From 200a2c81e9383c76b9188566576bece64f04e3ab Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 12 Mar 2024 09:09:40 +0100
Subject: [PATCH 01/17] Add automatic logging in Quickstart

---
 quickstart/fluid-openfoam/clean.sh |  1 +
 quickstart/fluid-openfoam/run.sh   | 10 ++++++----
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/quickstart/fluid-openfoam/clean.sh b/quickstart/fluid-openfoam/clean.sh
index c31d9fc76..fd7d42349 100755
--- a/quickstart/fluid-openfoam/clean.sh
+++ b/quickstart/fluid-openfoam/clean.sh
@@ -4,3 +4,4 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
+rm -fv fluid-openfoam.log
diff --git a/quickstart/fluid-openfoam/run.sh b/quickstart/fluid-openfoam/run.sh
index c191b9e48..1f49b73ed 100755
--- a/quickstart/fluid-openfoam/run.sh
+++ b/quickstart/fluid-openfoam/run.sh
@@ -1,8 +1,10 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-openfoam.foam
+CASENAME=fluid-openfoam
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+blockMesh | tee ${CASENAME}.log 2>&1
+touch ${CASENAME}.foam
+
+../../tools/run-openfoam.sh "$@"  | tee --append ${CASENAME}.log 2>&1
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs | tee --append ${CASENAME}.log 2>&1

From 32f7fc3a747069d398d83e73de79e9234632f110 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 12 Mar 2024 18:40:52 +0100
Subject: [PATCH 02/17] Generalize cleaning

---
 quickstart/fluid-openfoam/clean.sh |  1 -
 tools/cleaning-tools.sh            | 18 ++++++++++++++++++
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/quickstart/fluid-openfoam/clean.sh b/quickstart/fluid-openfoam/clean.sh
index fd7d42349..c31d9fc76 100755
--- a/quickstart/fluid-openfoam/clean.sh
+++ b/quickstart/fluid-openfoam/clean.sh
@@ -4,4 +4,3 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_openfoam .
-rm -fv fluid-openfoam.log
diff --git a/tools/cleaning-tools.sh b/tools/cleaning-tools.sh
index 7038b2219..c215ac488 100755
--- a/tools/cleaning-tools.sh
+++ b/tools/cleaning-tools.sh
@@ -44,6 +44,16 @@ clean_precice_logs() {
     )
 }
 
+clean_case_logs() {
+    (
+        set -e -u
+        cd "$1"
+        echo "- Cleaning up general case logs in $(pwd)"
+        CASENAME="$(readlink -f "$0" | xargs dirname | xargs basename)"
+        rm -fv "./$CASENAME.log"
+    )
+}
+
 clean_calculix() {
     (
         set -e -u
@@ -54,6 +64,7 @@ clean_calculix() {
         rm -fv ./*.eig
         rm -fv ./*.vtk
         clean_precice_logs .
+        clean_case_logs .
     )
 }
 
@@ -65,6 +76,7 @@ clean_codeaster() {
         rm -fv ./*.mess ./*.resu ./*.rmed
         rm -rfv ./REPE_OUT/*
         clean_precice_logs .
+        clean_case_logs .
     )
 }
 
@@ -75,6 +87,7 @@ clean_dealii() {
         echo "- Cleaning up deal.II case in $(pwd)"
         rm -rfv ./dealii-output/
         clean_precice_logs .
+        clean_case_logs .
     )
 }
 
@@ -85,6 +98,7 @@ clean_fenics() {
         echo "- Cleaning up FEniCS case in $(pwd)"
         rm -rfv ./output/
         clean_precice_logs .
+        clean_case_logs .
     )
 }
 
@@ -95,6 +109,7 @@ clean_nutils() {
         echo "- Cleaning up Nutils case in $(pwd)"
         rm -fv ./*.vtk
         clean_precice_logs .
+        clean_case_logs .
     )
 }
 
@@ -110,6 +125,7 @@ clean_openfoam() {
             rm -rfv 0/uniform/functionObjects/functionObjectProperties history
         fi
         clean_precice_logs .
+        clean_case_logs .
     )
 }
 
@@ -120,6 +136,7 @@ clean_su2() {
         echo "- Cleaning up SU2 case in $(pwd)"
         rm -fv ./restart_flow_*.dat forces_breakdown.dat ./surface_flow_*.csv ./flow_*.vtk ./history_*.vtk
         clean_precice_logs .
+        clean_case_logs .
     )
 }
 
@@ -143,6 +160,7 @@ clean_dune() {
         rm -fv ./*.vtu
         rm -rfv ./output/
         clean_precice_logs .
+        clean_case_logs .
     )
 }
 

From 7d86a029a6d576c489ce9c10e8be6244cc45a156 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 12 Mar 2024 18:41:39 +0100
Subject: [PATCH 03/17] Automatically deduce CASENAME

---
 quickstart/fluid-openfoam/run.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/quickstart/fluid-openfoam/run.sh b/quickstart/fluid-openfoam/run.sh
index 1f49b73ed..936a2b528 100755
--- a/quickstart/fluid-openfoam/run.sh
+++ b/quickstart/fluid-openfoam/run.sh
@@ -1,10 +1,10 @@
 #!/bin/sh
 set -e -u
 
-CASENAME=fluid-openfoam
+CASENAME="$(readlink -f "$0" | xargs dirname | xargs basename)"
 
-blockMesh | tee ${CASENAME}.log 2>&1
-touch ${CASENAME}.foam
+blockMesh | tee "$CASENAME.log" 2>&1
+touch "$CASENAME.foam"
 
-../../tools/run-openfoam.sh "$@"  | tee --append ${CASENAME}.log 2>&1
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs | tee --append ${CASENAME}.log 2>&1
+../../tools/run-openfoam.sh "$@"  | tee --append "$CASENAME.log" 2>&1
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs | tee --append "$CASENAME.log" 2>&1

From 52cfd4756fe4c8095d0306b76314d1171df90259 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 12 Mar 2024 18:47:35 +0100
Subject: [PATCH 04/17] Move CASENAME deduction to tools/get-case-name.sh

---
 quickstart/fluid-openfoam/run.sh | 2 +-
 tools/get-case-name.sh           | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 tools/get-case-name.sh

diff --git a/quickstart/fluid-openfoam/run.sh b/quickstart/fluid-openfoam/run.sh
index 936a2b528..d84db9b76 100755
--- a/quickstart/fluid-openfoam/run.sh
+++ b/quickstart/fluid-openfoam/run.sh
@@ -1,7 +1,7 @@
 #!/bin/sh
 set -e -u
 
-CASENAME="$(readlink -f "$0" | xargs dirname | xargs basename)"
+. ../../tools/get-case-name.sh
 
 blockMesh | tee "$CASENAME.log" 2>&1
 touch "$CASENAME.foam"
diff --git a/tools/get-case-name.sh b/tools/get-case-name.sh
new file mode 100644
index 000000000..4b079cca9
--- /dev/null
+++ b/tools/get-case-name.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+set -e -u
+
+CASENAME="$(readlink -f "$0" | xargs dirname | xargs basename)"
+export CASENAME

From d7312de5090ee5ef3bd117a7b3588f67764912ba Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 12 Mar 2024 19:09:16 +0100
Subject: [PATCH 05/17] Simplify logging, add date at the begin/end

---
 quickstart/fluid-openfoam/run.sh   | 10 ++++++----
 tools/{get-case-name.sh => log.sh} |  6 ++++++
 2 files changed, 12 insertions(+), 4 deletions(-)
 rename tools/{get-case-name.sh => log.sh} (55%)

diff --git a/quickstart/fluid-openfoam/run.sh b/quickstart/fluid-openfoam/run.sh
index d84db9b76..be075dfd2 100755
--- a/quickstart/fluid-openfoam/run.sh
+++ b/quickstart/fluid-openfoam/run.sh
@@ -1,10 +1,12 @@
 #!/bin/sh
 set -e -u
 
-. ../../tools/get-case-name.sh
+. ../../tools/log.sh
 
-blockMesh | tee "$CASENAME.log" 2>&1
+log blockMesh
 touch "$CASENAME.foam"
 
-../../tools/run-openfoam.sh "$@"  | tee --append "$CASENAME.log" 2>&1
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs | tee --append "$CASENAME.log" 2>&1
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+
+log date
diff --git a/tools/get-case-name.sh b/tools/log.sh
similarity index 55%
rename from tools/get-case-name.sh
rename to tools/log.sh
index 4b079cca9..c957f3a00 100644
--- a/tools/get-case-name.sh
+++ b/tools/log.sh
@@ -3,3 +3,9 @@ set -e -u
 
 CASENAME="$(readlink -f "$0" | xargs dirname | xargs basename)"
 export CASENAME
+
+date > "$CASENAME.log"
+
+log() {
+    "$@" | tee --append "$CASENAME.log" 2>&1
+}

From 0c50f48e28539b3276e663bafe3e3a77390e99ca Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 15 Mar 2024 08:01:38 +0100
Subject: [PATCH 06/17] Add formatted start, end, duration

---
 quickstart/fluid-openfoam/run.sh |  2 +-
 tools/log.sh                     | 12 +++++++++++-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/quickstart/fluid-openfoam/run.sh b/quickstart/fluid-openfoam/run.sh
index be075dfd2..8f4fb1c36 100755
--- a/quickstart/fluid-openfoam/run.sh
+++ b/quickstart/fluid-openfoam/run.sh
@@ -9,4 +9,4 @@ touch "$CASENAME.foam"
 log ../../tools/run-openfoam.sh "$@"
 . ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
-log date
+close_log
diff --git a/tools/log.sh b/tools/log.sh
index c957f3a00..7dfb29497 100644
--- a/tools/log.sh
+++ b/tools/log.sh
@@ -4,8 +4,18 @@ set -e -u
 CASENAME="$(readlink -f "$0" | xargs dirname | xargs basename)"
 export CASENAME
 
-date > "$CASENAME.log"
+STARTDATE="$(date --rfc-email)"
+STARTTIME="$(date +%s)"
+echo "Started on: $STARTDATE" | tee "$CASENAME.log" 2>&1
 
 log() {
     "$@" | tee --append "$CASENAME.log" 2>&1
 }
+
+close_log() {
+    echo "Started on:  $STARTDATE" | tee --append "$CASENAME.log" 2>&1
+    ENDDATE="$(date --rfc-email)"
+    ENDTIME="$(date +%s)"
+    echo "Finished on: $ENDDATE" | tee --append "$CASENAME.log" 2>&1
+    echo "Duration:    $((ENDTIME-STARTTIME)) seconds" | tee --append "$CASENAME.log" 2>&1
+}

From 7c9ca19e31f922d836e9b55720a28c032fdd0dad Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Sat, 16 Mar 2024 06:53:47 +0100
Subject: [PATCH 07/17] Switch from readlink to pwd, move .foam generation to
 run-openfoam.sh

---
 quickstart/fluid-openfoam/run.sh | 1 -
 tools/log.sh                     | 2 +-
 tools/run-openfoam.sh            | 4 ++++
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/quickstart/fluid-openfoam/run.sh b/quickstart/fluid-openfoam/run.sh
index 8f4fb1c36..d0f8685db 100755
--- a/quickstart/fluid-openfoam/run.sh
+++ b/quickstart/fluid-openfoam/run.sh
@@ -4,7 +4,6 @@ set -e -u
 . ../../tools/log.sh
 
 log blockMesh
-touch "$CASENAME.foam"
 
 log ../../tools/run-openfoam.sh "$@"
 . ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
diff --git a/tools/log.sh b/tools/log.sh
index 7dfb29497..3a1c91dfe 100644
--- a/tools/log.sh
+++ b/tools/log.sh
@@ -1,7 +1,7 @@
 #!/bin/sh
 set -e -u
 
-CASENAME="$(readlink -f "$0" | xargs dirname | xargs basename)"
+CASENAME="$(pwd | xargs basename)"
 export CASENAME
 
 STARTDATE="$(date --rfc-email)"
diff --git a/tools/run-openfoam.sh b/tools/run-openfoam.sh
index e0667aa16..e3bf2c920 100755
--- a/tools/run-openfoam.sh
+++ b/tools/run-openfoam.sh
@@ -1,6 +1,10 @@
 #!/bin/sh
 set -e # Not setting -u as it gets triggered by the OpenFOAM RunFunctions
 
+# Prepare an (intentionally empty) .foam file for the ParaView OpenFOAM reader
+CASENAME="$(pwd | xargs basename)"
+touch "$CASENAME.foam"
+
 # 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"

From 0cb426e3c9c481655cd5d3fd06d9d4485b3b54d3 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Sat, 16 Mar 2024 06:56:20 +0100
Subject: [PATCH 08/17] Log quickstart/solid-cpp

---
 quickstart/solid-cpp/run.sh | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/quickstart/solid-cpp/run.sh b/quickstart/solid-cpp/run.sh
index 60b4fd3eb..19895306a 100755
--- a/quickstart/solid-cpp/run.sh
+++ b/quickstart/solid-cpp/run.sh
@@ -1,9 +1,13 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 solver=./rigid_body_solver
 if [ -f "${solver}" ]; then
-    ${solver}
+    log ${solver}
 else 
-    echo "Unable to locate the executable ${solver}. Have a look at the README for building instructions."
+    log echo "Unable to locate the executable ${solver}. Have a look at the README for building instructions."
 fi
+
+close_log

From 99a2fb3985dc0d0c64d6b0786ecd8e3a038e56ca Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Sat, 16 Mar 2024 07:54:03 +0100
Subject: [PATCH 09/17] Add logging to more run scripts

---
 breaking-dam-2d/fluid-openfoam/run.sh             | 15 +++++++++------
 breaking-dam-2d/solid-calculix/run.sh             |  6 +++++-
 channel-transport-reaction/chemical-fenics/run.sh |  6 +++++-
 channel-transport-reaction/clean-tutorial.sh      | 11 +++++++++++
 channel-transport-reaction/fluid-fenics/run.sh    |  6 +++++-
 channel-transport/fluid-nutils/run.sh             | 12 ++++++++----
 channel-transport/fluid-openfoam/run.sh           | 11 +++++++----
 channel-transport/transport-nutils/run.sh         | 12 ++++++++----
 elastic-tube-1d/fluid-cpp/run.sh                  | 12 ++++++++----
 elastic-tube-1d/fluid-python/run.sh               |  6 +++++-
 elastic-tube-1d/fluid-rust/run.sh                 |  6 +++++-
 elastic-tube-1d/solid-cpp/run.sh                  | 12 ++++++++----
 elastic-tube-1d/solid-python/run.sh               |  6 +++++-
 elastic-tube-1d/solid-rust/run.sh                 |  6 +++++-
 elastic-tube-3d/fluid-openfoam/run.sh             | 11 +++++++----
 elastic-tube-3d/solid-calculix/run.sh             |  6 +++++-
 quickstart/fluid-openfoam/run.sh                  |  3 ++-
 tools/log.sh                                      |  2 +-
 18 files changed, 109 insertions(+), 40 deletions(-)
 create mode 100755 channel-transport-reaction/clean-tutorial.sh

diff --git a/breaking-dam-2d/fluid-openfoam/run.sh b/breaking-dam-2d/fluid-openfoam/run.sh
index 33f5cdb23..bb9aebf15 100755
--- a/breaking-dam-2d/fluid-openfoam/run.sh
+++ b/breaking-dam-2d/fluid-openfoam/run.sh
@@ -1,10 +1,13 @@
 #!/bin/sh
 set -e -u
 
-cp 0/alpha.water_orig 0/alpha.water
-blockMesh
-setFields
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log cp 0/alpha.water_orig 0/alpha.water
+log blockMesh
+log setFields
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/breaking-dam-2d/solid-calculix/run.sh b/breaking-dam-2d/solid-calculix/run.sh
index 0cc701cc5..a12ac5937 100755
--- a/breaking-dam-2d/solid-calculix/run.sh
+++ b/breaking-dam-2d/solid-calculix/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-ccx_preCICE -i flap -precice-participant Solid
+. ../../tools/log.sh
+
+log ccx_preCICE -i flap -precice-participant Solid
+
+close_log
diff --git a/channel-transport-reaction/chemical-fenics/run.sh b/channel-transport-reaction/chemical-fenics/run.sh
index 9ee75e87c..ab6e02f37 100755
--- a/channel-transport-reaction/chemical-fenics/run.sh
+++ b/channel-transport-reaction/chemical-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 chemical-reaction-advection-diffusion.py
+. ../../tools/log.sh
+
+log python3 chemical-reaction-advection-diffusion.py
+
+close_log
diff --git a/channel-transport-reaction/clean-tutorial.sh b/channel-transport-reaction/clean-tutorial.sh
new file mode 100755
index 000000000..88f60e8c6
--- /dev/null
+++ b/channel-transport-reaction/clean-tutorial.sh
@@ -0,0 +1,11 @@
+#!/bin/sh
+set -e -u
+
+# shellcheck disable=SC1091
+. ../tools/cleaning-tools.sh
+
+clean_tutorial .
+clean_precice_logs .
+rm -fv ./*.log
+rm -fv ./*.vtu
+
diff --git a/channel-transport-reaction/fluid-fenics/run.sh b/channel-transport-reaction/fluid-fenics/run.sh
index 788f40d13..b17cd285e 100755
--- a/channel-transport-reaction/fluid-fenics/run.sh
+++ b/channel-transport-reaction/fluid-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 fluid.py
+. ../../tools/log.sh
+
+log python3 fluid.py
+
+close_log
diff --git a/channel-transport/fluid-nutils/run.sh b/channel-transport/fluid-nutils/run.sh
index 00b103a23..0e99d59f7 100755
--- a/channel-transport/fluid-nutils/run.sh
+++ b/channel-transport/fluid-nutils/run.sh
@@ -1,7 +1,11 @@
 #!/bin/sh
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-python3 fluid.py
+. ../../tools/log.sh
+
+log python3 -m venv .venv
+log . .venv/bin/activate
+log pip install -r requirements.txt
+log python3 fluid.py
+
+close_log
diff --git a/channel-transport/fluid-openfoam/run.sh b/channel-transport/fluid-openfoam/run.sh
index c191b9e48..864ca8c26 100755
--- a/channel-transport/fluid-openfoam/run.sh
+++ b/channel-transport/fluid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/channel-transport/transport-nutils/run.sh b/channel-transport/transport-nutils/run.sh
index c3048dffd..26bc8f71f 100755
--- a/channel-transport/transport-nutils/run.sh
+++ b/channel-transport/transport-nutils/run.sh
@@ -1,7 +1,11 @@
 #!/bin/sh
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-python3 transport.py
+. ../../tools/log.sh
+
+log python3 -m venv .venv
+log . .venv/bin/activate
+log pip install -r requirements.txt
+log python3 transport.py
+
+close_log
diff --git a/elastic-tube-1d/fluid-cpp/run.sh b/elastic-tube-1d/fluid-cpp/run.sh
index c6be7a9bd..7906d3981 100755
--- a/elastic-tube-1d/fluid-cpp/run.sh
+++ b/elastic-tube-1d/fluid-cpp/run.sh
@@ -1,10 +1,14 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 if [ ! -d build ]; then
-  mkdir build
-  cmake -S . -B build
-  cmake --build build
+  log mkdir build
+  log cmake -S . -B build
+  log cmake --build build
 fi
 
-./build/FluidSolver ../precice-config.xml
+log ./build/FluidSolver ../precice-config.xml
+
+close_log
diff --git a/elastic-tube-1d/fluid-python/run.sh b/elastic-tube-1d/fluid-python/run.sh
index 4272d9b77..36a1ca22b 100755
--- a/elastic-tube-1d/fluid-python/run.sh
+++ b/elastic-tube-1d/fluid-python/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ./FluidSolver.py ../precice-config.xml
+. ../../tools/log.sh
+
+log python3 ./FluidSolver.py ../precice-config.xml
+
+close_log
diff --git a/elastic-tube-1d/fluid-rust/run.sh b/elastic-tube-1d/fluid-rust/run.sh
index 79a022fa3..987cf781c 100755
--- a/elastic-tube-1d/fluid-rust/run.sh
+++ b/elastic-tube-1d/fluid-rust/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-cargo run --release ../precice-config.xml 
+. ../../tools/log.sh
+
+log cargo run --release ../precice-config.xml 
+
+close_log
diff --git a/elastic-tube-1d/solid-cpp/run.sh b/elastic-tube-1d/solid-cpp/run.sh
index 3b85f004b..6708de8c8 100755
--- a/elastic-tube-1d/solid-cpp/run.sh
+++ b/elastic-tube-1d/solid-cpp/run.sh
@@ -1,10 +1,14 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 if [ ! -d build ]; then
-  mkdir build
-  cmake -S . -B build
-  cmake --build build
+  log mkdir build
+  log cmake -S . -B build
+  log cmake --build build
 fi
 
-./build/SolidSolver ../precice-config.xml
+log ./build/SolidSolver ../precice-config.xml
+
+close_log
diff --git a/elastic-tube-1d/solid-python/run.sh b/elastic-tube-1d/solid-python/run.sh
index ad00c6c38..0c4e5dd52 100755
--- a/elastic-tube-1d/solid-python/run.sh
+++ b/elastic-tube-1d/solid-python/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ./SolidSolver.py ../precice-config.xml
+. ../../tools/log.sh
+
+log python3 ./SolidSolver.py ../precice-config.xml
+
+close_log
diff --git a/elastic-tube-1d/solid-rust/run.sh b/elastic-tube-1d/solid-rust/run.sh
index d9103ab27..49305ddf7 100755
--- a/elastic-tube-1d/solid-rust/run.sh
+++ b/elastic-tube-1d/solid-rust/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-cargo run --release ../precice-config.xml
+. ../../tools/log.sh
+
+log cargo run --release ../precice-config.xml
+
+close_log
diff --git a/elastic-tube-3d/fluid-openfoam/run.sh b/elastic-tube-3d/fluid-openfoam/run.sh
index c305d6d9b..5a90867ba 100755
--- a/elastic-tube-3d/fluid-openfoam/run.sh
+++ b/elastic-tube-3d/fluid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-cp -r constant/polyMesh.orig constant/polyMesh
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log cp -r constant/polyMesh.orig constant/polyMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/elastic-tube-3d/solid-calculix/run.sh b/elastic-tube-3d/solid-calculix/run.sh
index 5ebdaf5b2..2676d0c2a 100755
--- a/elastic-tube-3d/solid-calculix/run.sh
+++ b/elastic-tube-3d/solid-calculix/run.sh
@@ -1,6 +1,10 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
-ccx_preCICE -i tube -precice-participant Solid
+log ccx_preCICE -i tube -precice-participant Solid
+
+close_log
diff --git a/quickstart/fluid-openfoam/run.sh b/quickstart/fluid-openfoam/run.sh
index d0f8685db..e8baeb5e0 100755
--- a/quickstart/fluid-openfoam/run.sh
+++ b/quickstart/fluid-openfoam/run.sh
@@ -6,6 +6,7 @@ set -e -u
 log blockMesh
 
 log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
 
 close_log
diff --git a/tools/log.sh b/tools/log.sh
index 3a1c91dfe..8925148d1 100644
--- a/tools/log.sh
+++ b/tools/log.sh
@@ -17,5 +17,5 @@ close_log() {
     ENDDATE="$(date --rfc-email)"
     ENDTIME="$(date +%s)"
     echo "Finished on: $ENDDATE" | tee --append "$CASENAME.log" 2>&1
-    echo "Duration:    $((ENDTIME-STARTTIME)) seconds" | tee --append "$CASENAME.log" 2>&1
+    echo "Duration:    $((ENDTIME-STARTTIME)) seconds (wall-clock time, including time waiting for participants)" | tee --append "$CASENAME.log" 2>&1
 }

From 22971b5df188358d2d804757016f2f18909890d6 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Wed, 20 Mar 2024 08:59:50 +0100
Subject: [PATCH 10/17] Add logging to the rest of the cases

---
 .../controller-fmi/run.sh                     | 22 +++++++-----
 .../fluid-openfoam/run.sh                     | 18 +++++-----
 .../solid-python/run.sh                       |  4 ++-
 .../fluid-openfoam/run.sh                     | 11 +++---
 .../solid-openfoam/run.sh                     | 11 +++---
 .../fluid1-openfoam/run.sh                    | 11 +++---
 .../fluid2-openfoam/run.sh                    | 11 +++---
 .../solid-openfoam/run.sh                     | 11 +++---
 .../fluid-openfoam/run.sh                     | 11 +++---
 .../solid-codeaster/run.sh                    | 16 +++++----
 .../fluid-openfoam/run.sh                     | 11 +++---
 .../solid-calculix/run.sh                     |  8 +++--
 flow-over-heated-plate/fluid-openfoam/run.sh  | 11 +++---
 flow-over-heated-plate/solid-dunefem/run.sh   |  5 ++-
 flow-over-heated-plate/solid-fenics/run.sh    |  6 +++-
 flow-over-heated-plate/solid-nutils/run.sh    | 12 ++++---
 flow-over-heated-plate/solid-openfoam/run.sh  | 11 +++---
 .../fluid-bottom-openfoam/run.sh              | 11 +++---
 .../fluid-top-openfoam/run.sh                 | 11 +++---
 .../solid-calculix/run.sh                     |  8 +++--
 heat-exchanger/fluid-inner-openfoam/run.sh    |  8 +++--
 heat-exchanger/fluid-outer-openfoam/run.sh    |  8 +++--
 heat-exchanger/solid-calculix/run.sh          |  8 +++--
 .../fluid-openfoam/run.sh                     | 11 +++---
 oscillator-overlap/mass-left-python/run.sh    |  6 +++-
 oscillator-overlap/mass-right-python/run.sh   |  6 +++-
 oscillator/fmi/run.sh                         | 34 +++++++++++--------
 oscillator/python/run.sh                      | 14 +++++---
 .../fluid1-openfoam/run.sh                    | 11 +++---
 .../fluid2-openfoam/run.sh                    | 11 +++---
 .../dirichlet-calculix/run.sh                 |  6 +++-
 .../neumann-calculix/run.sh                   |  6 +++-
 .../dirichlet-fenics/run.sh                   |  6 +++-
 .../neumann-fenics/run.sh                     |  6 +++-
 .../nutils/run.sh                             | 22 +++++++-----
 .../left-fenics/run.sh                        |  6 +++-
 .../right-fenics/run.sh                       |  6 +++-
 .../dirichlet-fenics/run.sh                   |  6 +++-
 .../dirichlet-openfoam/run.sh                 | 14 +++++---
 partitioned-heat-conduction/fenicsx/run.sh    | 10 ++++--
 .../neumann-fenics/run.sh                     |  6 +++-
 .../neumann-openfoam/run.sh                   | 13 ++++---
 .../fluid1-openfoam/run.sh                    | 15 ++++----
 .../fluid2-openfoam/run.sh                    | 15 ++++----
 partitioned-pipe-two-phase/monolithic/run.sh  | 15 ++++----
 .../fluid1-openfoam-pimplefoam/run.sh         | 14 ++++----
 .../fluid1-openfoam-sonicliquidfoam/run.sh    | 11 +++---
 .../fluid2-openfoam-pimplefoam/run.sh         | 14 ++++----
 .../fluid2-openfoam-sonicliquidfoam/run.sh    | 11 +++---
 perpendicular-flap/fluid-nutils/run.sh        | 12 ++++---
 perpendicular-flap/fluid-openfoam/run.sh      | 11 +++---
 perpendicular-flap/fluid-su2/run.sh           |  8 +++--
 perpendicular-flap/solid-calculix/run.sh      | 16 +++++----
 perpendicular-flap/solid-dune/run.sh          |  6 +++-
 perpendicular-flap/solid-fenics/run.sh        |  6 +++-
 perpendicular-flap/solid-nutils/run.sh        | 12 ++++---
 perpendicular-flap/solid-openfoam/run.sh      | 13 ++++---
 perpendicular-flap/solid-solids4foam/run.sh   | 11 +++---
 turek-hron-fsi3/fluid-openfoam/run.sh         | 11 +++---
 two-scale-heat-conduction/macro-dumux/run.sh  |  6 +++-
 two-scale-heat-conduction/macro-nutils/run.sh | 12 ++++---
 two-scale-heat-conduction/micro-dumux/run.sh  | 14 +++++---
 two-scale-heat-conduction/micro-nutils/run.sh | 20 ++++++-----
 volume-coupled-diffusion/fenics/run.sh        | 12 ++++---
 volume-coupled-flow/fluid-openfoam/run.sh     | 13 ++++---
 volume-coupled-flow/source-nutils/run.sh      |  6 +++-
 66 files changed, 477 insertions(+), 251 deletions(-)

diff --git a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
index 0b55398ac..790f73384 100755
--- a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
+++ b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
@@ -1,15 +1,19 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 if [ ! -f PIDcontroller.fmu ]; then
-  cd fmu
-  rm -rf build
-  mkdir build
-  cd build
-  cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
-  make
-  cp ./PIDcontroller.fmu ../..
-  cd ../../
+  log cd fmu
+  log rm -rf build
+  log mkdir build
+  log cd build
+  log cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
+  log make
+  log cp ./PIDcontroller.fmu ../..
+  log cd ../../
 fi
 
-fmiprecice ./fmi-settings.json ./precice-settings.json
+log fmiprecice ./fmi-settings.json ./precice-settings.json
+
+close_log
diff --git a/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh b/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh
index 797f27984..19ade3233 100755
--- a/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh
+++ b/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh
@@ -1,14 +1,16 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-transformPoints -scale '(0.0016  0.0016 1)'
-transformPoints -translate '(0.0  0.0 -0.05)'
+. ../../tools/log.sh
 
-rm -rf 0
-cp -r 0.orig 0
+log blockMesh
+log transformPoints -scale '(0.0016  0.0016 1)'
+log transformPoints -translate '(0.0  0.0 -0.05)'
 
-touch fluid-openfoam.foam
+log rm -rf 0
+log cp -r 0.orig 0
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/flow-around-controlled-moving-cylinder/solid-python/run.sh b/flow-around-controlled-moving-cylinder/solid-python/run.sh
index dbf7a6708..9494ca643 100755
--- a/flow-around-controlled-moving-cylinder/solid-python/run.sh
+++ b/flow-around-controlled-moving-cylinder/solid-python/run.sh
@@ -1,6 +1,8 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
 
-python3 solid.py ../precice-config.xml
+log python3 solid.py ../precice-config.xml
 
+close_log
diff --git a/flow-over-heated-plate-nearest-projection/fluid-openfoam/run.sh b/flow-over-heated-plate-nearest-projection/fluid-openfoam/run.sh
index c191b9e48..864ca8c26 100755
--- a/flow-over-heated-plate-nearest-projection/fluid-openfoam/run.sh
+++ b/flow-over-heated-plate-nearest-projection/fluid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/flow-over-heated-plate-nearest-projection/solid-openfoam/run.sh b/flow-over-heated-plate-nearest-projection/solid-openfoam/run.sh
index 57e9395ee..864ca8c26 100755
--- a/flow-over-heated-plate-nearest-projection/solid-openfoam/run.sh
+++ b/flow-over-heated-plate-nearest-projection/solid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch solid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/flow-over-heated-plate-partitioned-flow/fluid1-openfoam/run.sh b/flow-over-heated-plate-partitioned-flow/fluid1-openfoam/run.sh
index 8c4083b4a..864ca8c26 100755
--- a/flow-over-heated-plate-partitioned-flow/fluid1-openfoam/run.sh
+++ b/flow-over-heated-plate-partitioned-flow/fluid1-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid1-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/flow-over-heated-plate-partitioned-flow/fluid2-openfoam/run.sh b/flow-over-heated-plate-partitioned-flow/fluid2-openfoam/run.sh
index 59f7967e7..864ca8c26 100755
--- a/flow-over-heated-plate-partitioned-flow/fluid2-openfoam/run.sh
+++ b/flow-over-heated-plate-partitioned-flow/fluid2-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid2-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/flow-over-heated-plate-partitioned-flow/solid-openfoam/run.sh b/flow-over-heated-plate-partitioned-flow/solid-openfoam/run.sh
index 57e9395ee..864ca8c26 100755
--- a/flow-over-heated-plate-partitioned-flow/solid-openfoam/run.sh
+++ b/flow-over-heated-plate-partitioned-flow/solid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch solid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/flow-over-heated-plate-steady-state/fluid-openfoam/run.sh b/flow-over-heated-plate-steady-state/fluid-openfoam/run.sh
index c191b9e48..864ca8c26 100755
--- a/flow-over-heated-plate-steady-state/fluid-openfoam/run.sh
+++ b/flow-over-heated-plate-steady-state/fluid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/flow-over-heated-plate-steady-state/solid-codeaster/run.sh b/flow-over-heated-plate-steady-state/solid-codeaster/run.sh
index 0af4b021f..c70dcdeef 100755
--- a/flow-over-heated-plate-steady-state/solid-codeaster/run.sh
+++ b/flow-over-heated-plate-steady-state/solid-codeaster/run.sh
@@ -1,12 +1,16 @@
 #!/bin/sh
 set -e -u
 
-echo "Warning: this case requires a manual preparation step for code_aster."
-echo "You also need to set an absolute path as exchange-directory in precice-config.xml."
-echo "See the tutorial and code_aster adapter documentation pages for more:"
-echo "https://precice.org/adapter-code_aster.html"
-echo ""
+. ../../tools/log.sh
+
+log echo "Warning: this case requires a manual preparation step for code_aster."
+log echo "You also need to set an absolute path as exchange-directory in precice-config.xml."
+log echo "See the tutorial and code_aster adapter documentation pages for more:"
+log echo "https://precice.org/adapter-code_aster.html"
+log echo ""
 
 export TUTORIAL_ROOT="${PWD}"
 export PRECICE_PARTICIPANT=Solid
-as_run --run solid.export
+log as_run --run solid.export
+
+close_log
diff --git a/flow-over-heated-plate-two-meshes/fluid-openfoam/run.sh b/flow-over-heated-plate-two-meshes/fluid-openfoam/run.sh
index c191b9e48..864ca8c26 100755
--- a/flow-over-heated-plate-two-meshes/fluid-openfoam/run.sh
+++ b/flow-over-heated-plate-two-meshes/fluid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/flow-over-heated-plate-two-meshes/solid-calculix/run.sh b/flow-over-heated-plate-two-meshes/solid-calculix/run.sh
index 8935f96af..832e75b61 100755
--- a/flow-over-heated-plate-two-meshes/solid-calculix/run.sh
+++ b/flow-over-heated-plate-two-meshes/solid-calculix/run.sh
@@ -1,5 +1,9 @@
 #!/bin/sh
 set -e -u
 
-python3 ./generate_mesh.py > all.msh
-ccx_preCICE -i solid -precice-participant Solid
+. ../../tools/log.sh
+
+log python3 ./generate_mesh.py > all.msh
+log ccx_preCICE -i solid -precice-participant Solid
+
+close_log
diff --git a/flow-over-heated-plate/fluid-openfoam/run.sh b/flow-over-heated-plate/fluid-openfoam/run.sh
index c191b9e48..864ca8c26 100755
--- a/flow-over-heated-plate/fluid-openfoam/run.sh
+++ b/flow-over-heated-plate/fluid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/flow-over-heated-plate/solid-dunefem/run.sh b/flow-over-heated-plate/solid-dunefem/run.sh
index 21bd5c3b1..536d0dea4 100755
--- a/flow-over-heated-plate/solid-dunefem/run.sh
+++ b/flow-over-heated-plate/solid-dunefem/run.sh
@@ -1,5 +1,8 @@
 #!/bin/bash
 set -e -u
 
-python3 solid.py
+. ../../tools/log.sh
 
+log python3 solid.py
+
+close_log
diff --git a/flow-over-heated-plate/solid-fenics/run.sh b/flow-over-heated-plate/solid-fenics/run.sh
index 15315c67d..ad66b6d1b 100755
--- a/flow-over-heated-plate/solid-fenics/run.sh
+++ b/flow-over-heated-plate/solid-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 solid.py
+. ../../tools/log.sh
+
+log python3 solid.py
+
+close_log
diff --git a/flow-over-heated-plate/solid-nutils/run.sh b/flow-over-heated-plate/solid-nutils/run.sh
index 8678a56d1..f216f8055 100755
--- a/flow-over-heated-plate/solid-nutils/run.sh
+++ b/flow-over-heated-plate/solid-nutils/run.sh
@@ -1,7 +1,11 @@
 #!/bin/bash
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-python3 solid.py
+. ../../tools/log.sh
+
+log python3 -m venv .venv
+log . .venv/bin/activate
+log pip install -r requirements.txt
+log python3 solid.py
+
+close_log
diff --git a/flow-over-heated-plate/solid-openfoam/run.sh b/flow-over-heated-plate/solid-openfoam/run.sh
index 57e9395ee..864ca8c26 100755
--- a/flow-over-heated-plate/solid-openfoam/run.sh
+++ b/flow-over-heated-plate/solid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch solid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/heat-exchanger-simplified/fluid-bottom-openfoam/run.sh b/heat-exchanger-simplified/fluid-bottom-openfoam/run.sh
index 5ecab7517..864ca8c26 100755
--- a/heat-exchanger-simplified/fluid-bottom-openfoam/run.sh
+++ b/heat-exchanger-simplified/fluid-bottom-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-bottom-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/heat-exchanger-simplified/fluid-top-openfoam/run.sh b/heat-exchanger-simplified/fluid-top-openfoam/run.sh
index 005bf5371..864ca8c26 100755
--- a/heat-exchanger-simplified/fluid-top-openfoam/run.sh
+++ b/heat-exchanger-simplified/fluid-top-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-top-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/heat-exchanger-simplified/solid-calculix/run.sh b/heat-exchanger-simplified/solid-calculix/run.sh
index 8935f96af..832e75b61 100755
--- a/heat-exchanger-simplified/solid-calculix/run.sh
+++ b/heat-exchanger-simplified/solid-calculix/run.sh
@@ -1,5 +1,9 @@
 #!/bin/sh
 set -e -u
 
-python3 ./generate_mesh.py > all.msh
-ccx_preCICE -i solid -precice-participant Solid
+. ../../tools/log.sh
+
+log python3 ./generate_mesh.py > all.msh
+log ccx_preCICE -i solid -precice-participant Solid
+
+close_log
diff --git a/heat-exchanger/fluid-inner-openfoam/run.sh b/heat-exchanger/fluid-inner-openfoam/run.sh
index 6f176ba93..c71009214 100755
--- a/heat-exchanger/fluid-inner-openfoam/run.sh
+++ b/heat-exchanger/fluid-inner-openfoam/run.sh
@@ -1,7 +1,9 @@
 #!/bin/sh
 set -e -u
 
-touch fluid-inner-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/heat-exchanger/fluid-outer-openfoam/run.sh b/heat-exchanger/fluid-outer-openfoam/run.sh
index 8816441f2..c71009214 100755
--- a/heat-exchanger/fluid-outer-openfoam/run.sh
+++ b/heat-exchanger/fluid-outer-openfoam/run.sh
@@ -1,7 +1,9 @@
 #!/bin/sh
 set -e -u
 
-touch fluid-outer-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/heat-exchanger/solid-calculix/run.sh b/heat-exchanger/solid-calculix/run.sh
index 33d6d65c3..bf264eb69 100755
--- a/heat-exchanger/solid-calculix/run.sh
+++ b/heat-exchanger/solid-calculix/run.sh
@@ -1,11 +1,15 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 if [ ! -f all.msh ]; then
-    echo "Mesh files not found. Use the Download_meshes script to download them."
+    log echo "Mesh files not found. Use the Download_meshes script to download them."
     exit
 fi
 
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
-ccx_preCICE -i solid -precice-participant Solid
+log ccx_preCICE -i solid -precice-participant Solid
+
+close_log
diff --git a/multiple-perpendicular-flaps/fluid-openfoam/run.sh b/multiple-perpendicular-flaps/fluid-openfoam/run.sh
index c191b9e48..864ca8c26 100755
--- a/multiple-perpendicular-flaps/fluid-openfoam/run.sh
+++ b/multiple-perpendicular-flaps/fluid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/oscillator-overlap/mass-left-python/run.sh b/oscillator-overlap/mass-left-python/run.sh
index 2784cfeba..23c30d4e3 100755
--- a/oscillator-overlap/mass-left-python/run.sh
+++ b/oscillator-overlap/mass-left-python/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ../solver-python/oscillator.py Mass-Left
\ No newline at end of file
+. ../../tools/log.sh
+
+log python3 ../solver-python/oscillator.py Mass-Left
+
+close_log
diff --git a/oscillator-overlap/mass-right-python/run.sh b/oscillator-overlap/mass-right-python/run.sh
index 775d6a83e..fb373fd33 100755
--- a/oscillator-overlap/mass-right-python/run.sh
+++ b/oscillator-overlap/mass-right-python/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ../solver-python/oscillator.py Mass-Right
\ No newline at end of file
+. ../../tools/log.sh
+
+log python3 ../solver-python/oscillator.py Mass-Right
+
+close_log
diff --git a/oscillator/fmi/run.sh b/oscillator/fmi/run.sh
index 3cc384bb9..d2945f76f 100755
--- a/oscillator/fmi/run.sh
+++ b/oscillator/fmi/run.sh
@@ -1,40 +1,44 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 usage() { echo "Usage: cmd [-l] [-r]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-	usage
+	log usage
 fi
 
 if [ ! -f Oscillator.fmu ]; then
-  cd fmu
-  rm -rf build
-  mkdir build
-  cd build
-  # Both FMI_VERSION=3 and FMI_VERSION=2 are supported
-  cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
-  make
-  cp ./Oscillator.fmu ../..
-  cd ../../
+  log cd fmu
+  log rm -rf build
+  log mkdir build
+  log cd build
+  log # Both FMI_VERSION=3 and FMI_VERSION=2 are supported
+  log cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
+  log make
+  log cp ./Oscillator.fmu ../..
+  log cd ../../
 fi
 
 # Select appropriate case
 while getopts ":lr" opt; do
   case ${opt} in
   l)
-    fmiprecice ./MassLeft/fmi-settings.json MassLeft/precice-settings.json
-    python3 calculate-error.py MassLeft/fmi-settings.json MassLeft/precice-settings.json MassRight/fmi-settings.json MassRight/precice-settings.json Mass-Left
+    log fmiprecice ./MassLeft/fmi-settings.json MassLeft/precice-settings.json
+    log python3 calculate-error.py MassLeft/fmi-settings.json MassLeft/precice-settings.json MassRight/fmi-settings.json MassRight/precice-settings.json Mass-Left
 
     ;;
   r)
-    fmiprecice MassRight/fmi-settings.json MassRight/precice-settings.json
-    python3 calculate-error.py MassLeft/fmi-settings.json MassLeft/precice-settings.json MassRight/fmi-settings.json MassRight/precice-settings.json Mass-Right
+    log fmiprecice MassRight/fmi-settings.json MassRight/precice-settings.json
+    log python3 calculate-error.py MassLeft/fmi-settings.json MassLeft/precice-settings.json MassRight/fmi-settings.json MassRight/precice-settings.json Mass-Right
 
     ;;
   *)
-    usage
+    log usage
     ;;
   esac
 done
+
+close_log
diff --git a/oscillator/python/run.sh b/oscillator/python/run.sh
index f20c841ec..131c7e55e 100755
--- a/oscillator/python/run.sh
+++ b/oscillator/python/run.sh
@@ -1,24 +1,28 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 usage() { echo "Usage: cmd [-l] [-r]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-	usage
+	log usage
 fi
 
 # Select appropriate case
 while getopts ":lr" opt; do
   case ${opt} in
   l)
-    python3 oscillator.py Mass-Left
+    log python3 oscillator.py Mass-Left
     ;;
   r)
-    python3 oscillator.py Mass-Right
+    log python3 oscillator.py Mass-Right
     ;;
   *)
-    usage
+    log usage
     ;;
   esac
-done
\ No newline at end of file
+done
+
+close_log
diff --git a/partitioned-backwards-facing-step/fluid1-openfoam/run.sh b/partitioned-backwards-facing-step/fluid1-openfoam/run.sh
index 8c4083b4a..864ca8c26 100755
--- a/partitioned-backwards-facing-step/fluid1-openfoam/run.sh
+++ b/partitioned-backwards-facing-step/fluid1-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid1-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/partitioned-backwards-facing-step/fluid2-openfoam/run.sh b/partitioned-backwards-facing-step/fluid2-openfoam/run.sh
index 59f7967e7..864ca8c26 100755
--- a/partitioned-backwards-facing-step/fluid2-openfoam/run.sh
+++ b/partitioned-backwards-facing-step/fluid2-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid2-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/partitioned-elastic-beam/dirichlet-calculix/run.sh b/partitioned-elastic-beam/dirichlet-calculix/run.sh
index 4e020fcd1..c825396f1 100755
--- a/partitioned-elastic-beam/dirichlet-calculix/run.sh
+++ b/partitioned-elastic-beam/dirichlet-calculix/run.sh
@@ -1,6 +1,10 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
-ccx_preCICE -i beam1 -precice-participant Calculix1
+log ccx_preCICE -i beam1 -precice-participant Calculix1
+
+close_log
diff --git a/partitioned-elastic-beam/neumann-calculix/run.sh b/partitioned-elastic-beam/neumann-calculix/run.sh
index e1730a420..2c7a6b96c 100755
--- a/partitioned-elastic-beam/neumann-calculix/run.sh
+++ b/partitioned-elastic-beam/neumann-calculix/run.sh
@@ -1,6 +1,10 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
-ccx_preCICE -i beam2 -precice-participant Calculix2
+log ccx_preCICE -i beam2 -precice-participant Calculix2
+
+close_log
diff --git a/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh b/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh
index 24dba5e2b..a9100a6db 100755
--- a/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh
+++ b/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ../solver-fenics/heat.py -d -i complex
\ No newline at end of file
+. ../../tools/log.sh
+
+log python3 ../solver-fenics/heat.py -d -i complex
+
+close_log
diff --git a/partitioned-heat-conduction-complex/neumann-fenics/run.sh b/partitioned-heat-conduction-complex/neumann-fenics/run.sh
index bc4e1d14e..c8c7bb9a0 100755
--- a/partitioned-heat-conduction-complex/neumann-fenics/run.sh
+++ b/partitioned-heat-conduction-complex/neumann-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ../solver-fenics/heat.py -n -i complex
\ No newline at end of file
+. ../../tools/log.sh
+
+log python3 ../solver-fenics/heat.py -n -i complex
+
+close_log
diff --git a/partitioned-heat-conduction-direct/nutils/run.sh b/partitioned-heat-conduction-direct/nutils/run.sh
index 9c146a51c..f81ed0d1c 100755
--- a/partitioned-heat-conduction-direct/nutils/run.sh
+++ b/partitioned-heat-conduction-direct/nutils/run.sh
@@ -1,29 +1,33 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 usage() { echo "Usage: cmd [-d] [-n]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-        usage
+        log usage
 fi
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
+log python3 -m venv .venv
+log . .venv/bin/activate
+log pip install -r requirements.txt
 
 while getopts ":dn" opt; do
   case ${opt} in
   d)
-    rm -rf Dirichlet-*.vtk
-    NUTILS_RICHOUTPUT=no python3 heat.py --side=Dirichlet
+    log rm -rf Dirichlet-*.vtk
+    log NUTILS_RICHOUTPUT=no python3 heat.py --side=Dirichlet
     ;;
   n)
-    rm -rf Neumann-*.vtk
-    NUTILS_RICHOUTPUT=no python3 heat.py --side=Neumann
+    log rm -rf Neumann-*.vtk
+    log NUTILS_RICHOUTPUT=no python3 heat.py --side=Neumann
     ;;
   *)
-    usage
+    log usage
     ;;
   esac
 done
+
+close_log
diff --git a/partitioned-heat-conduction-overlap/left-fenics/run.sh b/partitioned-heat-conduction-overlap/left-fenics/run.sh
index 266300e4b..af69be292 100755
--- a/partitioned-heat-conduction-overlap/left-fenics/run.sh
+++ b/partitioned-heat-conduction-overlap/left-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ../solver-fenics/heat.py Left
\ No newline at end of file
+. ../../tools/log.sh
+
+log python3 ../solver-fenics/heat.py Left
+
+close_log
diff --git a/partitioned-heat-conduction-overlap/right-fenics/run.sh b/partitioned-heat-conduction-overlap/right-fenics/run.sh
index 0e46fb5df..fc635bc2a 100755
--- a/partitioned-heat-conduction-overlap/right-fenics/run.sh
+++ b/partitioned-heat-conduction-overlap/right-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ../solver-fenics/heat.py Right
\ No newline at end of file
+. ../../tools/log.sh
+
+log python3 ../solver-fenics/heat.py Right
+
+close_log
diff --git a/partitioned-heat-conduction/dirichlet-fenics/run.sh b/partitioned-heat-conduction/dirichlet-fenics/run.sh
index 3fd32e580..5fa306a84 100755
--- a/partitioned-heat-conduction/dirichlet-fenics/run.sh
+++ b/partitioned-heat-conduction/dirichlet-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ../solver-fenics/heat.py Dirichlet
\ No newline at end of file
+. ../../tools/log.sh
+
+log python3 ../solver-fenics/heat.py Dirichlet
+
+close_log
diff --git a/partitioned-heat-conduction/dirichlet-openfoam/run.sh b/partitioned-heat-conduction/dirichlet-openfoam/run.sh
index d9334f454..7baacfb2c 100755
--- a/partitioned-heat-conduction/dirichlet-openfoam/run.sh
+++ b/partitioned-heat-conduction/dirichlet-openfoam/run.sh
@@ -1,9 +1,13 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch openfoam-dirichlet.foam
-./setInitialField.sh
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+
+log blockMesh
+log ./setInitialField.sh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/partitioned-heat-conduction/fenicsx/run.sh b/partitioned-heat-conduction/fenicsx/run.sh
index e31f07a10..1737dc040 100755
--- a/partitioned-heat-conduction/fenicsx/run.sh
+++ b/partitioned-heat-conduction/fenicsx/run.sh
@@ -1,16 +1,20 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 while getopts ":dn" opt; do
   case ${opt} in
   d)
-    python3 heat.py -d --error-tol 10e-3
+    log python3 heat.py -d --error-tol 10e-3
     ;;
   n)
-    python3 heat.py -n --error-tol 10e-3
+    log python3 heat.py -n --error-tol 10e-3
     ;;
   \?)
-    echo "Usage: cmd [-d] [-n]"
+    log echo "Usage: cmd [-d] [-n]"
     ;;
   esac
 done
+
+close_log
diff --git a/partitioned-heat-conduction/neumann-fenics/run.sh b/partitioned-heat-conduction/neumann-fenics/run.sh
index 7c3fba9c1..4d8da96f6 100755
--- a/partitioned-heat-conduction/neumann-fenics/run.sh
+++ b/partitioned-heat-conduction/neumann-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 ../solver-fenics/heat.py Neumann
\ No newline at end of file
+. ../../tools/log.sh
+
+log python3 ../solver-fenics/heat.py Neumann
+
+close_log
diff --git a/partitioned-heat-conduction/neumann-openfoam/run.sh b/partitioned-heat-conduction/neumann-openfoam/run.sh
index 78b68a942..7f360be5c 100755
--- a/partitioned-heat-conduction/neumann-openfoam/run.sh
+++ b/partitioned-heat-conduction/neumann-openfoam/run.sh
@@ -1,9 +1,12 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch openfoam-neumann.foam
-./setInitialField.sh
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+log ./setInitialField.sh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/partitioned-pipe-two-phase/fluid1-openfoam/run.sh b/partitioned-pipe-two-phase/fluid1-openfoam/run.sh
index d8230a576..dd6219e85 100755
--- a/partitioned-pipe-two-phase/fluid1-openfoam/run.sh
+++ b/partitioned-pipe-two-phase/fluid1-openfoam/run.sh
@@ -1,10 +1,13 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-cp -r 0.orig 0
-setFields
-touch fluid1.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+log cp -r 0.orig 0
+log setFields
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/partitioned-pipe-two-phase/fluid2-openfoam/run.sh b/partitioned-pipe-two-phase/fluid2-openfoam/run.sh
index 3f32494e4..dd6219e85 100755
--- a/partitioned-pipe-two-phase/fluid2-openfoam/run.sh
+++ b/partitioned-pipe-two-phase/fluid2-openfoam/run.sh
@@ -1,10 +1,13 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-cp -r 0.orig 0
-setFields
-touch fluid2.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+log cp -r 0.orig 0
+log setFields
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/partitioned-pipe-two-phase/monolithic/run.sh b/partitioned-pipe-two-phase/monolithic/run.sh
index 979c9147c..dd6219e85 100755
--- a/partitioned-pipe-two-phase/monolithic/run.sh
+++ b/partitioned-pipe-two-phase/monolithic/run.sh
@@ -1,10 +1,13 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-cp -r 0.orig 0
-setFields
-touch monolithic.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+log cp -r 0.orig 0
+log setFields
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh b/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh
index 9d3846e5d..a804c9a78 100755
--- a/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh
+++ b/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh
@@ -1,6 +1,8 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 use_skewed=false
 
 for arg in "$@"
@@ -11,14 +13,14 @@ do
 done
 
 if [ "$use_skewed" = true ]; then
-    blockMesh -dict system/blockMeshDictSkewed
+    log blockMesh -dict system/blockMeshDictSkewed
 else
-    blockMesh
+    log blockMesh
 fi
 
-touch fluid1-openfoam-pimplefoam.foam
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log postProcess -func "flowRatePatch(name=inlet)" -latestTime -noZero
 
-postProcess -func "flowRatePatch(name=inlet)" -latestTime -noZero
\ No newline at end of file
+close_log
diff --git a/partitioned-pipe/fluid1-openfoam-sonicliquidfoam/run.sh b/partitioned-pipe/fluid1-openfoam-sonicliquidfoam/run.sh
index 76e94cbc8..864ca8c26 100755
--- a/partitioned-pipe/fluid1-openfoam-sonicliquidfoam/run.sh
+++ b/partitioned-pipe/fluid1-openfoam-sonicliquidfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid1-openfoam-sonicliquidfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh b/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh
index 254c3f68c..a804c9a78 100755
--- a/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh
+++ b/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh
@@ -1,6 +1,8 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 use_skewed=false
 
 for arg in "$@"
@@ -11,14 +13,14 @@ do
 done
 
 if [ "$use_skewed" = true ]; then
-    blockMesh -dict system/blockMeshDictSkewed
+    log blockMesh -dict system/blockMeshDictSkewed
 else
-    blockMesh
+    log blockMesh
 fi
 
-touch fluid2-openfoam-pimplefoam.foam
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log postProcess -func "flowRatePatch(name=inlet)" -latestTime -noZero
 
-postProcess -func "flowRatePatch(name=inlet)" -latestTime -noZero
\ No newline at end of file
+close_log
diff --git a/partitioned-pipe/fluid2-openfoam-sonicliquidfoam/run.sh b/partitioned-pipe/fluid2-openfoam-sonicliquidfoam/run.sh
index 5a24175c5..864ca8c26 100755
--- a/partitioned-pipe/fluid2-openfoam-sonicliquidfoam/run.sh
+++ b/partitioned-pipe/fluid2-openfoam-sonicliquidfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid2-openfoam-sonicliquidfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/perpendicular-flap/fluid-nutils/run.sh b/perpendicular-flap/fluid-nutils/run.sh
index 00b103a23..0e99d59f7 100755
--- a/perpendicular-flap/fluid-nutils/run.sh
+++ b/perpendicular-flap/fluid-nutils/run.sh
@@ -1,7 +1,11 @@
 #!/bin/sh
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-python3 fluid.py
+. ../../tools/log.sh
+
+log python3 -m venv .venv
+log . .venv/bin/activate
+log pip install -r requirements.txt
+log python3 fluid.py
+
+close_log
diff --git a/perpendicular-flap/fluid-openfoam/run.sh b/perpendicular-flap/fluid-openfoam/run.sh
index c191b9e48..864ca8c26 100755
--- a/perpendicular-flap/fluid-openfoam/run.sh
+++ b/perpendicular-flap/fluid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/perpendicular-flap/fluid-su2/run.sh b/perpendicular-flap/fluid-su2/run.sh
index a827818b5..c3e6900f8 100755
--- a/perpendicular-flap/fluid-su2/run.sh
+++ b/perpendicular-flap/fluid-su2/run.sh
@@ -1,8 +1,12 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 if [ "${1:-}" = "-parallel" ]; then
-    mpirun -n 2 SU2_CFD euler_config_coupled.cfg
+    log mpirun -n 2 SU2_CFD euler_config_coupled.cfg
 else
-    SU2_CFD euler_config_coupled.cfg
+    log SU2_CFD euler_config_coupled.cfg
 fi
+
+close_log
diff --git a/perpendicular-flap/solid-calculix/run.sh b/perpendicular-flap/solid-calculix/run.sh
index 8c5a876fa..74f14a9d7 100755
--- a/perpendicular-flap/solid-calculix/run.sh
+++ b/perpendicular-flap/solid-calculix/run.sh
@@ -1,19 +1,23 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 usage() { echo "Usage: run.sh [-modal]" 1>&2; exit 1; }
 
 # There must be either 0 arguments or 1, which is modal.
 # Send an error otherwise
 if [ $# -ge 2 ] || { [ $# -eq 1 ] && [ "$1" != "-modal" ]; }; then
-    usage
+    log usage
 fi
 
 # No arg => regular simulation. Otherwise, it's modal
 if [ $# -eq 0 ]; then
-    ccx_preCICE -i flap -precice-participant Solid
+    log ccx_preCICE -i flap -precice-participant Solid
 else
-    ccx_preCICE -i frequency
-    mv frequency.eig flap_modal.eig
-    ccx_preCICE -i flap_modal -precice-participant Solid
-fi
\ No newline at end of file
+    log ccx_preCICE -i frequency
+    log mv frequency.eig flap_modal.eig
+    log ccx_preCICE -i flap_modal -precice-participant Solid
+fi
+
+close_log
diff --git a/perpendicular-flap/solid-dune/run.sh b/perpendicular-flap/solid-dune/run.sh
index bbe2d648c..c46407ade 100755
--- a/perpendicular-flap/solid-dune/run.sh
+++ b/perpendicular-flap/solid-dune/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-./dune-perpendicular-flap
+. ../../tools/log.sh
+
+log ./dune-perpendicular-flap
+
+close_log
diff --git a/perpendicular-flap/solid-fenics/run.sh b/perpendicular-flap/solid-fenics/run.sh
index 15315c67d..ad66b6d1b 100755
--- a/perpendicular-flap/solid-fenics/run.sh
+++ b/perpendicular-flap/solid-fenics/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 solid.py
+. ../../tools/log.sh
+
+log python3 solid.py
+
+close_log
diff --git a/perpendicular-flap/solid-nutils/run.sh b/perpendicular-flap/solid-nutils/run.sh
index b57faa9f2..73285978f 100755
--- a/perpendicular-flap/solid-nutils/run.sh
+++ b/perpendicular-flap/solid-nutils/run.sh
@@ -1,7 +1,11 @@
 #!/bin/sh
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-python3 solid.py richoutput=no
+. ../../tools/log.sh
+
+log python3 -m venv .venv
+log . .venv/bin/activate
+log pip install -r requirements.txt
+log python3 solid.py richoutput=no
+
+close_log
diff --git a/perpendicular-flap/solid-openfoam/run.sh b/perpendicular-flap/solid-openfoam/run.sh
index d56f9c8d6..c971873e2 100755
--- a/perpendicular-flap/solid-openfoam/run.sh
+++ b/perpendicular-flap/solid-openfoam/run.sh
@@ -1,10 +1,13 @@
 #!/bin/bash
 
-blockMesh
-touch solid-openfoam.foam
+. ../../tools/log.sh
+
+log blockMesh
 
 # Compile boundary condition
-(cd solidDisplacementFoamForce && wmake libso)
+(cd solidDisplacementFoamForce && log wmake libso)
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+close_log
diff --git a/perpendicular-flap/solid-solids4foam/run.sh b/perpendicular-flap/solid-solids4foam/run.sh
index 90f973a25..aba5de63d 100755
--- a/perpendicular-flap/solid-solids4foam/run.sh
+++ b/perpendicular-flap/solid-solids4foam/run.sh
@@ -1,7 +1,10 @@
 #!/bin/bash
 
-blockMesh
-touch solid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/turek-hron-fsi3/fluid-openfoam/run.sh b/turek-hron-fsi3/fluid-openfoam/run.sh
index c191b9e48..864ca8c26 100755
--- a/turek-hron-fsi3/fluid-openfoam/run.sh
+++ b/turek-hron-fsi3/fluid-openfoam/run.sh
@@ -1,8 +1,11 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/two-scale-heat-conduction/macro-dumux/run.sh b/two-scale-heat-conduction/macro-dumux/run.sh
index 7b3d98112..22671307e 100755
--- a/two-scale-heat-conduction/macro-dumux/run.sh
+++ b/two-scale-heat-conduction/macro-dumux/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-./macro_dumux params.input
+. ../../tools/log.sh
+
+log ./macro_dumux params.input
+
+close_log
diff --git a/two-scale-heat-conduction/macro-nutils/run.sh b/two-scale-heat-conduction/macro-nutils/run.sh
index fa2bfba16..c37669008 100755
--- a/two-scale-heat-conduction/macro-nutils/run.sh
+++ b/two-scale-heat-conduction/macro-nutils/run.sh
@@ -1,7 +1,11 @@
 #!/bin/sh
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-python3 macro.py richoutput=no
+. ../../tools/log.sh
+
+log python3 -m venv .venv
+log . .venv/bin/activate
+log pip install -r requirements.txt
+log python3 macro.py richoutput=no
+
+close_log
diff --git a/two-scale-heat-conduction/micro-dumux/run.sh b/two-scale-heat-conduction/micro-dumux/run.sh
index f07dce500..32412d570 100755
--- a/two-scale-heat-conduction/micro-dumux/run.sh
+++ b/two-scale-heat-conduction/micro-dumux/run.sh
@@ -1,24 +1,28 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-        echo "No input argument provided. Micro Manager is launched in serial"
-	python3 run_micro_manager.py params.input
+  log echo "No input argument provided. Micro Manager is launched in serial"
+	log python3 run_micro_manager.py params.input
 fi
 
 while getopts ":sp" opt; do
   case ${opt} in
   s)
-    python3 run_micro_manager.py params.input
+    log python3 run_micro_manager.py params.input
     ;;
   p)
-    mpiexec -n "$2" python3 run_micro_manager.py params.input
+    log mpiexec -n "$2" python3 run_micro_manager.py params.input
     ;;
   *)
-    usage
+    log usage
     ;;
   esac
 done
+
+close_log
diff --git a/two-scale-heat-conduction/micro-nutils/run.sh b/two-scale-heat-conduction/micro-nutils/run.sh
index 8edbe9445..b406d306e 100755
--- a/two-scale-heat-conduction/micro-nutils/run.sh
+++ b/two-scale-heat-conduction/micro-nutils/run.sh
@@ -1,28 +1,32 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
+log python3 -m venv .venv
+log . .venv/bin/activate
+log pip install -r requirements.txt
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-        echo "No input argument provided. Micro Manager is launched in serial"
-	python3 run-micro-problems.py
+  log echo "No input argument provided. Micro Manager is launched in serial"
+	log python3 run-micro-problems.py
 fi
 
 while getopts ":sp" opt; do
   case ${opt} in
   s)
-    python3 run-micro-problems.py
+    log python3 run-micro-problems.py
     ;;
   p)
-    mpiexec -n "$2" python3 run-micro-problems.py
+    log mpiexec -n "$2" python3 run-micro-problems.py
     ;;
   *)
-    usage
+    log usage
     ;;
   esac
 done
+
+close_log
diff --git a/volume-coupled-diffusion/fenics/run.sh b/volume-coupled-diffusion/fenics/run.sh
index d15dd2163..98cc73f65 100755
--- a/volume-coupled-diffusion/fenics/run.sh
+++ b/volume-coupled-diffusion/fenics/run.sh
@@ -1,24 +1,28 @@
 #!/bin/sh
 set -e -u
 
+. ../../tools/log.sh
+
 usage() { echo "Usage: cmd [-s] [-d]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-	usage
+	log usage
 fi
 
 # Select appropriate case
 while getopts ":sd" opt; do
   case ${opt} in
   s)
-    python3 volume-coupled-diffusion.py --source
+    log python3 volume-coupled-diffusion.py --source
     ;;
   d)
-    python3 volume-coupled-diffusion.py --drain
+    log python3 volume-coupled-diffusion.py --drain
     ;;
   *)
-    usage
+    log usage
     ;;
   esac
 done
+
+close_log
diff --git a/volume-coupled-flow/fluid-openfoam/run.sh b/volume-coupled-flow/fluid-openfoam/run.sh
index 3418d12d1..4c61a814c 100755
--- a/volume-coupled-flow/fluid-openfoam/run.sh
+++ b/volume-coupled-flow/fluid-openfoam/run.sh
@@ -1,9 +1,12 @@
 #!/bin/sh
 set -e -u
 
-blockMesh
-topoSet
-touch fluid-openfoam.foam
+. ../../tools/log.sh
 
-../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
+log blockMesh
+log topoSet
+
+log ../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+
+close_log
diff --git a/volume-coupled-flow/source-nutils/run.sh b/volume-coupled-flow/source-nutils/run.sh
index 3ef84763d..39c1fb74b 100755
--- a/volume-coupled-flow/source-nutils/run.sh
+++ b/volume-coupled-flow/source-nutils/run.sh
@@ -1,4 +1,8 @@
 #!/bin/sh
 set -e -u
 
-python3 source.py
+. ../../tools/log.sh
+
+log python3 source.py
+
+close_log

From 6a36e5ebf62f9e2d581a4067edd8c2cc2ce13436 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Wed, 20 Mar 2024 09:05:44 +0100
Subject: [PATCH 11/17] two-scale-heat-conduction: tabs to spaces

---
 two-scale-heat-conduction/micro-dumux/run.sh  | 2 +-
 two-scale-heat-conduction/micro-nutils/run.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/two-scale-heat-conduction/micro-dumux/run.sh b/two-scale-heat-conduction/micro-dumux/run.sh
index 32412d570..48ffd12bd 100755
--- a/two-scale-heat-conduction/micro-dumux/run.sh
+++ b/two-scale-heat-conduction/micro-dumux/run.sh
@@ -8,7 +8,7 @@ usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
   log echo "No input argument provided. Micro Manager is launched in serial"
-	log python3 run_micro_manager.py params.input
+  log python3 run_micro_manager.py params.input
 fi
 
 while getopts ":sp" opt; do
diff --git a/two-scale-heat-conduction/micro-nutils/run.sh b/two-scale-heat-conduction/micro-nutils/run.sh
index b406d306e..d3ab76305 100755
--- a/two-scale-heat-conduction/micro-nutils/run.sh
+++ b/two-scale-heat-conduction/micro-nutils/run.sh
@@ -12,7 +12,7 @@ log pip install -r requirements.txt
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
   log echo "No input argument provided. Micro Manager is launched in serial"
-	log python3 run-micro-problems.py
+  log python3 run-micro-problems.py
 fi
 
 while getopts ":sp" opt; do

From bf3d7d056a0f6b2e4dc50929310f40988c4b1782 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Wed, 20 Mar 2024 15:36:37 +0100
Subject: [PATCH 12/17] Add clean_case_logs to raw clean.sh scripts

---
 elastic-tube-1d/fluid-cpp/clean.sh            |  1 +
 elastic-tube-1d/fluid-python/clean.sh         |  1 +
 elastic-tube-1d/fluid-rust/clean.sh           |  1 +
 elastic-tube-1d/solid-cpp/clean.sh            |  1 +
 elastic-tube-1d/solid-python/clean.sh         |  1 +
 elastic-tube-1d/solid-rust/clean.sh           |  1 +
 .../controller-fmi/clean.sh                   |  3 +--
 .../solid-python/clean.sh                     |  2 ++
 oscillator-overlap/mass-left-python/clean.sh  |  1 +
 oscillator-overlap/mass-right-python/clean.sh |  1 +
 oscillator/fmi/clean.sh                       |  4 +---
 oscillator/python/clean.sh                    |  1 +
 quickstart/solid-cpp/clean.sh                 |  1 +
 tools/cleaning-tools.sh                       | 21 ++++++++++++++-----
 14 files changed, 30 insertions(+), 10 deletions(-)

diff --git a/elastic-tube-1d/fluid-cpp/clean.sh b/elastic-tube-1d/fluid-cpp/clean.sh
index ff2895ffa..f84ab182f 100755
--- a/elastic-tube-1d/fluid-cpp/clean.sh
+++ b/elastic-tube-1d/fluid-cpp/clean.sh
@@ -5,3 +5,4 @@ set -e -u
 
 rm -rvf ./output/*.vtk
 clean_precice_logs .
+clean_case_logs .
diff --git a/elastic-tube-1d/fluid-python/clean.sh b/elastic-tube-1d/fluid-python/clean.sh
index ff2895ffa..f84ab182f 100755
--- a/elastic-tube-1d/fluid-python/clean.sh
+++ b/elastic-tube-1d/fluid-python/clean.sh
@@ -5,3 +5,4 @@ set -e -u
 
 rm -rvf ./output/*.vtk
 clean_precice_logs .
+clean_case_logs .
diff --git a/elastic-tube-1d/fluid-rust/clean.sh b/elastic-tube-1d/fluid-rust/clean.sh
index ff2895ffa..f84ab182f 100755
--- a/elastic-tube-1d/fluid-rust/clean.sh
+++ b/elastic-tube-1d/fluid-rust/clean.sh
@@ -5,3 +5,4 @@ set -e -u
 
 rm -rvf ./output/*.vtk
 clean_precice_logs .
+clean_case_logs .
diff --git a/elastic-tube-1d/solid-cpp/clean.sh b/elastic-tube-1d/solid-cpp/clean.sh
index 7330c8aaa..4c864fb36 100755
--- a/elastic-tube-1d/solid-cpp/clean.sh
+++ b/elastic-tube-1d/solid-cpp/clean.sh
@@ -4,3 +4,4 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_precice_logs .
+clean_case_logs .
diff --git a/elastic-tube-1d/solid-python/clean.sh b/elastic-tube-1d/solid-python/clean.sh
index 7330c8aaa..4c864fb36 100755
--- a/elastic-tube-1d/solid-python/clean.sh
+++ b/elastic-tube-1d/solid-python/clean.sh
@@ -4,3 +4,4 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_precice_logs .
+clean_case_logs .
diff --git a/elastic-tube-1d/solid-rust/clean.sh b/elastic-tube-1d/solid-rust/clean.sh
index 7330c8aaa..4c864fb36 100755
--- a/elastic-tube-1d/solid-rust/clean.sh
+++ b/elastic-tube-1d/solid-rust/clean.sh
@@ -4,3 +4,4 @@ set -e -u
 . ../../tools/cleaning-tools.sh
 
 clean_precice_logs .
+clean_case_logs .
diff --git a/flow-around-controlled-moving-cylinder/controller-fmi/clean.sh b/flow-around-controlled-moving-cylinder/controller-fmi/clean.sh
index f7f371eab..d4e26a453 100755
--- a/flow-around-controlled-moving-cylinder/controller-fmi/clean.sh
+++ b/flow-around-controlled-moving-cylinder/controller-fmi/clean.sh
@@ -3,5 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-rm -rfv ./output/
-clean_precice_logs .
+clean_fmi .
diff --git a/flow-around-controlled-moving-cylinder/solid-python/clean.sh b/flow-around-controlled-moving-cylinder/solid-python/clean.sh
index fa3b754f1..9e559af3b 100755
--- a/flow-around-controlled-moving-cylinder/solid-python/clean.sh
+++ b/flow-around-controlled-moving-cylinder/solid-python/clean.sh
@@ -1,4 +1,6 @@
 #!/bin/sh
 
 . ../../tools/cleaning-tools.sh
+
 clean_precice_logs .
+clean_case_logs .
diff --git a/oscillator-overlap/mass-left-python/clean.sh b/oscillator-overlap/mass-left-python/clean.sh
index c7e3552ac..91d01fde7 100755
--- a/oscillator-overlap/mass-left-python/clean.sh
+++ b/oscillator-overlap/mass-left-python/clean.sh
@@ -6,3 +6,4 @@ set -e -u
 rm -rfv ./output/
 
 clean_precice_logs .
+clean_case_logs .
diff --git a/oscillator-overlap/mass-right-python/clean.sh b/oscillator-overlap/mass-right-python/clean.sh
index c7e3552ac..91d01fde7 100755
--- a/oscillator-overlap/mass-right-python/clean.sh
+++ b/oscillator-overlap/mass-right-python/clean.sh
@@ -6,3 +6,4 @@ set -e -u
 rm -rfv ./output/
 
 clean_precice_logs .
+clean_case_logs .
diff --git a/oscillator/fmi/clean.sh b/oscillator/fmi/clean.sh
index c7e3552ac..d4e26a453 100755
--- a/oscillator/fmi/clean.sh
+++ b/oscillator/fmi/clean.sh
@@ -3,6 +3,4 @@ set -e -u
 
 . ../../tools/cleaning-tools.sh
 
-rm -rfv ./output/
-
-clean_precice_logs .
+clean_fmi .
diff --git a/oscillator/python/clean.sh b/oscillator/python/clean.sh
index c7e3552ac..91d01fde7 100755
--- a/oscillator/python/clean.sh
+++ b/oscillator/python/clean.sh
@@ -6,3 +6,4 @@ set -e -u
 rm -rfv ./output/
 
 clean_precice_logs .
+clean_case_logs .
diff --git a/quickstart/solid-cpp/clean.sh b/quickstart/solid-cpp/clean.sh
index a0ed77ed3..c05807870 100755
--- a/quickstart/solid-cpp/clean.sh
+++ b/quickstart/solid-cpp/clean.sh
@@ -5,3 +5,4 @@ set -e -u
 
 rm -rfv coupling-meshes
 clean_precice_logs .
+clean_case_logs .
diff --git a/tools/cleaning-tools.sh b/tools/cleaning-tools.sh
index c215ac488..3cea7742b 100755
--- a/tools/cleaning-tools.sh
+++ b/tools/cleaning-tools.sh
@@ -167,11 +167,22 @@ clean_dune() {
 clean_dumux() {
    (
         set -e -u
-	cd "$1"
-	echo "- Cleaning up DuMuX case in $(pwd)"
-	rm -fv ./*.vtu
-	rm -fv ./*.pvd
-	clean_precice_logs .
+        cd "$1"
+        echo "- Cleaning up DuMuX case in $(pwd)"
+        rm -fv ./*.vtu
+        rm -fv ./*.pvd
+        clean_precice_logs .
+        clean_case_logs .
    )
+}
 
+clean_fmi() {
+    (
+        set -e -u
+        cd "$1"
+        echo "- Cleaning up FMI case in $(pwd)"
+        rm -rfv ./output/
+        clean_precice_logs .
+        clean_case_logs .
+    )
 }

From aa2faa7e73416777551a9df66c16e338be27e454 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Wed, 20 Mar 2024 15:37:24 +0100
Subject: [PATCH 13/17] Update
 flow-around-controlled-moving-cylinder/controller-fmi/run.sh

Co-authored-by: Benjamin Uekermann <benjamin.uekermann@gmail.com>
---
 .../controller-fmi/run.sh                            | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
index 790f73384..cb63130f8 100755
--- a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
+++ b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
@@ -4,14 +4,14 @@ set -e -u
 . ../../tools/log.sh
 
 if [ ! -f PIDcontroller.fmu ]; then
-  log cd fmu
-  log rm -rf build
-  log mkdir build
-  log cd build
+  cd fmu
+  rm -rf build
+  mkdir build
+  cd build
   log cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
   log make
-  log cp ./PIDcontroller.fmu ../..
-  log cd ../../
+  cp ./PIDcontroller.fmu ../..
+  cd ../../
 fi
 
 log fmiprecice ./fmi-settings.json ./precice-settings.json

From b622692e9052888ed6eec5d5cf10056b0f3a098f Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Wed, 20 Mar 2024 15:37:33 +0100
Subject: [PATCH 14/17] Update oscillator/fmi/run.sh

Co-authored-by: Benjamin Uekermann <benjamin.uekermann@gmail.com>
---
 oscillator/fmi/run.sh | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/oscillator/fmi/run.sh b/oscillator/fmi/run.sh
index d2945f76f..a12a334d5 100755
--- a/oscillator/fmi/run.sh
+++ b/oscillator/fmi/run.sh
@@ -11,15 +11,15 @@ if [ -z "$*" ] ; then
 fi
 
 if [ ! -f Oscillator.fmu ]; then
-  log cd fmu
-  log rm -rf build
-  log mkdir build
-  log cd build
-  log # Both FMI_VERSION=3 and FMI_VERSION=2 are supported
+  cd fmu
+  rm -rf build
+  mkdir build
+  cd build
+  # Both FMI_VERSION=3 and FMI_VERSION=2 are supported
   log cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
   log make
-  log cp ./Oscillator.fmu ../..
-  log cd ../../
+  cp ./Oscillator.fmu ../..
+  cd ../../
 fi
 
 # Select appropriate case

From 8306727bf558b5830d8909c91fab6cdfaac58cd3 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Wed, 20 Mar 2024 15:40:32 +0100
Subject: [PATCH 15/17] Remove log from cd, cp, mv, rm, mkdir

---
 breaking-dam-2d/fluid-openfoam/run.sh                        | 2 +-
 elastic-tube-1d/fluid-cpp/run.sh                             | 2 +-
 elastic-tube-1d/solid-cpp/run.sh                             | 2 +-
 elastic-tube-3d/fluid-openfoam/run.sh                        | 2 +-
 flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh | 4 ++--
 partitioned-heat-conduction-direct/nutils/run.sh             | 4 ++--
 partitioned-pipe-two-phase/fluid1-openfoam/run.sh            | 2 +-
 partitioned-pipe-two-phase/fluid2-openfoam/run.sh            | 2 +-
 partitioned-pipe-two-phase/monolithic/run.sh                 | 2 +-
 perpendicular-flap/solid-calculix/run.sh                     | 2 +-
 10 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/breaking-dam-2d/fluid-openfoam/run.sh b/breaking-dam-2d/fluid-openfoam/run.sh
index bb9aebf15..a0296976c 100755
--- a/breaking-dam-2d/fluid-openfoam/run.sh
+++ b/breaking-dam-2d/fluid-openfoam/run.sh
@@ -3,7 +3,7 @@ set -e -u
 
 . ../../tools/log.sh
 
-log cp 0/alpha.water_orig 0/alpha.water
+cp 0/alpha.water_orig 0/alpha.water
 log blockMesh
 log setFields
 
diff --git a/elastic-tube-1d/fluid-cpp/run.sh b/elastic-tube-1d/fluid-cpp/run.sh
index 7906d3981..bc40e63ec 100755
--- a/elastic-tube-1d/fluid-cpp/run.sh
+++ b/elastic-tube-1d/fluid-cpp/run.sh
@@ -4,7 +4,7 @@ set -e -u
 . ../../tools/log.sh
 
 if [ ! -d build ]; then
-  log mkdir build
+  mkdir build
   log cmake -S . -B build
   log cmake --build build
 fi
diff --git a/elastic-tube-1d/solid-cpp/run.sh b/elastic-tube-1d/solid-cpp/run.sh
index 6708de8c8..649201774 100755
--- a/elastic-tube-1d/solid-cpp/run.sh
+++ b/elastic-tube-1d/solid-cpp/run.sh
@@ -4,7 +4,7 @@ set -e -u
 . ../../tools/log.sh
 
 if [ ! -d build ]; then
-  log mkdir build
+  mkdir build
   log cmake -S . -B build
   log cmake --build build
 fi
diff --git a/elastic-tube-3d/fluid-openfoam/run.sh b/elastic-tube-3d/fluid-openfoam/run.sh
index 5a90867ba..d253a51fe 100755
--- a/elastic-tube-3d/fluid-openfoam/run.sh
+++ b/elastic-tube-3d/fluid-openfoam/run.sh
@@ -3,7 +3,7 @@ set -e -u
 
 . ../../tools/log.sh
 
-log cp -r constant/polyMesh.orig constant/polyMesh
+cp -r constant/polyMesh.orig constant/polyMesh
 
 log ../../tools/run-openfoam.sh "$@"
 . ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
diff --git a/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh b/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh
index 19ade3233..f9c4a9f62 100755
--- a/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh
+++ b/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh
@@ -7,8 +7,8 @@ log blockMesh
 log transformPoints -scale '(0.0016  0.0016 1)'
 log transformPoints -translate '(0.0  0.0 -0.05)'
 
-log rm -rf 0
-log cp -r 0.orig 0
+rm -rf 0
+cp -r 0.orig 0
 
 log ../../tools/run-openfoam.sh "$@"
 . ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
diff --git a/partitioned-heat-conduction-direct/nutils/run.sh b/partitioned-heat-conduction-direct/nutils/run.sh
index f81ed0d1c..0c9de3146 100755
--- a/partitioned-heat-conduction-direct/nutils/run.sh
+++ b/partitioned-heat-conduction-direct/nutils/run.sh
@@ -17,11 +17,11 @@ log pip install -r requirements.txt
 while getopts ":dn" opt; do
   case ${opt} in
   d)
-    log rm -rf Dirichlet-*.vtk
+    rm -rf Dirichlet-*.vtk
     log NUTILS_RICHOUTPUT=no python3 heat.py --side=Dirichlet
     ;;
   n)
-    log rm -rf Neumann-*.vtk
+    rm -rf Neumann-*.vtk
     log NUTILS_RICHOUTPUT=no python3 heat.py --side=Neumann
     ;;
   *)
diff --git a/partitioned-pipe-two-phase/fluid1-openfoam/run.sh b/partitioned-pipe-two-phase/fluid1-openfoam/run.sh
index dd6219e85..50646029c 100755
--- a/partitioned-pipe-two-phase/fluid1-openfoam/run.sh
+++ b/partitioned-pipe-two-phase/fluid1-openfoam/run.sh
@@ -4,7 +4,7 @@ set -e -u
 . ../../tools/log.sh
 
 log blockMesh
-log cp -r 0.orig 0
+cp -r 0.orig 0
 log setFields
 
 log ../../tools/run-openfoam.sh "$@"
diff --git a/partitioned-pipe-two-phase/fluid2-openfoam/run.sh b/partitioned-pipe-two-phase/fluid2-openfoam/run.sh
index dd6219e85..50646029c 100755
--- a/partitioned-pipe-two-phase/fluid2-openfoam/run.sh
+++ b/partitioned-pipe-two-phase/fluid2-openfoam/run.sh
@@ -4,7 +4,7 @@ set -e -u
 . ../../tools/log.sh
 
 log blockMesh
-log cp -r 0.orig 0
+cp -r 0.orig 0
 log setFields
 
 log ../../tools/run-openfoam.sh "$@"
diff --git a/partitioned-pipe-two-phase/monolithic/run.sh b/partitioned-pipe-two-phase/monolithic/run.sh
index dd6219e85..50646029c 100755
--- a/partitioned-pipe-two-phase/monolithic/run.sh
+++ b/partitioned-pipe-two-phase/monolithic/run.sh
@@ -4,7 +4,7 @@ set -e -u
 . ../../tools/log.sh
 
 log blockMesh
-log cp -r 0.orig 0
+cp -r 0.orig 0
 log setFields
 
 log ../../tools/run-openfoam.sh "$@"
diff --git a/perpendicular-flap/solid-calculix/run.sh b/perpendicular-flap/solid-calculix/run.sh
index 74f14a9d7..3d4333eb4 100755
--- a/perpendicular-flap/solid-calculix/run.sh
+++ b/perpendicular-flap/solid-calculix/run.sh
@@ -16,7 +16,7 @@ if [ $# -eq 0 ]; then
     log ccx_preCICE -i flap -precice-participant Solid
 else
     log ccx_preCICE -i frequency
-    log mv frequency.eig flap_modal.eig
+    mv frequency.eig flap_modal.eig
     log ccx_preCICE -i flap_modal -precice-participant Solid
 fi
 

From d02b018c1252ee1a7d895ded25135f1714b40513 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Wed, 20 Mar 2024 16:13:39 +0100
Subject: [PATCH 16/17] Simplify logging of everything, switch to bash

---
 breaking-dam-2d/fluid-openfoam/run.sh          | 11 ++++++-----
 breaking-dam-2d/solid-calculix/run.sh          |  5 +++--
 .../chemical-fenics/run.sh                     |  5 +++--
 channel-transport-reaction/fluid-fenics/run.sh |  5 +++--
 channel-transport/fluid-nutils/run.sh          | 11 ++++++-----
 channel-transport/fluid-openfoam/run.sh        |  9 +++++----
 channel-transport/transport-nutils/run.sh      | 11 ++++++-----
 elastic-tube-1d/fluid-cpp/run.sh               |  8 ++++----
 elastic-tube-1d/fluid-python/run.sh            |  5 +++--
 elastic-tube-1d/fluid-rust/run.sh              |  5 +++--
 elastic-tube-1d/solid-cpp/run.sh               |  8 ++++----
 elastic-tube-1d/solid-python/run.sh            |  5 +++--
 elastic-tube-1d/solid-rust/run.sh              |  5 +++--
 elastic-tube-3d/fluid-openfoam/run.sh          |  6 +++---
 elastic-tube-3d/solid-calculix/run.sh          |  4 ++--
 elastic-tube-3d/solid-fenics/run.sh            |  2 +-
 .../controller-fmi/run.sh                      |  8 ++++----
 .../fluid-openfoam/run.sh                      | 13 +++++++------
 .../solid-python/run.sh                        |  5 +++--
 .../fluid-openfoam/run.sh                      |  9 +++++----
 .../solid-openfoam/run.sh                      |  9 +++++----
 .../fluid1-openfoam/run.sh                     |  9 +++++----
 .../fluid2-openfoam/run.sh                     |  9 +++++----
 .../solid-openfoam/run.sh                      |  9 +++++----
 .../fluid-openfoam/run.sh                      |  9 +++++----
 .../solid-codeaster/run.sh                     | 15 ++++++++-------
 .../fluid-openfoam/run.sh                      |  9 +++++----
 .../solid-calculix/run.sh                      |  7 ++++---
 flow-over-heated-plate/fluid-openfoam/run.sh   |  9 +++++----
 flow-over-heated-plate/solid-dunefem/run.sh    |  3 ++-
 flow-over-heated-plate/solid-fenics/run.sh     |  5 +++--
 flow-over-heated-plate/solid-nutils/run.sh     |  9 +++++----
 flow-over-heated-plate/solid-openfoam/run.sh   |  9 +++++----
 .../fluid-bottom-openfoam/run.sh               |  9 +++++----
 .../fluid-top-openfoam/run.sh                  |  9 +++++----
 .../solid-calculix/run.sh                      |  7 ++++---
 heat-exchanger/fluid-inner-openfoam/run.sh     |  7 ++++---
 heat-exchanger/fluid-outer-openfoam/run.sh     |  7 ++++---
 heat-exchanger/solid-calculix/run.sh           |  6 +++---
 .../fluid-openfoam/run.sh                      |  9 +++++----
 oscillator-overlap/mass-left-python/run.sh     |  5 +++--
 oscillator-overlap/mass-right-python/run.sh    |  5 +++--
 oscillator/fmi/run.sh                          | 18 +++++++++---------
 oscillator/python/run.sh                       | 10 +++++-----
 .../fluid1-openfoam/run.sh                     |  9 +++++----
 .../fluid2-openfoam/run.sh                     |  9 +++++----
 .../dirichlet-calculix/run.sh                  |  4 ++--
 .../neumann-calculix/run.sh                    |  4 ++--
 .../dirichlet-fenics/run.sh                    |  5 +++--
 .../neumann-fenics/run.sh                      |  5 +++--
 .../nutils/run.sh                              | 16 ++++++++--------
 .../left-fenics/run.sh                         |  5 +++--
 .../right-fenics/run.sh                        |  5 +++--
 .../dirichlet-fenics/run.sh                    |  5 +++--
 .../dirichlet-openfoam/run.sh                  | 10 +++++-----
 partitioned-heat-conduction/fenicsx/run.sh     |  8 ++++----
 .../neumann-fenics/run.sh                      |  5 +++--
 .../neumann-openfoam/run.sh                    | 11 ++++++-----
 partitioned-heat-conduction/nutils/run.sh      |  2 +-
 .../fluid1-openfoam/run.sh                     | 11 ++++++-----
 .../fluid2-openfoam/run.sh                     | 11 ++++++-----
 partitioned-pipe-two-phase/monolithic/run.sh   | 11 ++++++-----
 .../fluid1-openfoam-pimplefoam/run.sh          | 12 ++++++------
 .../fluid1-openfoam-sonicliquidfoam/run.sh     |  9 +++++----
 .../fluid2-openfoam-pimplefoam/run.sh          | 12 ++++++------
 .../fluid2-openfoam-sonicliquidfoam/run.sh     |  9 +++++----
 perpendicular-flap/fluid-nutils/run.sh         | 11 ++++++-----
 perpendicular-flap/fluid-openfoam/run.sh       |  9 +++++----
 perpendicular-flap/fluid-su2/run.sh            |  6 +++---
 perpendicular-flap/solid-calculix/run.sh       | 10 +++++-----
 perpendicular-flap/solid-dune/run.sh           |  5 +++--
 perpendicular-flap/solid-fenics/run.sh         |  5 +++--
 perpendicular-flap/solid-nutils/run.sh         | 11 ++++++-----
 perpendicular-flap/solid-openfoam/run.sh       |  9 +++++----
 perpendicular-flap/solid-solids4foam/run.sh    |  7 ++++---
 quickstart/fluid-openfoam/run.sh               |  9 +++++----
 quickstart/solid-cpp/run.sh                    |  7 ++++---
 tools/log.sh                                   | 15 ++++++---------
 tools/run-dealii.sh                            |  2 +-
 turek-hron-fsi3/fluid-openfoam/run.sh          |  9 +++++----
 two-scale-heat-conduction/macro-dumux/run.sh   |  5 +++--
 two-scale-heat-conduction/macro-nutils/run.sh  | 11 ++++++-----
 two-scale-heat-conduction/micro-dumux/run.sh   | 12 ++++++------
 two-scale-heat-conduction/micro-nutils/run.sh  | 18 +++++++++---------
 volume-coupled-diffusion/fenics/run.sh         | 10 +++++-----
 volume-coupled-flow/fluid-openfoam/run.sh      | 11 ++++++-----
 volume-coupled-flow/source-nutils/run.sh       |  5 +++--
 87 files changed, 384 insertions(+), 324 deletions(-)

diff --git a/breaking-dam-2d/fluid-openfoam/run.sh b/breaking-dam-2d/fluid-openfoam/run.sh
index a0296976c..d1c9bfbd5 100755
--- a/breaking-dam-2d/fluid-openfoam/run.sh
+++ b/breaking-dam-2d/fluid-openfoam/run.sh
@@ -1,13 +1,14 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 cp 0/alpha.water_orig 0/alpha.water
-log blockMesh
-log setFields
+blockMesh
+setFields
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/breaking-dam-2d/solid-calculix/run.sh b/breaking-dam-2d/solid-calculix/run.sh
index a12ac5937..3a9f49aae 100755
--- a/breaking-dam-2d/solid-calculix/run.sh
+++ b/breaking-dam-2d/solid-calculix/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log ccx_preCICE -i flap -precice-participant Solid
+ccx_preCICE -i flap -precice-participant Solid
 
 close_log
diff --git a/channel-transport-reaction/chemical-fenics/run.sh b/channel-transport-reaction/chemical-fenics/run.sh
index ab6e02f37..63712e999 100755
--- a/channel-transport-reaction/chemical-fenics/run.sh
+++ b/channel-transport-reaction/chemical-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 chemical-reaction-advection-diffusion.py
+python3 chemical-reaction-advection-diffusion.py
 
 close_log
diff --git a/channel-transport-reaction/fluid-fenics/run.sh b/channel-transport-reaction/fluid-fenics/run.sh
index b17cd285e..e25136551 100755
--- a/channel-transport-reaction/fluid-fenics/run.sh
+++ b/channel-transport-reaction/fluid-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 fluid.py
+python3 fluid.py
 
 close_log
diff --git a/channel-transport/fluid-nutils/run.sh b/channel-transport/fluid-nutils/run.sh
index 0e99d59f7..7094b61c8 100755
--- a/channel-transport/fluid-nutils/run.sh
+++ b/channel-transport/fluid-nutils/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 -m venv .venv
-log . .venv/bin/activate
-log pip install -r requirements.txt
-log python3 fluid.py
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+python3 fluid.py
 
 close_log
diff --git a/channel-transport/fluid-openfoam/run.sh b/channel-transport/fluid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/channel-transport/fluid-openfoam/run.sh
+++ b/channel-transport/fluid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/channel-transport/transport-nutils/run.sh b/channel-transport/transport-nutils/run.sh
index 26bc8f71f..4430e392c 100755
--- a/channel-transport/transport-nutils/run.sh
+++ b/channel-transport/transport-nutils/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 -m venv .venv
-log . .venv/bin/activate
-log pip install -r requirements.txt
-log python3 transport.py
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+python3 transport.py
 
 close_log
diff --git a/elastic-tube-1d/fluid-cpp/run.sh b/elastic-tube-1d/fluid-cpp/run.sh
index bc40e63ec..e99dd09e5 100755
--- a/elastic-tube-1d/fluid-cpp/run.sh
+++ b/elastic-tube-1d/fluid-cpp/run.sh
@@ -1,14 +1,14 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 if [ ! -d build ]; then
   mkdir build
-  log cmake -S . -B build
-  log cmake --build build
+  cmake -S . -B build
+  cmake --build build
 fi
 
-log ./build/FluidSolver ../precice-config.xml
+./build/FluidSolver ../precice-config.xml
 
 close_log
diff --git a/elastic-tube-1d/fluid-python/run.sh b/elastic-tube-1d/fluid-python/run.sh
index 36a1ca22b..dcf4c901d 100755
--- a/elastic-tube-1d/fluid-python/run.sh
+++ b/elastic-tube-1d/fluid-python/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ./FluidSolver.py ../precice-config.xml
+python3 ./FluidSolver.py ../precice-config.xml
 
 close_log
diff --git a/elastic-tube-1d/fluid-rust/run.sh b/elastic-tube-1d/fluid-rust/run.sh
index 987cf781c..9985f982b 100755
--- a/elastic-tube-1d/fluid-rust/run.sh
+++ b/elastic-tube-1d/fluid-rust/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log cargo run --release ../precice-config.xml 
+cargo run --release ../precice-config.xml 
 
 close_log
diff --git a/elastic-tube-1d/solid-cpp/run.sh b/elastic-tube-1d/solid-cpp/run.sh
index 649201774..84261afbc 100755
--- a/elastic-tube-1d/solid-cpp/run.sh
+++ b/elastic-tube-1d/solid-cpp/run.sh
@@ -1,14 +1,14 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 if [ ! -d build ]; then
   mkdir build
-  log cmake -S . -B build
-  log cmake --build build
+  cmake -S . -B build
+  cmake --build build
 fi
 
-log ./build/SolidSolver ../precice-config.xml
+./build/SolidSolver ../precice-config.xml
 
 close_log
diff --git a/elastic-tube-1d/solid-python/run.sh b/elastic-tube-1d/solid-python/run.sh
index 0c4e5dd52..6e772ed24 100755
--- a/elastic-tube-1d/solid-python/run.sh
+++ b/elastic-tube-1d/solid-python/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ./SolidSolver.py ../precice-config.xml
+python3 ./SolidSolver.py ../precice-config.xml
 
 close_log
diff --git a/elastic-tube-1d/solid-rust/run.sh b/elastic-tube-1d/solid-rust/run.sh
index 49305ddf7..85bee03f5 100755
--- a/elastic-tube-1d/solid-rust/run.sh
+++ b/elastic-tube-1d/solid-rust/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log cargo run --release ../precice-config.xml
+cargo run --release ../precice-config.xml
 
 close_log
diff --git a/elastic-tube-3d/fluid-openfoam/run.sh b/elastic-tube-3d/fluid-openfoam/run.sh
index d253a51fe..114671a2d 100755
--- a/elastic-tube-3d/fluid-openfoam/run.sh
+++ b/elastic-tube-3d/fluid-openfoam/run.sh
@@ -1,11 +1,11 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 cp -r constant/polyMesh.orig constant/polyMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/elastic-tube-3d/solid-calculix/run.sh b/elastic-tube-3d/solid-calculix/run.sh
index 2676d0c2a..a5925b868 100755
--- a/elastic-tube-3d/solid-calculix/run.sh
+++ b/elastic-tube-3d/solid-calculix/run.sh
@@ -1,10 +1,10 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
-log ccx_preCICE -i tube -precice-participant Solid
+ccx_preCICE -i tube -precice-participant Solid
 
 close_log
diff --git a/elastic-tube-3d/solid-fenics/run.sh b/elastic-tube-3d/solid-fenics/run.sh
index 15315c67d..2c9d2da09 100755
--- a/elastic-tube-3d/solid-fenics/run.sh
+++ b/elastic-tube-3d/solid-fenics/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 python3 solid.py
diff --git a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
index cb63130f8..9827e49c9 100755
--- a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
+++ b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -8,12 +8,12 @@ if [ ! -f PIDcontroller.fmu ]; then
   rm -rf build
   mkdir build
   cd build
-  log cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
-  log make
+  cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
+  make
   cp ./PIDcontroller.fmu ../..
   cd ../../
 fi
 
-log fmiprecice ./fmi-settings.json ./precice-settings.json
+fmiprecice ./fmi-settings.json ./precice-settings.json
 
 close_log
diff --git a/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh b/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh
index f9c4a9f62..e2a8415a0 100755
--- a/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh
+++ b/flow-around-controlled-moving-cylinder/fluid-openfoam/run.sh
@@ -1,16 +1,17 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
-log transformPoints -scale '(0.0016  0.0016 1)'
-log transformPoints -translate '(0.0  0.0 -0.05)'
+blockMesh
+transformPoints -scale '(0.0016  0.0016 1)'
+transformPoints -translate '(0.0  0.0 -0.05)'
 
 rm -rf 0
 cp -r 0.orig 0
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/flow-around-controlled-moving-cylinder/solid-python/run.sh b/flow-around-controlled-moving-cylinder/solid-python/run.sh
index 9494ca643..678a825eb 100755
--- a/flow-around-controlled-moving-cylinder/solid-python/run.sh
+++ b/flow-around-controlled-moving-cylinder/solid-python/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 solid.py ../precice-config.xml
+python3 solid.py ../precice-config.xml
 
 close_log
diff --git a/flow-over-heated-plate-nearest-projection/fluid-openfoam/run.sh b/flow-over-heated-plate-nearest-projection/fluid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/flow-over-heated-plate-nearest-projection/fluid-openfoam/run.sh
+++ b/flow-over-heated-plate-nearest-projection/fluid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/flow-over-heated-plate-nearest-projection/solid-openfoam/run.sh b/flow-over-heated-plate-nearest-projection/solid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/flow-over-heated-plate-nearest-projection/solid-openfoam/run.sh
+++ b/flow-over-heated-plate-nearest-projection/solid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/flow-over-heated-plate-partitioned-flow/fluid1-openfoam/run.sh b/flow-over-heated-plate-partitioned-flow/fluid1-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/flow-over-heated-plate-partitioned-flow/fluid1-openfoam/run.sh
+++ b/flow-over-heated-plate-partitioned-flow/fluid1-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/flow-over-heated-plate-partitioned-flow/fluid2-openfoam/run.sh b/flow-over-heated-plate-partitioned-flow/fluid2-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/flow-over-heated-plate-partitioned-flow/fluid2-openfoam/run.sh
+++ b/flow-over-heated-plate-partitioned-flow/fluid2-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/flow-over-heated-plate-partitioned-flow/solid-openfoam/run.sh b/flow-over-heated-plate-partitioned-flow/solid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/flow-over-heated-plate-partitioned-flow/solid-openfoam/run.sh
+++ b/flow-over-heated-plate-partitioned-flow/solid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/flow-over-heated-plate-steady-state/fluid-openfoam/run.sh b/flow-over-heated-plate-steady-state/fluid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/flow-over-heated-plate-steady-state/fluid-openfoam/run.sh
+++ b/flow-over-heated-plate-steady-state/fluid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/flow-over-heated-plate-steady-state/solid-codeaster/run.sh b/flow-over-heated-plate-steady-state/solid-codeaster/run.sh
index c70dcdeef..e3075712b 100755
--- a/flow-over-heated-plate-steady-state/solid-codeaster/run.sh
+++ b/flow-over-heated-plate-steady-state/solid-codeaster/run.sh
@@ -1,16 +1,17 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log echo "Warning: this case requires a manual preparation step for code_aster."
-log echo "You also need to set an absolute path as exchange-directory in precice-config.xml."
-log echo "See the tutorial and code_aster adapter documentation pages for more:"
-log echo "https://precice.org/adapter-code_aster.html"
-log echo ""
+echo "Warning: this case requires a manual preparation step for code_aster."
+echo "You also need to set an absolute path as exchange-directory in precice-config.xml."
+echo "See the tutorial and code_aster adapter documentation pages for more:"
+echo "https://precice.org/adapter-code_aster.html"
+echo ""
 
 export TUTORIAL_ROOT="${PWD}"
 export PRECICE_PARTICIPANT=Solid
-log as_run --run solid.export
+as_run --run solid.export
 
 close_log
diff --git a/flow-over-heated-plate-two-meshes/fluid-openfoam/run.sh b/flow-over-heated-plate-two-meshes/fluid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/flow-over-heated-plate-two-meshes/fluid-openfoam/run.sh
+++ b/flow-over-heated-plate-two-meshes/fluid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/flow-over-heated-plate-two-meshes/solid-calculix/run.sh b/flow-over-heated-plate-two-meshes/solid-calculix/run.sh
index 832e75b61..460b914bd 100755
--- a/flow-over-heated-plate-two-meshes/solid-calculix/run.sh
+++ b/flow-over-heated-plate-two-meshes/solid-calculix/run.sh
@@ -1,9 +1,10 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ./generate_mesh.py > all.msh
-log ccx_preCICE -i solid -precice-participant Solid
+python3 ./generate_mesh.py > all.msh
+ccx_preCICE -i solid -precice-participant Solid
 
 close_log
diff --git a/flow-over-heated-plate/fluid-openfoam/run.sh b/flow-over-heated-plate/fluid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/flow-over-heated-plate/fluid-openfoam/run.sh
+++ b/flow-over-heated-plate/fluid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/flow-over-heated-plate/solid-dunefem/run.sh b/flow-over-heated-plate/solid-dunefem/run.sh
index 536d0dea4..6d5da4496 100755
--- a/flow-over-heated-plate/solid-dunefem/run.sh
+++ b/flow-over-heated-plate/solid-dunefem/run.sh
@@ -2,7 +2,8 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 solid.py
+python3 solid.py
 
 close_log
diff --git a/flow-over-heated-plate/solid-fenics/run.sh b/flow-over-heated-plate/solid-fenics/run.sh
index ad66b6d1b..6d5da4496 100755
--- a/flow-over-heated-plate/solid-fenics/run.sh
+++ b/flow-over-heated-plate/solid-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 solid.py
+python3 solid.py
 
 close_log
diff --git a/flow-over-heated-plate/solid-nutils/run.sh b/flow-over-heated-plate/solid-nutils/run.sh
index f216f8055..125686c9e 100755
--- a/flow-over-heated-plate/solid-nutils/run.sh
+++ b/flow-over-heated-plate/solid-nutils/run.sh
@@ -2,10 +2,11 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 -m venv .venv
-log . .venv/bin/activate
-log pip install -r requirements.txt
-log python3 solid.py
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+python3 solid.py
 
 close_log
diff --git a/flow-over-heated-plate/solid-openfoam/run.sh b/flow-over-heated-plate/solid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/flow-over-heated-plate/solid-openfoam/run.sh
+++ b/flow-over-heated-plate/solid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/heat-exchanger-simplified/fluid-bottom-openfoam/run.sh b/heat-exchanger-simplified/fluid-bottom-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/heat-exchanger-simplified/fluid-bottom-openfoam/run.sh
+++ b/heat-exchanger-simplified/fluid-bottom-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/heat-exchanger-simplified/fluid-top-openfoam/run.sh b/heat-exchanger-simplified/fluid-top-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/heat-exchanger-simplified/fluid-top-openfoam/run.sh
+++ b/heat-exchanger-simplified/fluid-top-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/heat-exchanger-simplified/solid-calculix/run.sh b/heat-exchanger-simplified/solid-calculix/run.sh
index 832e75b61..460b914bd 100755
--- a/heat-exchanger-simplified/solid-calculix/run.sh
+++ b/heat-exchanger-simplified/solid-calculix/run.sh
@@ -1,9 +1,10 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ./generate_mesh.py > all.msh
-log ccx_preCICE -i solid -precice-participant Solid
+python3 ./generate_mesh.py > all.msh
+ccx_preCICE -i solid -precice-participant Solid
 
 close_log
diff --git a/heat-exchanger/fluid-inner-openfoam/run.sh b/heat-exchanger/fluid-inner-openfoam/run.sh
index c71009214..71a1313ae 100755
--- a/heat-exchanger/fluid-inner-openfoam/run.sh
+++ b/heat-exchanger/fluid-inner-openfoam/run.sh
@@ -1,9 +1,10 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/heat-exchanger/fluid-outer-openfoam/run.sh b/heat-exchanger/fluid-outer-openfoam/run.sh
index c71009214..71a1313ae 100755
--- a/heat-exchanger/fluid-outer-openfoam/run.sh
+++ b/heat-exchanger/fluid-outer-openfoam/run.sh
@@ -1,9 +1,10 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/heat-exchanger/solid-calculix/run.sh b/heat-exchanger/solid-calculix/run.sh
index bf264eb69..c57ccc311 100755
--- a/heat-exchanger/solid-calculix/run.sh
+++ b/heat-exchanger/solid-calculix/run.sh
@@ -1,15 +1,15 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 if [ ! -f all.msh ]; then
-    log echo "Mesh files not found. Use the Download_meshes script to download them."
+    echo "Mesh files not found. Use the Download_meshes script to download them."
     exit
 fi
 
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
-log ccx_preCICE -i solid -precice-participant Solid
+ccx_preCICE -i solid -precice-participant Solid
 
 close_log
diff --git a/multiple-perpendicular-flaps/fluid-openfoam/run.sh b/multiple-perpendicular-flaps/fluid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/multiple-perpendicular-flaps/fluid-openfoam/run.sh
+++ b/multiple-perpendicular-flaps/fluid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/oscillator-overlap/mass-left-python/run.sh b/oscillator-overlap/mass-left-python/run.sh
index 23c30d4e3..d2e5f9515 100755
--- a/oscillator-overlap/mass-left-python/run.sh
+++ b/oscillator-overlap/mass-left-python/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ../solver-python/oscillator.py Mass-Left
+python3 ../solver-python/oscillator.py Mass-Left
 
 close_log
diff --git a/oscillator-overlap/mass-right-python/run.sh b/oscillator-overlap/mass-right-python/run.sh
index fb373fd33..4bd290c63 100755
--- a/oscillator-overlap/mass-right-python/run.sh
+++ b/oscillator-overlap/mass-right-python/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ../solver-python/oscillator.py Mass-Right
+python3 ../solver-python/oscillator.py Mass-Right
 
 close_log
diff --git a/oscillator/fmi/run.sh b/oscillator/fmi/run.sh
index a12a334d5..8e6fbfbe5 100755
--- a/oscillator/fmi/run.sh
+++ b/oscillator/fmi/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -7,7 +7,7 @@ usage() { echo "Usage: cmd [-l] [-r]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-	log usage
+	usage
 fi
 
 if [ ! -f Oscillator.fmu ]; then
@@ -16,8 +16,8 @@ if [ ! -f Oscillator.fmu ]; then
   mkdir build
   cd build
   # Both FMI_VERSION=3 and FMI_VERSION=2 are supported
-  log cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
-  log make
+  cmake -DFMI_TYPE=CS -DFMI_VERSION=3 ..
+  make
   cp ./Oscillator.fmu ../..
   cd ../../
 fi
@@ -26,17 +26,17 @@ fi
 while getopts ":lr" opt; do
   case ${opt} in
   l)
-    log fmiprecice ./MassLeft/fmi-settings.json MassLeft/precice-settings.json
-    log python3 calculate-error.py MassLeft/fmi-settings.json MassLeft/precice-settings.json MassRight/fmi-settings.json MassRight/precice-settings.json Mass-Left
+    fmiprecice ./MassLeft/fmi-settings.json MassLeft/precice-settings.json
+    python3 calculate-error.py MassLeft/fmi-settings.json MassLeft/precice-settings.json MassRight/fmi-settings.json MassRight/precice-settings.json Mass-Left
 
     ;;
   r)
-    log fmiprecice MassRight/fmi-settings.json MassRight/precice-settings.json
-    log python3 calculate-error.py MassLeft/fmi-settings.json MassLeft/precice-settings.json MassRight/fmi-settings.json MassRight/precice-settings.json Mass-Right
+    fmiprecice MassRight/fmi-settings.json MassRight/precice-settings.json
+    python3 calculate-error.py MassLeft/fmi-settings.json MassLeft/precice-settings.json MassRight/fmi-settings.json MassRight/precice-settings.json Mass-Right
 
     ;;
   *)
-    log usage
+    usage
     ;;
   esac
 done
diff --git a/oscillator/python/run.sh b/oscillator/python/run.sh
index 131c7e55e..3e4fb0209 100755
--- a/oscillator/python/run.sh
+++ b/oscillator/python/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -7,20 +7,20 @@ usage() { echo "Usage: cmd [-l] [-r]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-	log usage
+	usage
 fi
 
 # Select appropriate case
 while getopts ":lr" opt; do
   case ${opt} in
   l)
-    log python3 oscillator.py Mass-Left
+    python3 oscillator.py Mass-Left
     ;;
   r)
-    log python3 oscillator.py Mass-Right
+    python3 oscillator.py Mass-Right
     ;;
   *)
-    log usage
+    usage
     ;;
   esac
 done
diff --git a/partitioned-backwards-facing-step/fluid1-openfoam/run.sh b/partitioned-backwards-facing-step/fluid1-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/partitioned-backwards-facing-step/fluid1-openfoam/run.sh
+++ b/partitioned-backwards-facing-step/fluid1-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/partitioned-backwards-facing-step/fluid2-openfoam/run.sh b/partitioned-backwards-facing-step/fluid2-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/partitioned-backwards-facing-step/fluid2-openfoam/run.sh
+++ b/partitioned-backwards-facing-step/fluid2-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/partitioned-elastic-beam/dirichlet-calculix/run.sh b/partitioned-elastic-beam/dirichlet-calculix/run.sh
index c825396f1..d0a6bac87 100755
--- a/partitioned-elastic-beam/dirichlet-calculix/run.sh
+++ b/partitioned-elastic-beam/dirichlet-calculix/run.sh
@@ -1,10 +1,10 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
-log ccx_preCICE -i beam1 -precice-participant Calculix1
+ccx_preCICE -i beam1 -precice-participant Calculix1
 
 close_log
diff --git a/partitioned-elastic-beam/neumann-calculix/run.sh b/partitioned-elastic-beam/neumann-calculix/run.sh
index 2c7a6b96c..bbc7ecfe6 100755
--- a/partitioned-elastic-beam/neumann-calculix/run.sh
+++ b/partitioned-elastic-beam/neumann-calculix/run.sh
@@ -1,10 +1,10 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
-log ccx_preCICE -i beam2 -precice-participant Calculix2
+ccx_preCICE -i beam2 -precice-participant Calculix2
 
 close_log
diff --git a/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh b/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh
index a9100a6db..e4c1a798c 100755
--- a/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh
+++ b/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ../solver-fenics/heat.py -d -i complex
+python3 ../solver-fenics/heat.py -d -i complex
 
 close_log
diff --git a/partitioned-heat-conduction-complex/neumann-fenics/run.sh b/partitioned-heat-conduction-complex/neumann-fenics/run.sh
index c8c7bb9a0..4f0ae3402 100755
--- a/partitioned-heat-conduction-complex/neumann-fenics/run.sh
+++ b/partitioned-heat-conduction-complex/neumann-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ../solver-fenics/heat.py -n -i complex
+python3 ../solver-fenics/heat.py -n -i complex
 
 close_log
diff --git a/partitioned-heat-conduction-direct/nutils/run.sh b/partitioned-heat-conduction-direct/nutils/run.sh
index 0c9de3146..b6d8dc781 100755
--- a/partitioned-heat-conduction-direct/nutils/run.sh
+++ b/partitioned-heat-conduction-direct/nutils/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -7,25 +7,25 @@ usage() { echo "Usage: cmd [-d] [-n]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-        log usage
+        usage
 fi
 
-log python3 -m venv .venv
-log . .venv/bin/activate
-log pip install -r requirements.txt
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
 
 while getopts ":dn" opt; do
   case ${opt} in
   d)
     rm -rf Dirichlet-*.vtk
-    log NUTILS_RICHOUTPUT=no python3 heat.py --side=Dirichlet
+    NUTILS_RICHOUTPUT=no python3 heat.py --side=Dirichlet
     ;;
   n)
     rm -rf Neumann-*.vtk
-    log NUTILS_RICHOUTPUT=no python3 heat.py --side=Neumann
+    NUTILS_RICHOUTPUT=no python3 heat.py --side=Neumann
     ;;
   *)
-    log usage
+    usage
     ;;
   esac
 done
diff --git a/partitioned-heat-conduction-overlap/left-fenics/run.sh b/partitioned-heat-conduction-overlap/left-fenics/run.sh
index af69be292..df525cc51 100755
--- a/partitioned-heat-conduction-overlap/left-fenics/run.sh
+++ b/partitioned-heat-conduction-overlap/left-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ../solver-fenics/heat.py Left
+python3 ../solver-fenics/heat.py Left
 
 close_log
diff --git a/partitioned-heat-conduction-overlap/right-fenics/run.sh b/partitioned-heat-conduction-overlap/right-fenics/run.sh
index fc635bc2a..ae72b4d1b 100755
--- a/partitioned-heat-conduction-overlap/right-fenics/run.sh
+++ b/partitioned-heat-conduction-overlap/right-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ../solver-fenics/heat.py Right
+python3 ../solver-fenics/heat.py Right
 
 close_log
diff --git a/partitioned-heat-conduction/dirichlet-fenics/run.sh b/partitioned-heat-conduction/dirichlet-fenics/run.sh
index 5fa306a84..874a00a5a 100755
--- a/partitioned-heat-conduction/dirichlet-fenics/run.sh
+++ b/partitioned-heat-conduction/dirichlet-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ../solver-fenics/heat.py Dirichlet
+python3 ../solver-fenics/heat.py Dirichlet
 
 close_log
diff --git a/partitioned-heat-conduction/dirichlet-openfoam/run.sh b/partitioned-heat-conduction/dirichlet-openfoam/run.sh
index 7baacfb2c..c71f80da2 100755
--- a/partitioned-heat-conduction/dirichlet-openfoam/run.sh
+++ b/partitioned-heat-conduction/dirichlet-openfoam/run.sh
@@ -1,13 +1,13 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 
-log blockMesh
-log ./setInitialField.sh
+blockMesh
+./setInitialField.sh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/partitioned-heat-conduction/fenicsx/run.sh b/partitioned-heat-conduction/fenicsx/run.sh
index 1737dc040..948a4f66b 100755
--- a/partitioned-heat-conduction/fenicsx/run.sh
+++ b/partitioned-heat-conduction/fenicsx/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -6,13 +6,13 @@ set -e -u
 while getopts ":dn" opt; do
   case ${opt} in
   d)
-    log python3 heat.py -d --error-tol 10e-3
+    python3 heat.py -d --error-tol 10e-3
     ;;
   n)
-    log python3 heat.py -n --error-tol 10e-3
+    python3 heat.py -n --error-tol 10e-3
     ;;
   \?)
-    log echo "Usage: cmd [-d] [-n]"
+    echo "Usage: cmd [-d] [-n]"
     ;;
   esac
 done
diff --git a/partitioned-heat-conduction/neumann-fenics/run.sh b/partitioned-heat-conduction/neumann-fenics/run.sh
index 4d8da96f6..8c02791c1 100755
--- a/partitioned-heat-conduction/neumann-fenics/run.sh
+++ b/partitioned-heat-conduction/neumann-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 ../solver-fenics/heat.py Neumann
+python3 ../solver-fenics/heat.py Neumann
 
 close_log
diff --git a/partitioned-heat-conduction/neumann-openfoam/run.sh b/partitioned-heat-conduction/neumann-openfoam/run.sh
index 7f360be5c..e75dacd3d 100755
--- a/partitioned-heat-conduction/neumann-openfoam/run.sh
+++ b/partitioned-heat-conduction/neumann-openfoam/run.sh
@@ -1,12 +1,13 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
-log ./setInitialField.sh
+blockMesh
+./setInitialField.sh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/partitioned-heat-conduction/nutils/run.sh b/partitioned-heat-conduction/nutils/run.sh
index 21341a572..11bcd5318 100755
--- a/partitioned-heat-conduction/nutils/run.sh
+++ b/partitioned-heat-conduction/nutils/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 usage() { echo "Usage: cmd [-d] [-n]" 1>&2; exit 1; }
diff --git a/partitioned-pipe-two-phase/fluid1-openfoam/run.sh b/partitioned-pipe-two-phase/fluid1-openfoam/run.sh
index 50646029c..63adb50c4 100755
--- a/partitioned-pipe-two-phase/fluid1-openfoam/run.sh
+++ b/partitioned-pipe-two-phase/fluid1-openfoam/run.sh
@@ -1,13 +1,14 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 cp -r 0.orig 0
-log setFields
+setFields
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/partitioned-pipe-two-phase/fluid2-openfoam/run.sh b/partitioned-pipe-two-phase/fluid2-openfoam/run.sh
index 50646029c..63adb50c4 100755
--- a/partitioned-pipe-two-phase/fluid2-openfoam/run.sh
+++ b/partitioned-pipe-two-phase/fluid2-openfoam/run.sh
@@ -1,13 +1,14 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 cp -r 0.orig 0
-log setFields
+setFields
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/partitioned-pipe-two-phase/monolithic/run.sh b/partitioned-pipe-two-phase/monolithic/run.sh
index 50646029c..63adb50c4 100755
--- a/partitioned-pipe-two-phase/monolithic/run.sh
+++ b/partitioned-pipe-two-phase/monolithic/run.sh
@@ -1,13 +1,14 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 cp -r 0.orig 0
-log setFields
+setFields
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh b/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh
index a804c9a78..33ff84014 100755
--- a/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh
+++ b/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -13,14 +13,14 @@ do
 done
 
 if [ "$use_skewed" = true ]; then
-    log blockMesh -dict system/blockMeshDictSkewed
+    blockMesh -dict system/blockMeshDictSkewed
 else
-    log blockMesh
+    blockMesh
 fi
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
-log postProcess -func "flowRatePatch(name=inlet)" -latestTime -noZero
+postProcess -func "flowRatePatch(name=inlet)" -latestTime -noZero
 
 close_log
diff --git a/partitioned-pipe/fluid1-openfoam-sonicliquidfoam/run.sh b/partitioned-pipe/fluid1-openfoam-sonicliquidfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/partitioned-pipe/fluid1-openfoam-sonicliquidfoam/run.sh
+++ b/partitioned-pipe/fluid1-openfoam-sonicliquidfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh b/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh
index a804c9a78..33ff84014 100755
--- a/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh
+++ b/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -13,14 +13,14 @@ do
 done
 
 if [ "$use_skewed" = true ]; then
-    log blockMesh -dict system/blockMeshDictSkewed
+    blockMesh -dict system/blockMeshDictSkewed
 else
-    log blockMesh
+    blockMesh
 fi
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
-log postProcess -func "flowRatePatch(name=inlet)" -latestTime -noZero
+postProcess -func "flowRatePatch(name=inlet)" -latestTime -noZero
 
 close_log
diff --git a/partitioned-pipe/fluid2-openfoam-sonicliquidfoam/run.sh b/partitioned-pipe/fluid2-openfoam-sonicliquidfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/partitioned-pipe/fluid2-openfoam-sonicliquidfoam/run.sh
+++ b/partitioned-pipe/fluid2-openfoam-sonicliquidfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/perpendicular-flap/fluid-nutils/run.sh b/perpendicular-flap/fluid-nutils/run.sh
index 0e99d59f7..7094b61c8 100755
--- a/perpendicular-flap/fluid-nutils/run.sh
+++ b/perpendicular-flap/fluid-nutils/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 -m venv .venv
-log . .venv/bin/activate
-log pip install -r requirements.txt
-log python3 fluid.py
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+python3 fluid.py
 
 close_log
diff --git a/perpendicular-flap/fluid-openfoam/run.sh b/perpendicular-flap/fluid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/perpendicular-flap/fluid-openfoam/run.sh
+++ b/perpendicular-flap/fluid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/perpendicular-flap/fluid-su2/run.sh b/perpendicular-flap/fluid-su2/run.sh
index c3e6900f8..4b7eda062 100755
--- a/perpendicular-flap/fluid-su2/run.sh
+++ b/perpendicular-flap/fluid-su2/run.sh
@@ -1,12 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 if [ "${1:-}" = "-parallel" ]; then
-    log mpirun -n 2 SU2_CFD euler_config_coupled.cfg
+    mpirun -n 2 SU2_CFD euler_config_coupled.cfg
 else
-    log SU2_CFD euler_config_coupled.cfg
+    SU2_CFD euler_config_coupled.cfg
 fi
 
 close_log
diff --git a/perpendicular-flap/solid-calculix/run.sh b/perpendicular-flap/solid-calculix/run.sh
index 3d4333eb4..fd38f4581 100755
--- a/perpendicular-flap/solid-calculix/run.sh
+++ b/perpendicular-flap/solid-calculix/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -8,16 +8,16 @@ usage() { echo "Usage: run.sh [-modal]" 1>&2; exit 1; }
 # There must be either 0 arguments or 1, which is modal.
 # Send an error otherwise
 if [ $# -ge 2 ] || { [ $# -eq 1 ] && [ "$1" != "-modal" ]; }; then
-    log usage
+    usage
 fi
 
 # No arg => regular simulation. Otherwise, it's modal
 if [ $# -eq 0 ]; then
-    log ccx_preCICE -i flap -precice-participant Solid
+    ccx_preCICE -i flap -precice-participant Solid
 else
-    log ccx_preCICE -i frequency
+    ccx_preCICE -i frequency
     mv frequency.eig flap_modal.eig
-    log ccx_preCICE -i flap_modal -precice-participant Solid
+    ccx_preCICE -i flap_modal -precice-participant Solid
 fi
 
 close_log
diff --git a/perpendicular-flap/solid-dune/run.sh b/perpendicular-flap/solid-dune/run.sh
index c46407ade..7cf8e187a 100755
--- a/perpendicular-flap/solid-dune/run.sh
+++ b/perpendicular-flap/solid-dune/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log ./dune-perpendicular-flap
+./dune-perpendicular-flap
 
 close_log
diff --git a/perpendicular-flap/solid-fenics/run.sh b/perpendicular-flap/solid-fenics/run.sh
index ad66b6d1b..6d5da4496 100755
--- a/perpendicular-flap/solid-fenics/run.sh
+++ b/perpendicular-flap/solid-fenics/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 solid.py
+python3 solid.py
 
 close_log
diff --git a/perpendicular-flap/solid-nutils/run.sh b/perpendicular-flap/solid-nutils/run.sh
index 73285978f..43cc739cd 100755
--- a/perpendicular-flap/solid-nutils/run.sh
+++ b/perpendicular-flap/solid-nutils/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 -m venv .venv
-log . .venv/bin/activate
-log pip install -r requirements.txt
-log python3 solid.py richoutput=no
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+python3 solid.py richoutput=no
 
 close_log
diff --git a/perpendicular-flap/solid-openfoam/run.sh b/perpendicular-flap/solid-openfoam/run.sh
index c971873e2..7996753e3 100755
--- a/perpendicular-flap/solid-openfoam/run.sh
+++ b/perpendicular-flap/solid-openfoam/run.sh
@@ -1,13 +1,14 @@
 #!/bin/bash
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
 # Compile boundary condition
-(cd solidDisplacementFoamForce && log wmake libso)
+(cd solidDisplacementFoamForce && wmake libso)
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/perpendicular-flap/solid-solids4foam/run.sh b/perpendicular-flap/solid-solids4foam/run.sh
index aba5de63d..4f2b797ab 100755
--- a/perpendicular-flap/solid-solids4foam/run.sh
+++ b/perpendicular-flap/solid-solids4foam/run.sh
@@ -1,10 +1,11 @@
 #!/bin/bash
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/quickstart/fluid-openfoam/run.sh b/quickstart/fluid-openfoam/run.sh
index e8baeb5e0..40cd648cf 100755
--- a/quickstart/fluid-openfoam/run.sh
+++ b/quickstart/fluid-openfoam/run.sh
@@ -1,12 +1,13 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
+../../tools/run-openfoam.sh "$@"
 
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/quickstart/solid-cpp/run.sh b/quickstart/solid-cpp/run.sh
index 19895306a..c764a8f73 100755
--- a/quickstart/solid-cpp/run.sh
+++ b/quickstart/solid-cpp/run.sh
@@ -1,13 +1,14 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 solver=./rigid_body_solver
 if [ -f "${solver}" ]; then
-    log ${solver}
+    ${solver}
 else 
-    log echo "Unable to locate the executable ${solver}. Have a look at the README for building instructions."
+    echo "Unable to locate the executable ${solver}. Have a look at the README for building instructions."
 fi
 
 close_log
diff --git a/tools/log.sh b/tools/log.sh
index 8925148d1..76cd533d1 100644
--- a/tools/log.sh
+++ b/tools/log.sh
@@ -1,21 +1,18 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 CASENAME="$(pwd | xargs basename)"
-export CASENAME
+LOGFILE="$CASENAME.log"
+export LOGFILE
 
 STARTDATE="$(date --rfc-email)"
 STARTTIME="$(date +%s)"
 echo "Started on: $STARTDATE" | tee "$CASENAME.log" 2>&1
 
-log() {
-    "$@" | tee --append "$CASENAME.log" 2>&1
-}
-
 close_log() {
-    echo "Started on:  $STARTDATE" | tee --append "$CASENAME.log" 2>&1
+    echo "Started on:  $STARTDATE" | tee --append "$LOGFILE" 2>&1
     ENDDATE="$(date --rfc-email)"
     ENDTIME="$(date +%s)"
-    echo "Finished on: $ENDDATE" | tee --append "$CASENAME.log" 2>&1
-    echo "Duration:    $((ENDTIME-STARTTIME)) seconds (wall-clock time, including time waiting for participants)" | tee --append "$CASENAME.log" 2>&1
+    echo "Finished on: $ENDDATE" | tee --append "$LOGFILE" 2>&1
+    echo "Duration:    $((ENDTIME-STARTTIME)) seconds (wall-clock time, including time waiting for participants)" | tee --append "$LOGFILE" 2>&1
 }
diff --git a/tools/run-dealii.sh b/tools/run-dealii.sh
index 318bb5143..64148aa6f 100755
--- a/tools/run-dealii.sh
+++ b/tools/run-dealii.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 EXE=""
diff --git a/turek-hron-fsi3/fluid-openfoam/run.sh b/turek-hron-fsi3/fluid-openfoam/run.sh
index 864ca8c26..da82a9ba2 100755
--- a/turek-hron-fsi3/fluid-openfoam/run.sh
+++ b/turek-hron-fsi3/fluid-openfoam/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
+blockMesh
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/two-scale-heat-conduction/macro-dumux/run.sh b/two-scale-heat-conduction/macro-dumux/run.sh
index 22671307e..920352b8d 100755
--- a/two-scale-heat-conduction/macro-dumux/run.sh
+++ b/two-scale-heat-conduction/macro-dumux/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log ./macro_dumux params.input
+./macro_dumux params.input
 
 close_log
diff --git a/two-scale-heat-conduction/macro-nutils/run.sh b/two-scale-heat-conduction/macro-nutils/run.sh
index c37669008..5ae6ac050 100755
--- a/two-scale-heat-conduction/macro-nutils/run.sh
+++ b/two-scale-heat-conduction/macro-nutils/run.sh
@@ -1,11 +1,12 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 -m venv .venv
-log . .venv/bin/activate
-log pip install -r requirements.txt
-log python3 macro.py richoutput=no
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+python3 macro.py richoutput=no
 
 close_log
diff --git a/two-scale-heat-conduction/micro-dumux/run.sh b/two-scale-heat-conduction/micro-dumux/run.sh
index 48ffd12bd..7b739e57e 100755
--- a/two-scale-heat-conduction/micro-dumux/run.sh
+++ b/two-scale-heat-conduction/micro-dumux/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -7,20 +7,20 @@ usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-  log echo "No input argument provided. Micro Manager is launched in serial"
-  log python3 run_micro_manager.py params.input
+  echo "No input argument provided. Micro Manager is launched in serial"
+  python3 run_micro_manager.py params.input
 fi
 
 while getopts ":sp" opt; do
   case ${opt} in
   s)
-    log python3 run_micro_manager.py params.input
+    python3 run_micro_manager.py params.input
     ;;
   p)
-    log mpiexec -n "$2" python3 run_micro_manager.py params.input
+    mpiexec -n "$2" python3 run_micro_manager.py params.input
     ;;
   *)
-    log usage
+    usage
     ;;
   esac
 done
diff --git a/two-scale-heat-conduction/micro-nutils/run.sh b/two-scale-heat-conduction/micro-nutils/run.sh
index d3ab76305..0b9846c86 100755
--- a/two-scale-heat-conduction/micro-nutils/run.sh
+++ b/two-scale-heat-conduction/micro-nutils/run.sh
@@ -1,30 +1,30 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
 
 usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
 
-log python3 -m venv .venv
-log . .venv/bin/activate
-log pip install -r requirements.txt
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-  log echo "No input argument provided. Micro Manager is launched in serial"
-  log python3 run-micro-problems.py
+  echo "No input argument provided. Micro Manager is launched in serial"
+  python3 run-micro-problems.py
 fi
 
 while getopts ":sp" opt; do
   case ${opt} in
   s)
-    log python3 run-micro-problems.py
+    python3 run-micro-problems.py
     ;;
   p)
-    log mpiexec -n "$2" python3 run-micro-problems.py
+    mpiexec -n "$2" python3 run-micro-problems.py
     ;;
   *)
-    log usage
+    usage
     ;;
   esac
 done
diff --git a/volume-coupled-diffusion/fenics/run.sh b/volume-coupled-diffusion/fenics/run.sh
index 98cc73f65..213c47471 100755
--- a/volume-coupled-diffusion/fenics/run.sh
+++ b/volume-coupled-diffusion/fenics/run.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
@@ -7,20 +7,20 @@ usage() { echo "Usage: cmd [-s] [-d]" 1>&2; exit 1; }
 
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
-	log usage
+	usage
 fi
 
 # Select appropriate case
 while getopts ":sd" opt; do
   case ${opt} in
   s)
-    log python3 volume-coupled-diffusion.py --source
+    python3 volume-coupled-diffusion.py --source
     ;;
   d)
-    log python3 volume-coupled-diffusion.py --drain
+    python3 volume-coupled-diffusion.py --drain
     ;;
   *)
-    log usage
+    usage
     ;;
   esac
 done
diff --git a/volume-coupled-flow/fluid-openfoam/run.sh b/volume-coupled-flow/fluid-openfoam/run.sh
index 4c61a814c..75b56f415 100755
--- a/volume-coupled-flow/fluid-openfoam/run.sh
+++ b/volume-coupled-flow/fluid-openfoam/run.sh
@@ -1,12 +1,13 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log blockMesh
-log topoSet
+blockMesh
+topoSet
 
-log ../../tools/run-openfoam.sh "$@"
-. ../../tools/openfoam-remove-empty-dirs.sh && log openfoam_remove_empty_dirs
+../../tools/run-openfoam.sh "$@"
+. ../../tools/openfoam-remove-empty-dirs.sh && openfoam_remove_empty_dirs
 
 close_log
diff --git a/volume-coupled-flow/source-nutils/run.sh b/volume-coupled-flow/source-nutils/run.sh
index 39c1fb74b..716fe373b 100755
--- a/volume-coupled-flow/source-nutils/run.sh
+++ b/volume-coupled-flow/source-nutils/run.sh
@@ -1,8 +1,9 @@
-#!/bin/sh
+#!/bin/bash
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
-log python3 source.py
+python3 source.py
 
 close_log

From 48d76dc9710c76a8fc013d460523326d82bc2baf Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Wed, 20 Mar 2024 16:25:09 +0100
Subject: [PATCH 17/17] Port more cases

---
 elastic-tube-1d/fluid-cpp/run.sh                             | 1 +
 elastic-tube-1d/solid-cpp/run.sh                             | 1 +
 elastic-tube-3d/fluid-openfoam/run.sh                        | 1 +
 elastic-tube-3d/solid-calculix/run.sh                        | 1 +
 flow-around-controlled-moving-cylinder/controller-fmi/run.sh | 1 +
 heat-exchanger/solid-calculix/run.sh                         | 1 +
 oscillator/fmi/run.sh                                        | 1 +
 oscillator/python/run.sh                                     | 1 +
 partitioned-elastic-beam/dirichlet-calculix/run.sh           | 1 +
 partitioned-elastic-beam/neumann-calculix/run.sh             | 1 +
 partitioned-heat-conduction-direct/nutils/run.sh             | 1 +
 partitioned-heat-conduction/dirichlet-openfoam/run.sh        | 2 +-
 partitioned-heat-conduction/fenicsx/run.sh                   | 1 +
 partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh           | 1 +
 partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh           | 1 +
 perpendicular-flap/fluid-su2/run.sh                          | 1 +
 perpendicular-flap/solid-calculix/run.sh                     | 1 +
 two-scale-heat-conduction/micro-dumux/run.sh                 | 1 +
 two-scale-heat-conduction/micro-nutils/run.sh                | 1 +
 volume-coupled-diffusion/fenics/run.sh                       | 1 +
 20 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/elastic-tube-1d/fluid-cpp/run.sh b/elastic-tube-1d/fluid-cpp/run.sh
index e99dd09e5..0e005451e 100755
--- a/elastic-tube-1d/fluid-cpp/run.sh
+++ b/elastic-tube-1d/fluid-cpp/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 if [ ! -d build ]; then
   mkdir build
diff --git a/elastic-tube-1d/solid-cpp/run.sh b/elastic-tube-1d/solid-cpp/run.sh
index 84261afbc..fe674287d 100755
--- a/elastic-tube-1d/solid-cpp/run.sh
+++ b/elastic-tube-1d/solid-cpp/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 if [ ! -d build ]; then
   mkdir build
diff --git a/elastic-tube-3d/fluid-openfoam/run.sh b/elastic-tube-3d/fluid-openfoam/run.sh
index 114671a2d..9d072bcda 100755
--- a/elastic-tube-3d/fluid-openfoam/run.sh
+++ b/elastic-tube-3d/fluid-openfoam/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 cp -r constant/polyMesh.orig constant/polyMesh
 
diff --git a/elastic-tube-3d/solid-calculix/run.sh b/elastic-tube-3d/solid-calculix/run.sh
index a5925b868..6e8b5a83f 100755
--- a/elastic-tube-3d/solid-calculix/run.sh
+++ b/elastic-tube-3d/solid-calculix/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
diff --git a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
index 9827e49c9..46a4f217d 100755
--- a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
+++ b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 if [ ! -f PIDcontroller.fmu ]; then
   cd fmu
diff --git a/heat-exchanger/solid-calculix/run.sh b/heat-exchanger/solid-calculix/run.sh
index c57ccc311..f1f5b3aef 100755
--- a/heat-exchanger/solid-calculix/run.sh
+++ b/heat-exchanger/solid-calculix/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 if [ ! -f all.msh ]; then
     echo "Mesh files not found. Use the Download_meshes script to download them."
diff --git a/oscillator/fmi/run.sh b/oscillator/fmi/run.sh
index 8e6fbfbe5..7928ee03f 100755
--- a/oscillator/fmi/run.sh
+++ b/oscillator/fmi/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 usage() { echo "Usage: cmd [-l] [-r]" 1>&2; exit 1; }
 
diff --git a/oscillator/python/run.sh b/oscillator/python/run.sh
index 3e4fb0209..fdc19ba4b 100755
--- a/oscillator/python/run.sh
+++ b/oscillator/python/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 usage() { echo "Usage: cmd [-l] [-r]" 1>&2; exit 1; }
 
diff --git a/partitioned-elastic-beam/dirichlet-calculix/run.sh b/partitioned-elastic-beam/dirichlet-calculix/run.sh
index d0a6bac87..a7266841a 100755
--- a/partitioned-elastic-beam/dirichlet-calculix/run.sh
+++ b/partitioned-elastic-beam/dirichlet-calculix/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
diff --git a/partitioned-elastic-beam/neumann-calculix/run.sh b/partitioned-elastic-beam/neumann-calculix/run.sh
index bbc7ecfe6..b8dfea3d6 100755
--- a/partitioned-elastic-beam/neumann-calculix/run.sh
+++ b/partitioned-elastic-beam/neumann-calculix/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 export OMP_NUM_THREADS=1
 export CCX_NPROC_EQUATION_SOLVER=1
diff --git a/partitioned-heat-conduction-direct/nutils/run.sh b/partitioned-heat-conduction-direct/nutils/run.sh
index b6d8dc781..ae66a8256 100755
--- a/partitioned-heat-conduction-direct/nutils/run.sh
+++ b/partitioned-heat-conduction-direct/nutils/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 usage() { echo "Usage: cmd [-d] [-n]" 1>&2; exit 1; }
 
diff --git a/partitioned-heat-conduction/dirichlet-openfoam/run.sh b/partitioned-heat-conduction/dirichlet-openfoam/run.sh
index c71f80da2..e75dacd3d 100755
--- a/partitioned-heat-conduction/dirichlet-openfoam/run.sh
+++ b/partitioned-heat-conduction/dirichlet-openfoam/run.sh
@@ -2,7 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
-
+exec > >(tee --append "$LOGFILE") 2>&1
 
 blockMesh
 ./setInitialField.sh
diff --git a/partitioned-heat-conduction/fenicsx/run.sh b/partitioned-heat-conduction/fenicsx/run.sh
index 948a4f66b..c4cf97cc4 100755
--- a/partitioned-heat-conduction/fenicsx/run.sh
+++ b/partitioned-heat-conduction/fenicsx/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 while getopts ":dn" opt; do
   case ${opt} in
diff --git a/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh b/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh
index 33ff84014..198f58108 100755
--- a/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh
+++ b/partitioned-pipe/fluid1-openfoam-pimplefoam/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 use_skewed=false
 
diff --git a/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh b/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh
index 33ff84014..198f58108 100755
--- a/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh
+++ b/partitioned-pipe/fluid2-openfoam-pimplefoam/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 use_skewed=false
 
diff --git a/perpendicular-flap/fluid-su2/run.sh b/perpendicular-flap/fluid-su2/run.sh
index 4b7eda062..529a74f75 100755
--- a/perpendicular-flap/fluid-su2/run.sh
+++ b/perpendicular-flap/fluid-su2/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 if [ "${1:-}" = "-parallel" ]; then
     mpirun -n 2 SU2_CFD euler_config_coupled.cfg
diff --git a/perpendicular-flap/solid-calculix/run.sh b/perpendicular-flap/solid-calculix/run.sh
index fd38f4581..1954b6584 100755
--- a/perpendicular-flap/solid-calculix/run.sh
+++ b/perpendicular-flap/solid-calculix/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 usage() { echo "Usage: run.sh [-modal]" 1>&2; exit 1; }
 
diff --git a/two-scale-heat-conduction/micro-dumux/run.sh b/two-scale-heat-conduction/micro-dumux/run.sh
index 7b739e57e..7ce4c9a0b 100755
--- a/two-scale-heat-conduction/micro-dumux/run.sh
+++ b/two-scale-heat-conduction/micro-dumux/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
 
diff --git a/two-scale-heat-conduction/micro-nutils/run.sh b/two-scale-heat-conduction/micro-nutils/run.sh
index 0b9846c86..49d74d2ce 100755
--- a/two-scale-heat-conduction/micro-nutils/run.sh
+++ b/two-scale-heat-conduction/micro-nutils/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
 
diff --git a/volume-coupled-diffusion/fenics/run.sh b/volume-coupled-diffusion/fenics/run.sh
index 213c47471..b894cafeb 100755
--- a/volume-coupled-diffusion/fenics/run.sh
+++ b/volume-coupled-diffusion/fenics/run.sh
@@ -2,6 +2,7 @@
 set -e -u
 
 . ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
 
 usage() { echo "Usage: cmd [-s] [-d]" 1>&2; exit 1; }