Read capytaine functionality #464

akeeste · 2020-11-19T17:57:40Z

This PR adds read capytaine functionality to BEMIO. The BEMIO examples used for NEMOH and WAMIT have been recreated with Capytaine. The current read_capytaine script accomplishes as much as possible given Capytaine's current functionality. A method to add hydrostatics data is included in examples/BEMIO/CAPYTAINE/call_capy.py. This function must be used to output hydrostatics data in the correct format for read_capytaine.m

As Capytaine is still under development, it is important to know how it is being run for these cases to work correctly with BEMIO.
The specific python file that calls Capytaine and creates the .nc output is included in each case for this reason.

Files:
run_cases.py - Runs Capytaine for all cases
call_capytaine.py - Takes in input parameters, setups up Capytaine, runs hydrodynamics, and runs Capytaine
CASE.py - Setups up the input parameters that are sent to call_capytaine
CASE.nc - Capytaine output file for each case. This is read by the BEMIO function Read_CAPYTAINE.m

Notes:

Hydrostatics included with additional meshmagick function (see call_capy.py)
GBM should be supported, but has not been tested yet with B2B

…. More IRR issues but closer to WAMIT

kmruehl

@akeeste nice work! I didn't realize that you created all of the BEMIO runs too, that's great. I know it's still in progress, but you've gotten a lot done already.

kmruehl · 2020-12-16T21:54:56Z

examples/BEMIO/CAPYTAINE/Cubes/cubes.py

@@ -0,0 +1,54 @@
+"""


@akeeste are these the Capytaine input files?

The *.py scripts in each case directory set all of the Capytaine input parameters and run capytaine for each case (assuming Capytaine is already installed).

kmruehl · 2020-12-16T21:56:10Z

examples/BEMIO/CAPYTAINE/Cubes/t_cube.GDF

@@ -0,0 +1,9220 @@
+Rhino->WAMIT file export (mesh)
+1 9.81 	ULEN GRAV


If this is the same mesh as used for WAMIT, perhaps we should point to the WAMIT directory so we aren't uploading the same file twice?

Yes these are the same meshes in the other BEMIO examples. I can change case scripts to point to these meshes instead.

kmruehl · 2020-12-16T21:59:42Z

examples/BEMIO/CAPYTAINE/run_cases.py

+@author: akeeste
+
+This script runs all of the current cases for WEC-Sim bemio examples.
+


This runs all BEMIO runs, or just the Capytaine ones?

This script runs Capytaine for each case not BEMIO. I included this and call_capytaine.py so that everyone can see how Capytaine is being run for each case because there is an additional function required (hydrostatics)

kmruehl · 2020-12-24T01:28:52Z

@akeeste we need to re-open this PR. I went ahead and created a new dev branch and re-opened the PR

…_capytaine

…ngly

akeeste · 2021-01-15T18:59:52Z

@dav-og when you have some time, can you test the read_capytaine() function in this PR with any previous Capytaine output that you have? I want to ensure its working before we merge with master for the MECC groups

dav-og · 2021-01-22T06:08:40Z

@dav-og when you have some time, can you test the read_capytaine() function in this PR with any previous Capytaine output that you have? I want to ensure its working before we merge with master for the MECC groups

Hey Adam,

I ran your function on some old .nc files I had which don't have the hydrostatic stiffness matrix (C) included, so I get the following error message from normalize:

Warning: Hydrostatics data not included in Capytaine output. No value for C.
In Read_CAPYTAINE (line 205)
Reference to non-existent field 'C'.
Error in Normalize (line 50)
hydro(F).C = hydro(F).C/(hydro(F).g*hydro(F).rho);

Not sure what the best approach to this is 🤔. Obviously the user needs C to run WEC-Sim...But most of the time I would just use meshmagick to compute C separately, so ideally I'd prefer to have the option to pass C separately from the .nc file (i.e. just read from a text file such as 'KH.dat', as we do for Nemoh).

Other options for me in this instance could be to re-run Capytaine (which seems uneccessary just for C...especially if there are a lot of panels and/or frequencies to compute). Or manually edit the .nc files in hdfview or Python to include C...which could introduce errors/become tedious if you have a lot of .nc files.

I think if you want to merge this function as is, thats fine - I guess most people will just run Capytaine with hydrostatics and the function will read it straight from the .nc file? But if we could eventually have the option to read a separate 'KH.dat' file, as we do with Nemoh, I think that would be handy 👍

akeeste · 2021-01-22T17:20:51Z

@dav-og
Thanks for running this! I actually did change the read_capytaine function and made the hydrostatics (cg,cb,vo,C) use the same KH.dat and Hydrostatics.dat files that read_NEMOH() uses. I agree that since hydrostatics is not formally implemented in Capytaine, then we shouldn't require them in the .nc file. That would get messy and hard to fix..

I think the warning message is a bit ambiguous, I will change it to an error and point to those .dat files more obviously.

dav-og · 2021-01-22T17:24:24Z

Sounds good!

akeeste added 4 commits November 19, 2020 10:04

first revision of read_capytaine script

5ff134c

add Capy BEMIO cases to WEC-Sim/examples

b3ca411

minor bemio update. dof is size 1xNb and typically takes value of 6

ccec572

cleanup bemio files, read_capytaine, call_capytaine

6474e59

akeeste added the BEM/BEMIO related to BEMIO or BEM hydro data label Nov 19, 2020

akeeste self-assigned this Nov 19, 2020

akeeste added 7 commits November 19, 2020 15:52

clarify change to capytaine source code for hydrostatics to work

cf32661

add oswec BEMIO example

1692c36

starting b2b functionality

5b25cb4

working read_capytaine_b2b

34329cf

update capytaine script and B2B cases with correct B2B implementation…

7ff3565

…. More IRR issues but closer to WAMIT

clean up

058a543

update bemio script for easier comparison

8a6c8c0

kmruehl reviewed Dec 16, 2020

View reviewed changes

kmruehl closed this Dec 23, 2020

kmruehl deleted the branch WEC-Sim:dev December 23, 2020 23:05

kmruehl added the Feature new feature request label Dec 24, 2020

kmruehl reopened this Dec 24, 2020

akeeste added 2 commits January 4, 2021 08:43

Merge branch 'master' of https://github.com/WEC-Sim/WEC-Sim into read…

630d4ac

…_capytaine

update documentation with Capytaine references

3230070

dav-og self-requested a review January 6, 2021 23:34

akeeste added 3 commits January 13, 2021 08:28

Capytaine example in source bemio script

b79c32d

add distinct hydrostatics files, change how to call Capytaine accordi…

a74a317

…ngly

update Read_capytaine HS reading and lengthen some BEMIO irfs

e006258

akeeste marked this pull request as ready for review January 13, 2021 23:15

akeeste added 2 commits January 15, 2021 14:30

clean up comments and gbm dof sorting

98af472

GBM example with capytaine

0beb1e8

clarify hydrostatics error message

05a0f68

change 2nd hydrostatics error message

3ea9a38

dav-og approved these changes Jan 22, 2021

View reviewed changes

kmruehl merged commit ff731db into WEC-Sim:dev Jan 29, 2021

kmruehl deleted the read_capytaine branch January 29, 2021 16:40

		@@ -0,0 +1,9220 @@
		Rhino->WAMIT file export (mesh)
		1 9.81 ULEN GRAV

		@author: akeeste

		This script runs all of the current cases for WEC-Sim bemio examples.

Read capytaine functionality #464

Read capytaine functionality #464

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