From fa820d04ef6ff13fd4c1a7f24d9cd8753e51bad2 Mon Sep 17 00:00:00 2001 From: Niklas Date: Mon, 19 Aug 2024 15:17:03 +0200 Subject: [PATCH 1/9] Add requirements to oscillator tutorial --- oscillator/mass-left-python/requirements.txt | 2 ++ oscillator/mass-left-python/run.sh | 4 ++++ oscillator/mass-right-python/requirements.txt | 2 ++ oscillator/mass-right-python/run.sh | 4 ++++ 4 files changed, 12 insertions(+) create mode 100644 oscillator/mass-left-python/requirements.txt create mode 100644 oscillator/mass-right-python/requirements.txt diff --git a/oscillator/mass-left-python/requirements.txt b/oscillator/mass-left-python/requirements.txt new file mode 100644 index 000000000..dbffa144f --- /dev/null +++ b/oscillator/mass-left-python/requirements.txt @@ -0,0 +1,2 @@ +numpy >1, <2 +pyprecice~=3.0 diff --git a/oscillator/mass-left-python/run.sh b/oscillator/mass-left-python/run.sh index 2a3902739..f8949a10c 100755 --- a/oscillator/mass-left-python/run.sh +++ b/oscillator/mass-left-python/run.sh @@ -1,6 +1,10 @@ #!/usr/bin/env bash set -e -u +python3 -m venv .venv +. .venv/bin/activate +pip install -r requirements.txt + . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 diff --git a/oscillator/mass-right-python/requirements.txt b/oscillator/mass-right-python/requirements.txt new file mode 100644 index 000000000..dbffa144f --- /dev/null +++ b/oscillator/mass-right-python/requirements.txt @@ -0,0 +1,2 @@ +numpy >1, <2 +pyprecice~=3.0 diff --git a/oscillator/mass-right-python/run.sh b/oscillator/mass-right-python/run.sh index e34e0aa8d..7fe22e7de 100755 --- a/oscillator/mass-right-python/run.sh +++ b/oscillator/mass-right-python/run.sh @@ -1,6 +1,10 @@ #!/usr/bin/env bash set -e -u +python3 -m venv .venv +. .venv/bin/activate +pip install -r requirements.txt + . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 From 48a0a04ec155682d2cf00e5571d2e41197dd63b1 Mon Sep 17 00:00:00 2001 From: Benjamin Rodenberg Date: Thu, 29 Aug 2024 11:36:49 +0200 Subject: [PATCH 2/9] Apply suggestions from code review --- oscillator/mass-left-python/requirements.txt | 1 + oscillator/mass-right-python/requirements.txt | 1 + 2 files changed, 2 insertions(+) diff --git a/oscillator/mass-left-python/requirements.txt b/oscillator/mass-left-python/requirements.txt index dbffa144f..9dff131c5 100644 --- a/oscillator/mass-left-python/requirements.txt +++ b/oscillator/mass-left-python/requirements.txt @@ -1,2 +1,3 @@ numpy >1, <2 pyprecice~=3.0 +scipy diff --git a/oscillator/mass-right-python/requirements.txt b/oscillator/mass-right-python/requirements.txt index dbffa144f..9dff131c5 100644 --- a/oscillator/mass-right-python/requirements.txt +++ b/oscillator/mass-right-python/requirements.txt @@ -1,2 +1,3 @@ numpy >1, <2 pyprecice~=3.0 +scipy From 14c80f78f3cdc4ddccbab8ddeb9b0ce100afbbf1 Mon Sep 17 00:00:00 2001 From: Benjamin Rodenberg Date: Thu, 29 Aug 2024 11:55:49 +0200 Subject: [PATCH 3/9] Update run.sh and add requirements.txt for overlapping oscillator. --- oscillator-overlap/mass-left-python/requirements.txt | 3 +++ oscillator-overlap/mass-left-python/run.sh | 4 ++++ oscillator-overlap/mass-right-python/requirements.txt | 3 +++ oscillator-overlap/mass-right-python/run.sh | 4 ++++ 4 files changed, 14 insertions(+) create mode 100644 oscillator-overlap/mass-left-python/requirements.txt create mode 100644 oscillator-overlap/mass-right-python/requirements.txt diff --git a/oscillator-overlap/mass-left-python/requirements.txt b/oscillator-overlap/mass-left-python/requirements.txt new file mode 100644 index 000000000..9dff131c5 --- /dev/null +++ b/oscillator-overlap/mass-left-python/requirements.txt @@ -0,0 +1,3 @@ +numpy >1, <2 +pyprecice~=3.0 +scipy diff --git a/oscillator-overlap/mass-left-python/run.sh b/oscillator-overlap/mass-left-python/run.sh index 2a3902739..f8949a10c 100755 --- a/oscillator-overlap/mass-left-python/run.sh +++ b/oscillator-overlap/mass-left-python/run.sh @@ -1,6 +1,10 @@ #!/usr/bin/env bash set -e -u +python3 -m venv .venv +. .venv/bin/activate +pip install -r requirements.txt + . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 diff --git a/oscillator-overlap/mass-right-python/requirements.txt b/oscillator-overlap/mass-right-python/requirements.txt new file mode 100644 index 000000000..9dff131c5 --- /dev/null +++ b/oscillator-overlap/mass-right-python/requirements.txt @@ -0,0 +1,3 @@ +numpy >1, <2 +pyprecice~=3.0 +scipy diff --git a/oscillator-overlap/mass-right-python/run.sh b/oscillator-overlap/mass-right-python/run.sh index e34e0aa8d..7fe22e7de 100755 --- a/oscillator-overlap/mass-right-python/run.sh +++ b/oscillator-overlap/mass-right-python/run.sh @@ -1,6 +1,10 @@ #!/usr/bin/env bash set -e -u +python3 -m venv .venv +. .venv/bin/activate +pip install -r requirements.txt + . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 From 58f9e7ce34fc252479fdde844fdcc473ad6c7658 Mon Sep 17 00:00:00 2001 From: Niklas Date: Sat, 31 Aug 2024 14:33:22 +0200 Subject: [PATCH 4/9] Add requirements.txt for python tutorials and modified run scripts accordingly --- channel-transport-reaction/chemical-fenics/requirements.txt | 5 +++++ channel-transport-reaction/chemical-fenics/run.sh | 6 +++++- channel-transport-reaction/fluid-fenics/requirements.txt | 5 +++++ channel-transport-reaction/fluid-fenics/run.sh | 5 +++++ elastic-tube-1d/fluid-python/requirements.txt | 3 +++ elastic-tube-1d/fluid-python/run.sh | 5 +++++ elastic-tube-1d/solid-python/requirements.txt | 2 ++ elastic-tube-1d/solid-python/run.sh | 5 +++++ elastic-tube-3d/solid-fenics/requirements.txt | 4 ++++ elastic-tube-3d/solid-fenics/run.sh | 4 ++++ .../solid-python/requirements.txt | 2 ++ flow-around-controlled-moving-cylinder/solid-python/run.sh | 4 ++++ flow-over-heated-plate/solid-fenics/requirements.txt | 4 ++++ flow-over-heated-plate/solid-fenics/run.sh | 4 ++++ partitioned-heat-conduction-complex/dirichlet-fenics/run.sh | 4 ++++ partitioned-heat-conduction-complex/neumann-fenics/run.sh | 4 ++++ .../solver-fenics/requirements.txt | 5 +++++ partitioned-heat-conduction-overlap/left-fenics/run.sh | 4 ++++ partitioned-heat-conduction-overlap/right-fenics/run.sh | 4 ++++ .../solver-fenics/requirements.txt | 4 ++++ perpendicular-flap/solid-fenics/requirements.txt | 5 +++++ perpendicular-flap/solid-fenics/run.sh | 4 ++++ volume-coupled-diffusion/drain-fenics/run.sh | 4 ++++ volume-coupled-diffusion/solver-fenics/requirements.txt | 4 ++++ volume-coupled-diffusion/source-fenics/run.sh | 4 ++++ 25 files changed, 103 insertions(+), 1 deletion(-) create mode 100644 channel-transport-reaction/chemical-fenics/requirements.txt create mode 100644 channel-transport-reaction/fluid-fenics/requirements.txt create mode 100644 elastic-tube-1d/fluid-python/requirements.txt create mode 100644 elastic-tube-1d/solid-python/requirements.txt create mode 100644 elastic-tube-3d/solid-fenics/requirements.txt create mode 100644 flow-around-controlled-moving-cylinder/solid-python/requirements.txt create mode 100644 flow-over-heated-plate/solid-fenics/requirements.txt create mode 100644 partitioned-heat-conduction-complex/solver-fenics/requirements.txt create mode 100644 partitioned-heat-conduction-overlap/solver-fenics/requirements.txt create mode 100644 perpendicular-flap/solid-fenics/requirements.txt create mode 100644 volume-coupled-diffusion/solver-fenics/requirements.txt diff --git a/channel-transport-reaction/chemical-fenics/requirements.txt b/channel-transport-reaction/chemical-fenics/requirements.txt new file mode 100644 index 000000000..69a4edeb3 --- /dev/null +++ b/channel-transport-reaction/chemical-fenics/requirements.txt @@ -0,0 +1,5 @@ +numpy >1, <2 +pyprecice~=3.0 +mpi4py < 4 +fenicsprecice + diff --git a/channel-transport-reaction/chemical-fenics/run.sh b/channel-transport-reaction/chemical-fenics/run.sh index a1579fe12..960376a1a 100755 --- a/channel-transport-reaction/chemical-fenics/run.sh +++ b/channel-transport-reaction/chemical-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-package .venv +. .venv/bin/activate +pip install -r requirements.txt + python3 chemical-reaction-advection-diffusion.py -close_log +close_log \ No newline at end of file diff --git a/channel-transport-reaction/fluid-fenics/requirements.txt b/channel-transport-reaction/fluid-fenics/requirements.txt new file mode 100644 index 000000000..de06348da --- /dev/null +++ b/channel-transport-reaction/fluid-fenics/requirements.txt @@ -0,0 +1,5 @@ +numpy >1, <2 +pyprecice~=3.0 +mpi4py <4 +fenicsprecice + diff --git a/channel-transport-reaction/fluid-fenics/run.sh b/channel-transport-reaction/fluid-fenics/run.sh index 7ff7118b0..a56ffe641 100755 --- a/channel-transport-reaction/fluid-fenics/run.sh +++ b/channel-transport-reaction/fluid-fenics/run.sh @@ -4,6 +4,11 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-package .venv +. .venv/bin/activate +pip install -r requirements.txt + + python3 fluid.py close_log diff --git a/elastic-tube-1d/fluid-python/requirements.txt b/elastic-tube-1d/fluid-python/requirements.txt new file mode 100644 index 000000000..ee1722131 --- /dev/null +++ b/elastic-tube-1d/fluid-python/requirements.txt @@ -0,0 +1,3 @@ +pyprecice~=3.0 +numpy +matplotlib \ No newline at end of file diff --git a/elastic-tube-1d/fluid-python/run.sh b/elastic-tube-1d/fluid-python/run.sh index 40f081acc..9e6bc80ba 100755 --- a/elastic-tube-1d/fluid-python/run.sh +++ b/elastic-tube-1d/fluid-python/run.sh @@ -4,6 +4,11 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv .venv +. .venv/bin/activate +pip install -r requirements.txt + + python3 ./FluidSolver.py ../precice-config.xml close_log diff --git a/elastic-tube-1d/solid-python/requirements.txt b/elastic-tube-1d/solid-python/requirements.txt new file mode 100644 index 000000000..4301cd5fd --- /dev/null +++ b/elastic-tube-1d/solid-python/requirements.txt @@ -0,0 +1,2 @@ +pyprecice~=3.0 +numpy \ No newline at end of file diff --git a/elastic-tube-1d/solid-python/run.sh b/elastic-tube-1d/solid-python/run.sh index e56711214..4485a43d9 100755 --- a/elastic-tube-1d/solid-python/run.sh +++ b/elastic-tube-1d/solid-python/run.sh @@ -4,6 +4,11 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv .venv +. .venv/bin/activate +pip install -r requirements.txt + + python3 ./SolidSolver.py ../precice-config.xml close_log diff --git a/elastic-tube-3d/solid-fenics/requirements.txt b/elastic-tube-3d/solid-fenics/requirements.txt new file mode 100644 index 000000000..41b3413a9 --- /dev/null +++ b/elastic-tube-3d/solid-fenics/requirements.txt @@ -0,0 +1,4 @@ +pyprecice~=3.0 +fenicsprecice +numpy +mpi4py <4 \ No newline at end of file diff --git a/elastic-tube-3d/solid-fenics/run.sh b/elastic-tube-3d/solid-fenics/run.sh index 7bab57c34..17d93f4a2 100755 --- a/elastic-tube-3d/solid-fenics/run.sh +++ b/elastic-tube-3d/solid-fenics/run.sh @@ -1,4 +1,8 @@ #!/usr/bin/env bash set -e -u +python3 -m venv --system-site-package .venv +. .venv/bin/activate +pip install -r requirements.txt + python3 solid.py diff --git a/flow-around-controlled-moving-cylinder/solid-python/requirements.txt b/flow-around-controlled-moving-cylinder/solid-python/requirements.txt new file mode 100644 index 000000000..4301cd5fd --- /dev/null +++ b/flow-around-controlled-moving-cylinder/solid-python/requirements.txt @@ -0,0 +1,2 @@ +pyprecice~=3.0 +numpy \ No newline at end of file diff --git a/flow-around-controlled-moving-cylinder/solid-python/run.sh b/flow-around-controlled-moving-cylinder/solid-python/run.sh index cdf08fb53..82c7c56a7 100755 --- a/flow-around-controlled-moving-cylinder/solid-python/run.sh +++ b/flow-around-controlled-moving-cylinder/solid-python/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv .venv +. .venv/bin/activate +pip install -r requirements.txt + python3 solid.py ../precice-config.xml close_log diff --git a/flow-over-heated-plate/solid-fenics/requirements.txt b/flow-over-heated-plate/solid-fenics/requirements.txt new file mode 100644 index 000000000..41b3413a9 --- /dev/null +++ b/flow-over-heated-plate/solid-fenics/requirements.txt @@ -0,0 +1,4 @@ +pyprecice~=3.0 +fenicsprecice +numpy +mpi4py <4 \ No newline at end of file diff --git a/flow-over-heated-plate/solid-fenics/run.sh b/flow-over-heated-plate/solid-fenics/run.sh index 9cc046223..867c1db13 100755 --- a/flow-over-heated-plate/solid-fenics/run.sh +++ b/flow-over-heated-plate/solid-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages .venv +. .venv/bin/activate +pip install -r requirements.txt + python3 solid.py close_log diff --git a/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh b/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh index 3142687cb..9a9ce7331 100755 --- a/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh +++ b/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages ../solver-fenics/.venv +. ../solver-fenics/.venv/bin/activate +pip install -r ../solver-fenics/requirements.txt + python3 ../solver-fenics/heat.py -d -i complex close_log diff --git a/partitioned-heat-conduction-complex/neumann-fenics/run.sh b/partitioned-heat-conduction-complex/neumann-fenics/run.sh index 081a7d492..4f189a03a 100755 --- a/partitioned-heat-conduction-complex/neumann-fenics/run.sh +++ b/partitioned-heat-conduction-complex/neumann-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages ../solver-fenics/.venv +. ../solver-fenics/.venv/bin/activate +pip install -r ../solver-fenics/requirements.txt + python3 ../solver-fenics/heat.py -n -i complex close_log diff --git a/partitioned-heat-conduction-complex/solver-fenics/requirements.txt b/partitioned-heat-conduction-complex/solver-fenics/requirements.txt new file mode 100644 index 000000000..c97879a7c --- /dev/null +++ b/partitioned-heat-conduction-complex/solver-fenics/requirements.txt @@ -0,0 +1,5 @@ +pyprecice~=3.0 +fenicsprecice +numpy +sympy +mpi4py <4 \ No newline at end of file diff --git a/partitioned-heat-conduction-overlap/left-fenics/run.sh b/partitioned-heat-conduction-overlap/left-fenics/run.sh index 3b948a4c8..e876c94c4 100755 --- a/partitioned-heat-conduction-overlap/left-fenics/run.sh +++ b/partitioned-heat-conduction-overlap/left-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages ../solver-fenics/.venv +. ../solver-fenics/.venv/bin/activate +pip install -r ../solver-fenics/requirements.txt + python3 ../solver-fenics/heat.py Left close_log diff --git a/partitioned-heat-conduction-overlap/right-fenics/run.sh b/partitioned-heat-conduction-overlap/right-fenics/run.sh index 4dbc48821..90f1a7a68 100755 --- a/partitioned-heat-conduction-overlap/right-fenics/run.sh +++ b/partitioned-heat-conduction-overlap/right-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages ../solver-fenics/.venv +. ../solver-fenics/.venv/bin/activate +pip install -r ../solver-fenics/requirements.txt + python3 ../solver-fenics/heat.py Right close_log diff --git a/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt b/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt new file mode 100644 index 000000000..41b3413a9 --- /dev/null +++ b/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt @@ -0,0 +1,4 @@ +pyprecice~=3.0 +fenicsprecice +numpy +mpi4py <4 \ No newline at end of file diff --git a/perpendicular-flap/solid-fenics/requirements.txt b/perpendicular-flap/solid-fenics/requirements.txt new file mode 100644 index 000000000..a64af1da5 --- /dev/null +++ b/perpendicular-flap/solid-fenics/requirements.txt @@ -0,0 +1,5 @@ +pyprecice~=3.0 +fenicsprecice +mpi4py <4 +numpy +matplotlib \ No newline at end of file diff --git a/perpendicular-flap/solid-fenics/run.sh b/perpendicular-flap/solid-fenics/run.sh index 9cc046223..867c1db13 100755 --- a/perpendicular-flap/solid-fenics/run.sh +++ b/perpendicular-flap/solid-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages .venv +. .venv/bin/activate +pip install -r requirements.txt + python3 solid.py close_log diff --git a/volume-coupled-diffusion/drain-fenics/run.sh b/volume-coupled-diffusion/drain-fenics/run.sh index 1ed222432..6060b7758 100755 --- a/volume-coupled-diffusion/drain-fenics/run.sh +++ b/volume-coupled-diffusion/drain-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages ../solver-fenics/.venv +. ../solver-fenics/.venv/bin/activate +pip install -r ../solver-fenics/requirements.txt + python3 ../solver-fenics/volume-coupled-diffusion.py --drain close_log diff --git a/volume-coupled-diffusion/solver-fenics/requirements.txt b/volume-coupled-diffusion/solver-fenics/requirements.txt new file mode 100644 index 000000000..31c8c49c8 --- /dev/null +++ b/volume-coupled-diffusion/solver-fenics/requirements.txt @@ -0,0 +1,4 @@ +fenicsprecice +pyprecice~=3.0 +mpi4py <4 +numpy \ No newline at end of file diff --git a/volume-coupled-diffusion/source-fenics/run.sh b/volume-coupled-diffusion/source-fenics/run.sh index aa19983c4..d6ff75a84 100755 --- a/volume-coupled-diffusion/source-fenics/run.sh +++ b/volume-coupled-diffusion/source-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages ../solver-fenics/.venv +. ../solver-fenics/.venv/bin/activate +pip install -r ../solver-fenics/requirements.txt + python3 ../solver-fenics/volume-coupled-diffusion.py --source close_log From fca16cc8650773b34a871e24629184c02a576c2c Mon Sep 17 00:00:00 2001 From: Niklas Date: Sat, 31 Aug 2024 15:20:55 +0200 Subject: [PATCH 5/9] Add requirements.txt for fmi cases --- .../controller-fmi/requirements.txt | 1 + flow-around-controlled-moving-cylinder/controller-fmi/run.sh | 4 ++++ oscillator/mass-left-fmi/requirements.txt | 1 + oscillator/mass-left-fmi/run.sh | 4 ++++ oscillator/mass-right-fmi/requirements.txt | 1 + oscillator/mass-right-fmi/run.sh | 4 ++++ oscillator/solver-fmi/requirements.txt | 1 + 7 files changed, 16 insertions(+) create mode 100644 flow-around-controlled-moving-cylinder/controller-fmi/requirements.txt create mode 100644 oscillator/mass-left-fmi/requirements.txt create mode 100644 oscillator/mass-right-fmi/requirements.txt create mode 100644 oscillator/solver-fmi/requirements.txt diff --git a/flow-around-controlled-moving-cylinder/controller-fmi/requirements.txt b/flow-around-controlled-moving-cylinder/controller-fmi/requirements.txt new file mode 100644 index 000000000..10f7ea9df --- /dev/null +++ b/flow-around-controlled-moving-cylinder/controller-fmi/requirements.txt @@ -0,0 +1 @@ +fmiprecice \ No newline at end of file diff --git a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh index bf0a7d15d..258970acc 100755 --- a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh +++ b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh @@ -15,6 +15,10 @@ if [ ! -f PIDcontroller.fmu ]; then cd ../../ fi +python3 -m venv .venv +. .venv/bin/activate +pip install -r requirements.txt + fmiprecice ./fmi-settings.json ./precice-settings.json close_log diff --git a/oscillator/mass-left-fmi/requirements.txt b/oscillator/mass-left-fmi/requirements.txt new file mode 100644 index 000000000..871b3ec2b --- /dev/null +++ b/oscillator/mass-left-fmi/requirements.txt @@ -0,0 +1 @@ + fmiprecice \ No newline at end of file diff --git a/oscillator/mass-left-fmi/run.sh b/oscillator/mass-left-fmi/run.sh index 0e5998c58..9fe8217b3 100755 --- a/oscillator/mass-left-fmi/run.sh +++ b/oscillator/mass-left-fmi/run.sh @@ -16,6 +16,10 @@ if [ ! -f ../solver-fmi/Oscillator.fmu ]; then cd ../../../mass-left-fmi fi +python3 -m venv ../sover-fmi/.venv +. ../sover-fmi/.venv/bin/activate +pip install -r requirements.txt + fmiprecice fmi-settings.json precice-settings.json python3 ../solver-fmi/calculate-error.py ../mass-left-fmi/fmi-settings.json ../mass-left-fmi/precice-settings.json ../mass-right-fmi/fmi-settings.json ../mass-right-fmi/precice-settings.json Mass-Left diff --git a/oscillator/mass-right-fmi/requirements.txt b/oscillator/mass-right-fmi/requirements.txt new file mode 100644 index 000000000..10f7ea9df --- /dev/null +++ b/oscillator/mass-right-fmi/requirements.txt @@ -0,0 +1 @@ +fmiprecice \ No newline at end of file diff --git a/oscillator/mass-right-fmi/run.sh b/oscillator/mass-right-fmi/run.sh index 20ecac035..26952b591 100755 --- a/oscillator/mass-right-fmi/run.sh +++ b/oscillator/mass-right-fmi/run.sh @@ -16,6 +16,10 @@ if [ ! -f ../solver-fmi/Oscillator.fmu ]; then cd ../../../mass-right-fmi fi +python3 -m venv ../sover-fmi/.venv +. ../sover-fmi/.venv/bin/activate +pip install -r requirements.txt + fmiprecice fmi-settings.json precice-settings.json python3 ../solver-fmi/calculate-error.py ../mass-left-fmi/fmi-settings.json ../mass-left-fmi/precice-settings.json ../mass-right-fmi/fmi-settings.json ../mass-right-fmi/precice-settings.json Mass-Right diff --git a/oscillator/solver-fmi/requirements.txt b/oscillator/solver-fmi/requirements.txt new file mode 100644 index 000000000..10f7ea9df --- /dev/null +++ b/oscillator/solver-fmi/requirements.txt @@ -0,0 +1 @@ +fmiprecice \ No newline at end of file From e1efdceb0654211d2dc13bf33d3f8a2b1de33012 Mon Sep 17 00:00:00 2001 From: Niklas Date: Sat, 31 Aug 2024 15:44:39 +0200 Subject: [PATCH 6/9] Add remaining requirements files and remove redundant requirements files --- oscillator-overlap/mass-left-python/run.sh | 8 ++++---- oscillator-overlap/mass-right-python/run.sh | 8 ++++---- .../{mass-left-python => solver-python}/requirements.txt | 0 oscillator/mass-left-python/requirements.txt | 3 --- oscillator/mass-left-python/run.sh | 8 ++++---- oscillator/mass-right-python/requirements.txt | 3 --- oscillator/mass-right-python/run.sh | 8 ++++---- .../solver-python}/requirements.txt | 0 partitioned-heat-conduction/dirichlet-fenics/run.sh | 4 ++++ partitioned-heat-conduction/neumann-fenics/run.sh | 4 ++++ .../solver-fenics/requirements.txt | 5 +++++ 11 files changed, 29 insertions(+), 22 deletions(-) rename oscillator-overlap/{mass-left-python => solver-python}/requirements.txt (100%) delete mode 100644 oscillator/mass-left-python/requirements.txt delete mode 100644 oscillator/mass-right-python/requirements.txt rename {oscillator-overlap/mass-right-python => oscillator/solver-python}/requirements.txt (100%) create mode 100644 partitioned-heat-conduction/solver-fenics/requirements.txt diff --git a/oscillator-overlap/mass-left-python/run.sh b/oscillator-overlap/mass-left-python/run.sh index f8949a10c..2a31e7e79 100755 --- a/oscillator-overlap/mass-left-python/run.sh +++ b/oscillator-overlap/mass-left-python/run.sh @@ -1,13 +1,13 @@ #!/usr/bin/env bash set -e -u -python3 -m venv .venv -. .venv/bin/activate -pip install -r requirements.txt - . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv ../solver-python/.venv +. ../solver-python/.venv/bin/activate +pip install -r ../solver-python/requirements.txt + 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 7fe22e7de..67d5a66ab 100755 --- a/oscillator-overlap/mass-right-python/run.sh +++ b/oscillator-overlap/mass-right-python/run.sh @@ -1,13 +1,13 @@ #!/usr/bin/env bash set -e -u -python3 -m venv .venv -. .venv/bin/activate -pip install -r requirements.txt - . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv ../solver-python/.venv +. ../solver-python/.venv/bin/activate +pip install -r ../solver-python/requirements.txt + python3 ../solver-python/oscillator.py Mass-Right close_log diff --git a/oscillator-overlap/mass-left-python/requirements.txt b/oscillator-overlap/solver-python/requirements.txt similarity index 100% rename from oscillator-overlap/mass-left-python/requirements.txt rename to oscillator-overlap/solver-python/requirements.txt diff --git a/oscillator/mass-left-python/requirements.txt b/oscillator/mass-left-python/requirements.txt deleted file mode 100644 index 9dff131c5..000000000 --- a/oscillator/mass-left-python/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -numpy >1, <2 -pyprecice~=3.0 -scipy diff --git a/oscillator/mass-left-python/run.sh b/oscillator/mass-left-python/run.sh index f8949a10c..2a31e7e79 100755 --- a/oscillator/mass-left-python/run.sh +++ b/oscillator/mass-left-python/run.sh @@ -1,13 +1,13 @@ #!/usr/bin/env bash set -e -u -python3 -m venv .venv -. .venv/bin/activate -pip install -r requirements.txt - . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv ../solver-python/.venv +. ../solver-python/.venv/bin/activate +pip install -r ../solver-python/requirements.txt + python3 ../solver-python/oscillator.py Mass-Left close_log diff --git a/oscillator/mass-right-python/requirements.txt b/oscillator/mass-right-python/requirements.txt deleted file mode 100644 index 9dff131c5..000000000 --- a/oscillator/mass-right-python/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -numpy >1, <2 -pyprecice~=3.0 -scipy diff --git a/oscillator/mass-right-python/run.sh b/oscillator/mass-right-python/run.sh index 7fe22e7de..67d5a66ab 100755 --- a/oscillator/mass-right-python/run.sh +++ b/oscillator/mass-right-python/run.sh @@ -1,13 +1,13 @@ #!/usr/bin/env bash set -e -u -python3 -m venv .venv -. .venv/bin/activate -pip install -r requirements.txt - . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv ../solver-python/.venv +. ../solver-python/.venv/bin/activate +pip install -r ../solver-python/requirements.txt + python3 ../solver-python/oscillator.py Mass-Right close_log diff --git a/oscillator-overlap/mass-right-python/requirements.txt b/oscillator/solver-python/requirements.txt similarity index 100% rename from oscillator-overlap/mass-right-python/requirements.txt rename to oscillator/solver-python/requirements.txt diff --git a/partitioned-heat-conduction/dirichlet-fenics/run.sh b/partitioned-heat-conduction/dirichlet-fenics/run.sh index 95cc2d28b..09311591f 100755 --- a/partitioned-heat-conduction/dirichlet-fenics/run.sh +++ b/partitioned-heat-conduction/dirichlet-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages ../solver-fenics/.venv +. ../solver-fenics/.venv/bin/activate +pip install -r ../solver-fenics/requirements.txt + python3 ../solver-fenics/heat.py Dirichlet close_log diff --git a/partitioned-heat-conduction/neumann-fenics/run.sh b/partitioned-heat-conduction/neumann-fenics/run.sh index 874fdec84..f97b09d76 100755 --- a/partitioned-heat-conduction/neumann-fenics/run.sh +++ b/partitioned-heat-conduction/neumann-fenics/run.sh @@ -4,6 +4,10 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 +python3 -m venv --system-site-packages ../solver-fenics/.venv +. ../solver-fenics/.venv/bin/activate +pip install -r ../solver-fenics/requirements.txt + python3 ../solver-fenics/heat.py Neumann close_log diff --git a/partitioned-heat-conduction/solver-fenics/requirements.txt b/partitioned-heat-conduction/solver-fenics/requirements.txt new file mode 100644 index 000000000..c97879a7c --- /dev/null +++ b/partitioned-heat-conduction/solver-fenics/requirements.txt @@ -0,0 +1,5 @@ +pyprecice~=3.0 +fenicsprecice +numpy +sympy +mpi4py <4 \ No newline at end of file From e1c6a36db3caea33499a8f8c1ea2d0ccb4241bed Mon Sep 17 00:00:00 2001 From: Niklas Date: Fri, 6 Sep 2024 00:13:20 +0200 Subject: [PATCH 7/9] Suggested changes --- .../chemical-fenics/requirements.txt | 10 +++++++--- .../fluid-fenics/requirements.txt | 9 ++++++--- elastic-tube-1d/fluid-python/requirements.txt | 2 +- elastic-tube-1d/solid-python/requirements.txt | 2 +- elastic-tube-3d/solid-fenics/requirements.txt | 10 +++++++--- .../solid-python/requirements.txt | 2 +- .../solid-fenics/requirements.txt | 12 ++++++++---- oscillator-overlap/mass-left-python/run.sh | 4 ++-- oscillator-overlap/mass-right-python/run.sh | 4 ++-- oscillator/mass-left-fmi/requirements.txt | 2 +- oscillator/mass-left-fmi/run.sh | 4 ++-- oscillator/mass-left-python/run.sh | 4 ++-- oscillator/mass-right-fmi/run.sh | 4 ++-- oscillator/mass-right-python/run.sh | 4 ++-- .../dirichlet-fenics/run.sh | 4 ++-- .../neumann-fenics/run.sh | 4 ++-- .../solver-fenics/requirements.txt | 12 ++++++++---- .../left-fenics/run.sh | 4 ++-- .../right-fenics/run.sh | 4 ++-- .../solver-fenics/requirements.txt | 12 ++++++++---- .../dirichlet-fenics/run.sh | 4 ++-- partitioned-heat-conduction/neumann-fenics/run.sh | 4 ++-- .../solver-fenics/requirements.txt | 12 ++++++++---- perpendicular-flap/solid-fenics/requirements.txt | 14 +++++++++----- volume-coupled-diffusion/drain-fenics/run.sh | 4 ++-- .../solver-fenics/requirements.txt | 12 ++++++++---- volume-coupled-diffusion/source-fenics/run.sh | 4 ++-- 27 files changed, 101 insertions(+), 66 deletions(-) diff --git a/channel-transport-reaction/chemical-fenics/requirements.txt b/channel-transport-reaction/chemical-fenics/requirements.txt index 69a4edeb3..26648ea94 100644 --- a/channel-transport-reaction/chemical-fenics/requirements.txt +++ b/channel-transport-reaction/chemical-fenics/requirements.txt @@ -1,5 +1,9 @@ numpy >1, <2 -pyprecice~=3.0 -mpi4py < 4 -fenicsprecice +fenicsprecice~=2.0 + +fenics-dijitso==2019.2.0.dev0 +fenics-dolfin==2019.2.0.13.dev0 +fenics-ffc==2019.2.0.dev0 +fenics-fiat==2019.2.0.dev0 +fenics-ufl-legacy==2022.3.0 diff --git a/channel-transport-reaction/fluid-fenics/requirements.txt b/channel-transport-reaction/fluid-fenics/requirements.txt index de06348da..65c0f5ef4 100644 --- a/channel-transport-reaction/fluid-fenics/requirements.txt +++ b/channel-transport-reaction/fluid-fenics/requirements.txt @@ -1,5 +1,8 @@ numpy >1, <2 -pyprecice~=3.0 -mpi4py <4 -fenicsprecice +fenicsprecice~=2.0 +fenics-dijitso==2019.2.0.dev0 +fenics-dolfin==2019.2.0.13.dev0 +fenics-ffc==2019.2.0.dev0 +fenics-fiat==2019.2.0.dev0 +fenics-ufl-legacy==2022.3.0 \ No newline at end of file diff --git a/elastic-tube-1d/fluid-python/requirements.txt b/elastic-tube-1d/fluid-python/requirements.txt index ee1722131..560b7fb9f 100644 --- a/elastic-tube-1d/fluid-python/requirements.txt +++ b/elastic-tube-1d/fluid-python/requirements.txt @@ -1,3 +1,3 @@ pyprecice~=3.0 -numpy +numpy >1, <2 matplotlib \ No newline at end of file diff --git a/elastic-tube-1d/solid-python/requirements.txt b/elastic-tube-1d/solid-python/requirements.txt index 4301cd5fd..8a45549cd 100644 --- a/elastic-tube-1d/solid-python/requirements.txt +++ b/elastic-tube-1d/solid-python/requirements.txt @@ -1,2 +1,2 @@ pyprecice~=3.0 -numpy \ No newline at end of file +numpy >1, <2 \ No newline at end of file diff --git a/elastic-tube-3d/solid-fenics/requirements.txt b/elastic-tube-3d/solid-fenics/requirements.txt index 41b3413a9..9614b5742 100644 --- a/elastic-tube-3d/solid-fenics/requirements.txt +++ b/elastic-tube-3d/solid-fenics/requirements.txt @@ -1,4 +1,8 @@ pyprecice~=3.0 -fenicsprecice -numpy -mpi4py <4 \ No newline at end of file +numpy >1, <2 + +fenics-dijitso==2019.2.0.dev0 +fenics-dolfin==2019.2.0.13.dev0 +fenics-ffc==2019.2.0.dev0 +fenics-fiat==2019.2.0.dev0 +fenics-ufl-legacy==2022.3.0 \ No newline at end of file diff --git a/flow-around-controlled-moving-cylinder/solid-python/requirements.txt b/flow-around-controlled-moving-cylinder/solid-python/requirements.txt index 4301cd5fd..8a45549cd 100644 --- a/flow-around-controlled-moving-cylinder/solid-python/requirements.txt +++ b/flow-around-controlled-moving-cylinder/solid-python/requirements.txt @@ -1,2 +1,2 @@ pyprecice~=3.0 -numpy \ No newline at end of file +numpy >1, <2 \ No newline at end of file diff --git a/flow-over-heated-plate/solid-fenics/requirements.txt b/flow-over-heated-plate/solid-fenics/requirements.txt index 41b3413a9..65c7aae96 100644 --- a/flow-over-heated-plate/solid-fenics/requirements.txt +++ b/flow-over-heated-plate/solid-fenics/requirements.txt @@ -1,4 +1,8 @@ -pyprecice~=3.0 -fenicsprecice -numpy -mpi4py <4 \ No newline at end of file +fenicsprecice~=2.0 +numpy >1, <2 + +fenics-dijitso==2019.2.0.dev0 +fenics-dolfin==2019.2.0.13.dev0 +fenics-ffc==2019.2.0.dev0 +fenics-fiat==2019.2.0.dev0 +fenics-ufl-legacy==2022.3.0 \ No newline at end of file diff --git a/oscillator-overlap/mass-left-python/run.sh b/oscillator-overlap/mass-left-python/run.sh index 2a31e7e79..8268553b8 100755 --- a/oscillator-overlap/mass-left-python/run.sh +++ b/oscillator-overlap/mass-left-python/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv ../solver-python/.venv -. ../solver-python/.venv/bin/activate +python3 -m venv .venv +. .venv/bin/activate pip install -r ../solver-python/requirements.txt python3 ../solver-python/oscillator.py Mass-Left diff --git a/oscillator-overlap/mass-right-python/run.sh b/oscillator-overlap/mass-right-python/run.sh index 67d5a66ab..51ddf0eac 100755 --- a/oscillator-overlap/mass-right-python/run.sh +++ b/oscillator-overlap/mass-right-python/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv ../solver-python/.venv -. ../solver-python/.venv/bin/activate +python3 -m venv .venv +. .venv/bin/activate pip install -r ../solver-python/requirements.txt python3 ../solver-python/oscillator.py Mass-Right diff --git a/oscillator/mass-left-fmi/requirements.txt b/oscillator/mass-left-fmi/requirements.txt index 871b3ec2b..10f7ea9df 100644 --- a/oscillator/mass-left-fmi/requirements.txt +++ b/oscillator/mass-left-fmi/requirements.txt @@ -1 +1 @@ - fmiprecice \ No newline at end of file +fmiprecice \ No newline at end of file diff --git a/oscillator/mass-left-fmi/run.sh b/oscillator/mass-left-fmi/run.sh index 9fe8217b3..a6f1f563a 100755 --- a/oscillator/mass-left-fmi/run.sh +++ b/oscillator/mass-left-fmi/run.sh @@ -16,8 +16,8 @@ if [ ! -f ../solver-fmi/Oscillator.fmu ]; then cd ../../../mass-left-fmi fi -python3 -m venv ../sover-fmi/.venv -. ../sover-fmi/.venv/bin/activate +python3 -m venv .venv +. .venv/bin/activate pip install -r requirements.txt fmiprecice fmi-settings.json precice-settings.json diff --git a/oscillator/mass-left-python/run.sh b/oscillator/mass-left-python/run.sh index 2a31e7e79..8268553b8 100755 --- a/oscillator/mass-left-python/run.sh +++ b/oscillator/mass-left-python/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv ../solver-python/.venv -. ../solver-python/.venv/bin/activate +python3 -m venv .venv +. .venv/bin/activate pip install -r ../solver-python/requirements.txt python3 ../solver-python/oscillator.py Mass-Left diff --git a/oscillator/mass-right-fmi/run.sh b/oscillator/mass-right-fmi/run.sh index 26952b591..4ca91f9dd 100755 --- a/oscillator/mass-right-fmi/run.sh +++ b/oscillator/mass-right-fmi/run.sh @@ -16,8 +16,8 @@ if [ ! -f ../solver-fmi/Oscillator.fmu ]; then cd ../../../mass-right-fmi fi -python3 -m venv ../sover-fmi/.venv -. ../sover-fmi/.venv/bin/activate +python3 -m venv .venv +. .venv/bin/activate pip install -r requirements.txt fmiprecice fmi-settings.json precice-settings.json diff --git a/oscillator/mass-right-python/run.sh b/oscillator/mass-right-python/run.sh index 67d5a66ab..51ddf0eac 100755 --- a/oscillator/mass-right-python/run.sh +++ b/oscillator/mass-right-python/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv ../solver-python/.venv -. ../solver-python/.venv/bin/activate +python3 -m venv .venv +. .venv/bin/activate pip install -r ../solver-python/requirements.txt python3 ../solver-python/oscillator.py Mass-Right diff --git a/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh b/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh index 9a9ce7331..655407447 100755 --- a/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh +++ b/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv --system-site-packages ../solver-fenics/.venv -. ../solver-fenics/.venv/bin/activate +python3 -m venv --system-site-packages .venv +. .venv/bin/activate pip install -r ../solver-fenics/requirements.txt python3 ../solver-fenics/heat.py -d -i complex diff --git a/partitioned-heat-conduction-complex/neumann-fenics/run.sh b/partitioned-heat-conduction-complex/neumann-fenics/run.sh index 4f189a03a..e9a09cd54 100755 --- a/partitioned-heat-conduction-complex/neumann-fenics/run.sh +++ b/partitioned-heat-conduction-complex/neumann-fenics/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv --system-site-packages ../solver-fenics/.venv -. ../solver-fenics/.venv/bin/activate +python3 -m venv --system-site-packages .venv +. .venv/bin/activate pip install -r ../solver-fenics/requirements.txt python3 ../solver-fenics/heat.py -n -i complex diff --git a/partitioned-heat-conduction-complex/solver-fenics/requirements.txt b/partitioned-heat-conduction-complex/solver-fenics/requirements.txt index c97879a7c..0fa35afc6 100644 --- a/partitioned-heat-conduction-complex/solver-fenics/requirements.txt +++ b/partitioned-heat-conduction-complex/solver-fenics/requirements.txt @@ -1,5 +1,9 @@ -pyprecice~=3.0 -fenicsprecice -numpy +fenicsprecice~=2.0 +numpy >1, <2 sympy -mpi4py <4 \ No newline at end of file + +fenics-dijitso==2019.2.0.dev0 +fenics-dolfin==2019.2.0.13.dev0 +fenics-ffc==2019.2.0.dev0 +fenics-fiat==2019.2.0.dev0 +fenics-ufl-legacy==2022.3.0 \ No newline at end of file diff --git a/partitioned-heat-conduction-overlap/left-fenics/run.sh b/partitioned-heat-conduction-overlap/left-fenics/run.sh index e876c94c4..5304329a4 100755 --- a/partitioned-heat-conduction-overlap/left-fenics/run.sh +++ b/partitioned-heat-conduction-overlap/left-fenics/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv --system-site-packages ../solver-fenics/.venv -. ../solver-fenics/.venv/bin/activate +python3 -m venv --system-site-packages .venv +. .venv/bin/activate pip install -r ../solver-fenics/requirements.txt python3 ../solver-fenics/heat.py Left diff --git a/partitioned-heat-conduction-overlap/right-fenics/run.sh b/partitioned-heat-conduction-overlap/right-fenics/run.sh index 90f1a7a68..1df24c1db 100755 --- a/partitioned-heat-conduction-overlap/right-fenics/run.sh +++ b/partitioned-heat-conduction-overlap/right-fenics/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv --system-site-packages ../solver-fenics/.venv -. ../solver-fenics/.venv/bin/activate +python3 -m venv --system-site-packages .venv +. .venv/bin/activate pip install -r ../solver-fenics/requirements.txt python3 ../solver-fenics/heat.py Right diff --git a/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt b/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt index 41b3413a9..65c7aae96 100644 --- a/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt +++ b/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt @@ -1,4 +1,8 @@ -pyprecice~=3.0 -fenicsprecice -numpy -mpi4py <4 \ No newline at end of file +fenicsprecice~=2.0 +numpy >1, <2 + +fenics-dijitso==2019.2.0.dev0 +fenics-dolfin==2019.2.0.13.dev0 +fenics-ffc==2019.2.0.dev0 +fenics-fiat==2019.2.0.dev0 +fenics-ufl-legacy==2022.3.0 \ No newline at end of file diff --git a/partitioned-heat-conduction/dirichlet-fenics/run.sh b/partitioned-heat-conduction/dirichlet-fenics/run.sh index 09311591f..207b8e433 100755 --- a/partitioned-heat-conduction/dirichlet-fenics/run.sh +++ b/partitioned-heat-conduction/dirichlet-fenics/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv --system-site-packages ../solver-fenics/.venv -. ../solver-fenics/.venv/bin/activate +python3 -m venv --system-site-packages .venv +. .venv/bin/activate pip install -r ../solver-fenics/requirements.txt python3 ../solver-fenics/heat.py Dirichlet diff --git a/partitioned-heat-conduction/neumann-fenics/run.sh b/partitioned-heat-conduction/neumann-fenics/run.sh index f97b09d76..57d8648b0 100755 --- a/partitioned-heat-conduction/neumann-fenics/run.sh +++ b/partitioned-heat-conduction/neumann-fenics/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv --system-site-packages ../solver-fenics/.venv -. ../solver-fenics/.venv/bin/activate +python3 -m venv --system-site-packages .venv +. .venv/bin/activate pip install -r ../solver-fenics/requirements.txt python3 ../solver-fenics/heat.py Neumann diff --git a/partitioned-heat-conduction/solver-fenics/requirements.txt b/partitioned-heat-conduction/solver-fenics/requirements.txt index c97879a7c..0fa35afc6 100644 --- a/partitioned-heat-conduction/solver-fenics/requirements.txt +++ b/partitioned-heat-conduction/solver-fenics/requirements.txt @@ -1,5 +1,9 @@ -pyprecice~=3.0 -fenicsprecice -numpy +fenicsprecice~=2.0 +numpy >1, <2 sympy -mpi4py <4 \ No newline at end of file + +fenics-dijitso==2019.2.0.dev0 +fenics-dolfin==2019.2.0.13.dev0 +fenics-ffc==2019.2.0.dev0 +fenics-fiat==2019.2.0.dev0 +fenics-ufl-legacy==2022.3.0 \ No newline at end of file diff --git a/perpendicular-flap/solid-fenics/requirements.txt b/perpendicular-flap/solid-fenics/requirements.txt index a64af1da5..9567a860e 100644 --- a/perpendicular-flap/solid-fenics/requirements.txt +++ b/perpendicular-flap/solid-fenics/requirements.txt @@ -1,5 +1,9 @@ -pyprecice~=3.0 -fenicsprecice -mpi4py <4 -numpy -matplotlib \ No newline at end of file +fenicsprecice~=2.0 +numpy >1, <2 +matplotlib + +fenics-dijitso==2019.2.0.dev0 +fenics-dolfin==2019.2.0.13.dev0 +fenics-ffc==2019.2.0.dev0 +fenics-fiat==2019.2.0.dev0 +fenics-ufl-legacy==2022.3.0 \ No newline at end of file diff --git a/volume-coupled-diffusion/drain-fenics/run.sh b/volume-coupled-diffusion/drain-fenics/run.sh index 6060b7758..47f434ab8 100755 --- a/volume-coupled-diffusion/drain-fenics/run.sh +++ b/volume-coupled-diffusion/drain-fenics/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv --system-site-packages ../solver-fenics/.venv -. ../solver-fenics/.venv/bin/activate +python3 -m venv --system-site-packages .venv +. .venv/bin/activate pip install -r ../solver-fenics/requirements.txt python3 ../solver-fenics/volume-coupled-diffusion.py --drain diff --git a/volume-coupled-diffusion/solver-fenics/requirements.txt b/volume-coupled-diffusion/solver-fenics/requirements.txt index 31c8c49c8..65c7aae96 100644 --- a/volume-coupled-diffusion/solver-fenics/requirements.txt +++ b/volume-coupled-diffusion/solver-fenics/requirements.txt @@ -1,4 +1,8 @@ -fenicsprecice -pyprecice~=3.0 -mpi4py <4 -numpy \ No newline at end of file +fenicsprecice~=2.0 +numpy >1, <2 + +fenics-dijitso==2019.2.0.dev0 +fenics-dolfin==2019.2.0.13.dev0 +fenics-ffc==2019.2.0.dev0 +fenics-fiat==2019.2.0.dev0 +fenics-ufl-legacy==2022.3.0 \ No newline at end of file diff --git a/volume-coupled-diffusion/source-fenics/run.sh b/volume-coupled-diffusion/source-fenics/run.sh index d6ff75a84..a0e1e60ca 100755 --- a/volume-coupled-diffusion/source-fenics/run.sh +++ b/volume-coupled-diffusion/source-fenics/run.sh @@ -4,8 +4,8 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -python3 -m venv --system-site-packages ../solver-fenics/.venv -. ../solver-fenics/.venv/bin/activate +python3 -m venv --system-site-packages .venv +. .venv/bin/activate pip install -r ../solver-fenics/requirements.txt python3 ../solver-fenics/volume-coupled-diffusion.py --source From 1df7f7683c7fcf18042735aeb34439077ba0c342 Mon Sep 17 00:00:00 2001 From: Niklas Date: Fri, 6 Sep 2024 12:22:13 +0200 Subject: [PATCH 8/9] Accidentally deleted requirement --- elastic-tube-3d/solid-fenics/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/elastic-tube-3d/solid-fenics/requirements.txt b/elastic-tube-3d/solid-fenics/requirements.txt index 9614b5742..4d26dcc80 100644 --- a/elastic-tube-3d/solid-fenics/requirements.txt +++ b/elastic-tube-3d/solid-fenics/requirements.txt @@ -1,4 +1,4 @@ -pyprecice~=3.0 +fenicsprecice~=2.0 numpy >1, <2 fenics-dijitso==2019.2.0.dev0 From c27d9ec91a274a0a0b47f8977e7b09b156d97132 Mon Sep 17 00:00:00 2001 From: Niklas Date: Sun, 15 Sep 2024 20:35:28 +0200 Subject: [PATCH 9/9] Add suggested changes --- channel-transport-reaction/chemical-fenics/requirements.txt | 2 ++ channel-transport-reaction/fluid-fenics/requirements.txt | 2 ++ elastic-tube-3d/solid-fenics/requirements.txt | 2 ++ elastic-tube-3d/solid-fenics/run.sh | 3 +++ flow-over-heated-plate/solid-fenics/requirements.txt | 2 ++ .../solver-fenics/requirements.txt | 2 ++ .../solver-fenics/requirements.txt | 2 ++ perpendicular-flap/solid-fenics/requirements.txt | 2 ++ volume-coupled-diffusion/solver-fenics/requirements.txt | 2 ++ 9 files changed, 19 insertions(+) diff --git a/channel-transport-reaction/chemical-fenics/requirements.txt b/channel-transport-reaction/chemical-fenics/requirements.txt index 26648ea94..a07390096 100644 --- a/channel-transport-reaction/chemical-fenics/requirements.txt +++ b/channel-transport-reaction/chemical-fenics/requirements.txt @@ -1,6 +1,8 @@ numpy >1, <2 fenicsprecice~=2.0 +# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/ +# Use --system-site-packages in venv fenics-dijitso==2019.2.0.dev0 fenics-dolfin==2019.2.0.13.dev0 fenics-ffc==2019.2.0.dev0 diff --git a/channel-transport-reaction/fluid-fenics/requirements.txt b/channel-transport-reaction/fluid-fenics/requirements.txt index 65c0f5ef4..f1abc0891 100644 --- a/channel-transport-reaction/fluid-fenics/requirements.txt +++ b/channel-transport-reaction/fluid-fenics/requirements.txt @@ -1,6 +1,8 @@ numpy >1, <2 fenicsprecice~=2.0 +# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/ +# Use --system-site-packages in venv fenics-dijitso==2019.2.0.dev0 fenics-dolfin==2019.2.0.13.dev0 fenics-ffc==2019.2.0.dev0 diff --git a/elastic-tube-3d/solid-fenics/requirements.txt b/elastic-tube-3d/solid-fenics/requirements.txt index 4d26dcc80..fc17fc9e0 100644 --- a/elastic-tube-3d/solid-fenics/requirements.txt +++ b/elastic-tube-3d/solid-fenics/requirements.txt @@ -1,6 +1,8 @@ fenicsprecice~=2.0 numpy >1, <2 +# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/ +# Use --system-site-packages in venv fenics-dijitso==2019.2.0.dev0 fenics-dolfin==2019.2.0.13.dev0 fenics-ffc==2019.2.0.dev0 diff --git a/elastic-tube-3d/solid-fenics/run.sh b/elastic-tube-3d/solid-fenics/run.sh index 17d93f4a2..be7d30880 100755 --- a/elastic-tube-3d/solid-fenics/run.sh +++ b/elastic-tube-3d/solid-fenics/run.sh @@ -1,6 +1,9 @@ #!/usr/bin/env bash set -e -u +. ../../tools/log.sh +exec > >(tee --append "$LOGFILE") 2>&1 + python3 -m venv --system-site-package .venv . .venv/bin/activate pip install -r requirements.txt diff --git a/flow-over-heated-plate/solid-fenics/requirements.txt b/flow-over-heated-plate/solid-fenics/requirements.txt index 65c7aae96..115509804 100644 --- a/flow-over-heated-plate/solid-fenics/requirements.txt +++ b/flow-over-heated-plate/solid-fenics/requirements.txt @@ -1,6 +1,8 @@ fenicsprecice~=2.0 numpy >1, <2 +# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/ +# Use --system-site-packages in venv fenics-dijitso==2019.2.0.dev0 fenics-dolfin==2019.2.0.13.dev0 fenics-ffc==2019.2.0.dev0 diff --git a/partitioned-heat-conduction-complex/solver-fenics/requirements.txt b/partitioned-heat-conduction-complex/solver-fenics/requirements.txt index 0fa35afc6..9c8eb54e7 100644 --- a/partitioned-heat-conduction-complex/solver-fenics/requirements.txt +++ b/partitioned-heat-conduction-complex/solver-fenics/requirements.txt @@ -2,6 +2,8 @@ fenicsprecice~=2.0 numpy >1, <2 sympy +# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/ +# Use --system-site-packages in venv fenics-dijitso==2019.2.0.dev0 fenics-dolfin==2019.2.0.13.dev0 fenics-ffc==2019.2.0.dev0 diff --git a/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt b/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt index 65c7aae96..115509804 100644 --- a/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt +++ b/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt @@ -1,6 +1,8 @@ fenicsprecice~=2.0 numpy >1, <2 +# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/ +# Use --system-site-packages in venv fenics-dijitso==2019.2.0.dev0 fenics-dolfin==2019.2.0.13.dev0 fenics-ffc==2019.2.0.dev0 diff --git a/perpendicular-flap/solid-fenics/requirements.txt b/perpendicular-flap/solid-fenics/requirements.txt index 9567a860e..fe29958de 100644 --- a/perpendicular-flap/solid-fenics/requirements.txt +++ b/perpendicular-flap/solid-fenics/requirements.txt @@ -2,6 +2,8 @@ fenicsprecice~=2.0 numpy >1, <2 matplotlib +# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/ +# Use --system-site-packages in venv fenics-dijitso==2019.2.0.dev0 fenics-dolfin==2019.2.0.13.dev0 fenics-ffc==2019.2.0.dev0 diff --git a/volume-coupled-diffusion/solver-fenics/requirements.txt b/volume-coupled-diffusion/solver-fenics/requirements.txt index 65c7aae96..115509804 100644 --- a/volume-coupled-diffusion/solver-fenics/requirements.txt +++ b/volume-coupled-diffusion/solver-fenics/requirements.txt @@ -1,6 +1,8 @@ fenicsprecice~=2.0 numpy >1, <2 +# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/ +# Use --system-site-packages in venv fenics-dijitso==2019.2.0.dev0 fenics-dolfin==2019.2.0.13.dev0 fenics-ffc==2019.2.0.dev0