Restructure runscripts and related resources #181

MakisH · 2021-04-10T22:57:32Z

Similarly to #169 and #166, this collects all the run scripts into common files, to reduce duplication.

OpenFOAM: separated between a "preparation" and an "execution" phase. The execution is same for every case, the preparation can differ. I did not find any reason to use a function, so I just call the general script from inside each case-specific script.
- I also took the opportunity to clean up some old crimes in the heat exchanger, so this also closes heat-exchanger OpenFOAM is missing run.sh #171.
- Since this case is special because we download some additional files, I added these extra files in smaller .gitignore files, so this also rouches aspects of Inconsistent .gitignore among cases #87.
deal.II: no changes.
CalculiX: I only removed unnecesary/inconsistent comments and variables. Some cases with large meshes already set (default) values for OpenMP, I assume that these actually work and can be useful.
SU2: We only have one case, I left it hard-coded and simplified it.
FEniCS: In some cases, I added a run.sh or a clean.sh that was missing. I guess that some of the cases are not yet in the fully restructured form, but these are elements we need anyway. I have not checked if the runscripts run. I also softened a bit an existing .gitignore file for a FEniCS case.
Nutils: Similarly to FEniCS. I also extended the clean_nutils to remove all ./*.vtk files. Not tested.
code_aster: Only formatting and consistency changes.

All scripts have been validated with shellcheck.

Before merging:

Check documentation for renamed scripts: plot displacements, download meshes, run.sh / runFluid / Allrun, ...
Check documentation for 0.orig (moved to 0 in most cases) . What happens when we use the cleaning scripts of the foundation version?

After merging:

Update Quickstart (@davidscn would be a good review/cross-check that you apply the same changes there and I review the separate PR)

davidscn

Very nice! I guess your checklist keeps track of already checked run scripts and we can check tomorrow if everything works.

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

MakisH · 2021-04-11T11:23:07Z

@davidscn ready for review! If you can easily run something with Nutils/FEniCS, please do. Other than than, any comments are welcome. Especially: did I forget anything? Is there anything in the documentation to fix?

MakisH · 2021-04-11T13:40:57Z

tools/cleaning-tools.sh

@@ -40,7 +41,7 @@ clean_calculix() {
        set -e -u
        cd "$1"
        echo "--- Cleaning up CalculiX case in $(pwd)"
-        rm -fv ./*.cvg ./*.dat ./*.frd ./*.sta ./*.12d spooles.out
+        rm -fv ./*.cvg ./*.dat ./*.frd ./*.sta ./*.12d spooles.out dummy


This dummy is generated at least in the heat exchanger CalculiX case, I have no idea where it comes from.

tools/cleaning-tools.sh

MakisH · 2021-04-11T13:41:56Z

tools/cleaning-tools.sh

@@ -81,6 +82,7 @@ clean_nutils() {
        set -e -u
        cd "$1"
        echo "--- Cleaning up Nutils case in $(pwd)"
+        rm -fv ./*.vtk


Now we delete all the VTK files inside Nutils cases. I guess not much can go wrong.

davidscn

A two more comments:

the OpenFOAM run ends for me with the following message ../../tools/run-openfoam.sh: 17: .: openfoam-remove-empty-dirs.sh: not found
I created the deal.II run script as symbolic link similar to our cleaning scripts. Do you want to keep it in case of OpenFOAM as it currently is?

I will adjust the quickstart in #145 and we can check the remaining parts during the coding days :)

MakisH · 2021-04-11T16:50:51Z

* the OpenFOAM run ends for me with the following message `../../tools/run-openfoam.sh: 17: .: openfoam-remove-empty-dirs.sh: not found `

Good catch, I fixed it by moving the cleaning part into run.sh as a separate step.

* I created the deal.II run script as symbolic link similar to our cleaning scripts. Do you want to keep it in case of OpenFOAM as it currently is?

In the way I see it, we cannot do this for OpenFOAM: some cases have different preparation steps and for all of them I create a named .foam file (opening two .foam files in ParaView should keep it clear what is what).

I will adjust the quickstart in #145 and we can check the remaining parts during the coding days :)

Then I don't wait for the Quickstart :).

MakisH · 2021-04-11T16:56:24Z

This PR is ready from my side. I also looked at the diff and it is as intended. Are there further comments or things to check?

Add common runscript for OpenFOAM

94127f6

MakisH self-assigned this Apr 10, 2021

davidscn self-requested a review April 11, 2021 07:17

davidscn reviewed Apr 11, 2021

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MakisH added 13 commits April 11, 2021 10:25

Format files

8df4866

More formatting

7cfe1ff

Format cleaning scripts

0046c10

perpendicular-flap OpenFOAM: move 0.orig to 0

37e9d1c

Drop 0.orig from most OpenFOAM cases

86f5fbc

Move 0.orig to 0 also for turek-hron-fsi3

e403b5f

Simplify CalculiX run scripts

54494d8

Simplify SU2 runscript

4aa795f

Remove duplicate plotDisplacement.sh

d9c9121

Remove deprecated log cleaning commands

cd2b619

Tidy up FEniCS run and clean scripts

43a6e31

Tidy up Nutils run and clean scripts

75fa649

Tidy up code_aster run script

2409738

MakisH marked this pull request as ready for review April 11, 2021 11:21

MakisH requested a review from davidscn April 11, 2021 11:22

Clarify heat exchanger CalculiX gitignore, add 'dummy' to clean targets

45b3876

MakisH commented Apr 11, 2021

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MakisH commented Apr 11, 2021

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Add warning for preparing code_aster case

5b5acab

davidscn reviewed Apr 11, 2021

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MakisH added 2 commits April 11, 2021 18:32

Update documentation

577af4f

Move call to openfoam_remove_empty_dirs to run.sh

e169ad3

MakisH changed the title ~~Restructure runscripts~~ Restructure runscripts and related resources Apr 11, 2021

Fix clean_fenics

4d584da

MakisH mentioned this pull request Apr 11, 2021

Add partitioned pipe tutorial (moved from openfoam-adapter) #182

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davidscn approved these changes Apr 12, 2021

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davidscn merged commit 07f770e into develop Apr 12, 2021

davidscn deleted the runscripts branch April 12, 2021 05:37

MakisH mentioned this pull request Apr 12, 2021

heat-exchanger OpenFOAM is missing run.sh #171

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Restructure runscripts and related resources #181

Restructure runscripts and related resources #181

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Restructure runscripts and related resources #181

Restructure runscripts and related resources #181

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