitioned-elastic-beam/neumann-calculix/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_calculix .
+clean_calculix .

partitioned-elastic-beam/neumann-calculix/run.sh

@@ -1,13 +1,6 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    # Run from this directory
+#!/bin/sh
+set -e -u
 
-# This script prepares and runs the CalculiX solver
-
-# =============== Participant: Solid ===========================
-Solver="ccx_preCICE"
-
-    # Run and get the process id
-    echo "Starting the CalculiX..."
-    export OMP_NUM_THREADS=1
-    export CCX_NPROC_EQUATION_SOLVER=1
-    ${Solver} -i beam2 -precice-participant Calculix2
+export OMP_NUM_THREADS=1
+export CCX_NPROC_EQUATION_SOLVER=1
+ccx_preCICE -i beam2 -precice-participant Calculix2

partitioned-heat-conduction-complex/fenics/clean.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+set -e -u
+
+. ../../tools/cleaning-tools.sh
+
+clean_fenics .

partitioned-heat-conduction-complex/fenics/run.sh

@@ -0,0 +1,16 @@
+#!/bin/sh
+set -e -u
+
+while getopts ":dn" opt; do
+  case ${opt} in
+  d)
+    python3 heat.py -d --error-tol 10e-3
+    ;;
+  n)
+    python3 heat.py -n --error-tol 10e-3
+    ;;
+  \?)
+    echo "Usage: cmd [-d] [-n]"
+    ;;
+  esac
+done

partitioned-heat-conduction/fenics/.gitignore

@@ -1,7 +1,2 @@
-*.txt
 venv
-.idea
 *.pyc
-out
-*.log
-*events.json

partitioned-heat-conduction/fenics/clean.sh

@@ -3,6 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-rm -rf out 
-rm -f *.log
-rm -f *-events.json
+clean_fenics .

partitioned-heat-conduction/fenics/run.sh

@@ -1,11 +1,16 @@
+#!/bin/sh
+set -e -u
+
 while getopts ":dn" opt; do
   case ${opt} in
-    d ) python3 heat.py -d --error-tol 10e-3
-      ;;
-    n ) python3 heat.py -n --error-tol 10e-3
-      ;;
-    \? ) echo "Usage: cmd [-d] [-n]"
-      ;;
+  d)
+    python3 heat.py -d --error-tol 10e-3
+    ;;
+  n)
+    python3 heat.py -n --error-tol 10e-3
+    ;;
+  \?)
+    echo "Usage: cmd [-d] [-n]"
+    ;;
   esac
 done
-

partitioned-heat-conduction/nutils/clean.sh

@@ -3,7 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-rm -f Dirichlet-*.vtk
-rm -f Neumann-*.vtk
-rm -f *.log
-rm -f *-events.json
+clean_nutils

partitioned-heat-conduction/nutils/run.sh

@@ -1,13 +1,18 @@
+#!/bin/sh
+set -e -u
+
 while getopts ":dn" opt; do
   case ${opt} in
-    d ) rm -rf Dirichlet-*.vtk
-        python3 heat.py --side=Dirichlet
-      ;;
-    n ) rm -rf Neumann-*.vtk
-	python3 heat.py --side=Neumann
-      ;;
-    \? ) echo "Usage: cmd [-d] [-n]"
-      ;;
+  d)
+    rm -rf Dirichlet-*.vtk
+    python3 heat.py --side=Dirichlet
+    ;;
+  n)
+    rm -rf Neumann-*.vtk
+    python3 heat.py --side=Neumann
+    ;;
+  \?)
+    echo "Usage: cmd [-d] [-n]"
+    ;;
   esac
 done
-

perpendicular-flap/fluid-nutils/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_nutils .
+clean_nutils .

perpendicular-flap/fluid-nutils/run.sh

@@ -1,7 +1,4 @@
-#!/bin/bash
+#!/bin/sh
+set -e -u
 
-# Solid participant
-
-# Run
 python3 nsale.py
-

perpendicular-flap/fluid-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

perpendicular-flap/fluid-openfoam/run.sh

@@ -1,40 +1,7 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    		    		# Run from this directory
-. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
+#!/bin/sh
+set -e -u
 
-# Fluid participant
-
-# Run this script in one terminal in order to start this participant.
-# Run this script with "-parallel" for parallel simulations
-
-# 1 for true, 0 for false
-parallel=0
-if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-
-rm -rfv 0/
-cp -r 0.orig/ 0/
 blockMesh
-checkMesh
 touch fluid-openfoam.foam
 
-# Run
-solver=$(getApplication)
-procs=$(getNumberOfProcessors)
-
-if [ $parallel -eq 1 ]; then
-    decomposePar -force
-    mpirun -np $procs $solver -parallel
-    reconstructPar
-else
-    $solver
-fi
-
-# Workaround for issue #26
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
-
-echo ""
-echo "### NOTE ### Make sure to use the correct solver for your OpenFOAM version! (pimpleFoam for OpenFOAM v1806, OpenFOAM 6, or newer, vs pimpleDyMFoam for older) You may change this in your Fluid/system/controlDict file, if needed."
+../../tools/run-openfoam.sh "$@"

perpendicular-flap/fluid-su2/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_su2 .
-rm -fv fluid-su2.log

perpendicular-flap/fluid-su2/run.sh

@@ -1,25 +1,8 @@
-#!/bin/bash
+#!/bin/sh
+set -e -u
 
-# Fluid participant
-
-# Run this script in one terminal and the "runSolid" script in another terminal.
-# These scripts present how the two participants would be started manually.
-# Alternatively, you may execute the "Allrun" script in one terminal.
-
-# Run this script with "-parallel" for parallel simulations
-
-# The script "Allclean" cleans-up the result and log files.
-
-# 1 for true, 0 for false
-parallel=0
 if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-
-if [ $parallel -eq 1 ]; then
-    mpirun -n 2 SU2_CFD euler_config_coupled.cfg 2>&1 | tee fluid-su2.log
+    mpirun -n 2 SU2_CFD euler_config_coupled.cfg
 else
-    SU2_CFD euler_config_coupled.cfg 2>&1 | tee fluid-su2.log
+    SU2_CFD euler_config_coupled.cfg
 fi

perpendicular-flap/solid-calculix/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_calculix .
-rm -fv Solid.log

perpendicular-flap/solid-calculix/run.sh

@@ -1,14 +1,4 @@
-#!/bin/bash
+#!/bin/sh
+set -e -u
 
-# Solid participant
-
-# Run this script in one terminal and the "runFluid" script in another terminal.
-# These scripts present how the two participants would be started manually.
-# Alternatively, you may execute the "Allrun" script in one terminal.
-
-# The script "Allclean" cleans-up the result and log files.
-
-echo "Running the Solid participant..."
-
-# Run
-ccx_preCICE -i flap -precice-participant Solid 2>&1 | tee Solid.log
+ccx_preCICE -i flap -precice-participant Solid

perpendicular-flap/solid-dealii/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_dealii .
+clean_dealii .

perpendicular-flap/solid-fenics/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_fenics .
+clean_fenics .

perpendicular-flap/solid-fenics/run.sh

@@ -1,14 +1,4 @@
-#!/bin/bash
+#!/bin/sh
+set -e -u
 
-# Solid participant
-
-# Run this script in one terminal and the "runFluid" script in another terminal.
-# These scripts present how the two participants would be started manually.
-# Alternatively, you may execute the "Allrun" script in one terminal.
-
-# The script "Allclean" cleans-up the result and log files.
-
-echo "Running the Solid participant..."
-
-# Run
-python3 perp-flap.py 2>&1 | tee solid-fenics.log
+python3 perp-flap.py

tools/clean-tutorial-base.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../tools/cleaning-tools.sh
 
-clean_tutorial .
+clean_tutorial .

tools/cleaning-tools.sh

@@ -1,7 +1,8 @@
 #!/bin/sh
 
 error() {
-    echo "Error: $1" >&2; exit 1;
+    echo "Error: $1" >&2
+    exit 1
 }
 
 clean_tutorial() {
@@ -14,7 +15,7 @@ clean_tutorial() {
         for case in */; do
             if [ "${case}" = images/ ]; then
                 continue
-            fi;
+            fi
             (cd "${case}" && ./clean.sh)
         done
     )
@@ -26,12 +27,12 @@ clean_precice_logs() {
         cd "$1"
         echo "---- Cleaning up preCICE logs in $(pwd)"
         rm -fv ./precice-*-iterations.log \
-               ./precice-*-convergence.log \
-               ./precice-*-events.json \
-               ./precice-*-events-summary.log \
-               ./precice-postProcessingInfo.log \
-               ./precice-*-watchpoint-*.log \
-               ./precice-*-watchintegral-*.log
+            ./precice-*-convergence.log \
+            ./precice-*-events.json \
+            ./precice-*-events-summary.log \
+            ./precice-postProcessingInfo.log \
+            ./precice-*-watchpoint-*.log \
+            ./precice-*-watchintegral-*.log
     )
 }
 
@@ -40,7 +41,7 @@ clean_calculix() {
         set -e -u
         cd "$1"
         echo "--- Cleaning up CalculiX case in $(pwd)"
-        rm -fv ./*.cvg ./*.dat ./*.frd ./*.sta ./*.12d spooles.out
+        rm -fv ./*.cvg ./*.dat ./*.frd ./*.sta ./*.12d spooles.out dummy
         clean_precice_logs .
     )
 }
@@ -71,7 +72,7 @@ clean_fenics() {
         set -e -u
         cd "$1"
         echo "--- Cleaning up FEniCS case in $(pwd)"
-        rm -fv ./*.pvd spooles.out FSI-S/*
+        rm -fv ./*.pvd spooles.out out FSI-S/*
         clean_precice_logs .
     )
 }
@@ -81,6 +82,7 @@ clean_nutils() {
         set -e -u
         cd "$1"
         echo "--- Cleaning up Nutils case in $(pwd)"
+        rm -fv ./*.vtk
         clean_precice_logs .
     )
 }
@@ -107,4 +109,4 @@ clean_su2() {
         rm -fv ./restart_flow_*.dat forces_breakdown.dat ./surface_flow_*.csv ./flow_*.vtk ./history_*.vtk
         clean_precice_logs .
     )
-}
+}

tools/openfoam-remove-empty-dirs.sh

@@ -2,24 +2,24 @@
 
 openfoam_remove_empty_dirs() {
 	(
-	set -e -u
-	echo "Looking for any time directories without results (e.g. stray functionObjectProperties files, see openfoam-adapter issue #26 on GitHub)..."
+		set -e -u
+		echo "Looking for any time directories without results (e.g. stray functionObjectProperties files, see openfoam-adapter issue #26 on GitHub)..."
 
-	for f in [0-9]* [0-9]*.[0-9]*; do
-		if ! [ -f "${f}/U" ] && ! [ -f "${f}/T" ]; then
-			rm -rfv "${f}"
-		fi
-	done
-	if [ -d processor0 ]; then
-		for d in processor*; do
-			cd "${d}"
-			for f in [0-9]* [0-9]*.[0-9]*; do
-				if ! [ -f "${f}"/U ] && ! [ -f "${f}"/T ]; then
-					rm -rfv "${f}"
-				fi
-			done
-			cd ..
+		for f in [0-9]* [0-9]*.[0-9]*; do
+			if ! [ -f "${f}/U" ] && ! [ -f "${f}/T" ]; then
+				rm -rfv "${f}"
+			fi
 		done
-	fi
+		if [ -d processor0 ]; then
+			for d in processor*; do
+				cd "${d}"
+				for f in [0-9]* [0-9]*.[0-9]*; do
+					if ! [ -f "${f}"/U ] && ! [ -f "${f}"/T ]; then
+						rm -rfv "${f}"
+					fi
+				done
+				cd ..
+			done
+		fi
 	)
 }

tools/run-dealii.sh

@@ -3,35 +3,34 @@ set -e -u
 
 EXE=""
 
-for i in "$@"
-do
-case $i in
-    -e=*|--exec=*)
-    EXE="${i#*=}"
-    shift # past argument=value
-    ;;
+for i in "$@"; do
+    case $i in
+    -e=* | --exec=*)
+        EXE="${i#*=}"
+        shift # past argument=value
+        ;;
     *)
-      # unknown option
-    ;;
-esac
+        # unknown option
+        ;;
+    esac
 done
 
 # If the executable has been defined
-if [ -n "${EXE}"  ]; then
+if [ -n "${EXE}" ]; then
     "${EXE}" parameters.prm
-    exit 0;
+    exit 0
 fi
 
 EXE="elasticity"
 # If it is in the global path
 if [ -n "$(command -v "${EXE}")" ]; then
-   "${EXE}" parameters.prm
-   exit 0;
+    "${EXE}" parameters.prm
+    exit 0
 fi
 
 # If it has been copied to the local directory
 if test -f "elasticity"; then
     ./"${EXE}" parameters.prm
-    else
+else
     echo "Unable to find the executable ${EXE}. Either specify the executable explicitly (-e=/path/to/elasticity) or make it discoverable at runtime (e.g. export PATH)"
 fi

tools/run-openfoam.sh

@@ -0,0 +1,17 @@
+#!/bin/sh
+set -e # Not setting -u as it gets triggered by the OpenFOAM RunFunctions
+
+# OpenFOAM run functions: getApplication, getNumberOfProcessors
+# shellcheck disable=SC1090 # This is an OpenFOAM file which we don't need to check
+. "${WM_PROJECT_DIR}/bin/tools/RunFunctions"
+solver=$(getApplication)
+if [ "${1:-}" = "-parallel" ]; then
+    procs=$(getNumberOfProcessors)
+    decomposePar -force
+    mpirun -np "${procs}" "${solver}" -parallel
+    reconstructPar
+else
+    ${solver}
+fi
+
+. openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs

turek-hron-fsi3/fluid-openfoam/clean.sh

@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -rfv ./0/ # in run.sh,0.orig/ is copied to 0/

turek-hron-fsi3/fluid-openfoam/run.sh

@@ -1,41 +1,7 @@
-#!/bin/bash
-cd ${0%/*} || exit 1    		    		# Run from this directory
-. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
+#!/bin/sh
+set -e -u
 
-# Fluid participant
-
-# Run this script in one terminal and the execute the coupled_elasto_dynamics bindary 
-# in another terminal.
-# These scripts present how the two participants would be started manually.
-
-# Run this script with "-parallel" for parallel simulations
-
-# The script "Allclean" cleans-up the result and log files.
-
-# 1 for true, 0 for false
-parallel=0
-if [ "$1" = "-parallel" ]; then
-    parallel=1
-fi
-
-echo "Preparing and running the Fluid participant..."
-
-rm -rfv 0/
-cp -r 0.orig/ 0/
 blockMesh
-checkMesh
 touch fluid-openfoam.foam
 
-# Run
-solver=$(getApplication)
-procs=$(getNumberOfProcessors)
-if [ $parallel -eq 1 ]; then
-    decomposePar -force
-    mpirun -np $procs $solver -parallel
-    reconstructPar
-else
-    $solver
-fi
-
-# Workaround for issue #26 (OF-adapter, relevant for OF .com versions) 
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"

turek-hron-fsi3/solid-dealii/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_dealii .
+clean_dealii .

turek-hron-fsi3/solid-fenics/clean.sh

@@ -3,4 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-clean_fenics .
+clean_fenics .

turek-hron-fsi3/solid-fenics/run.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+set -e -u
+
+python3 cyl-flap.py