Fix GEAR pressure floor

Big change to the pressure floor API and corresponding changes to the hydro flavours as we need to pass the engine-carried floor throughout. This also has consequences on the cooling API and on the feedback.

At the same time, cleaned up a bit the grackle cooling header.

Also added a few checks to prevent certain feedback modes and hydro models to run with the pressure floor where it is not implemented.

Cleaned up the Agora galaxy example.

Todo:

• Add doxygen strings.
• Apply the same API change to the other hydro schemes.
• Add the higher-res. ICs to the repo. Update run script.

added GEAR bug labels

requested review from @yvesrevaz

assigned to @matthieu

added 1 commit

• 3b60f493 - Also change the API in the 'none' pressure floor case

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I get the following error when compiling after configuring with:

./configure CC=cc MPICC=cc --with-chemistry=GEAR_10 --with-cooling=grackle_0 --with-pressure-floor=GEAR --with-stars=GEAR --with-star-formation=GEAR --with-feedback=GEAR -enable-mpi --enable-mpi-mesh-gravity --with-hdf5=$HDF5_ROOT/bin/h5pcc --with-gsl=$GSL_ROOT --with-parmetis=$PARMETIS_ROOT --with-fftw=$FFTW_ROOT --with-grackle=$GRACKLE_ROOT

No idea what this MHD variant is...

Thanks.

In file included from space_split.c:26:
In file included from In file included from space_rebuild.c./space.h::2636:
:
In file included from In file included from ./space.h./part.h::3684:
:
In file included from In file included from ./part.h././hydro/SPHENIX/hydro_part.h::8434:
:
In file included from ./mhd_struct.h././hydro/SPHENIX/hydro_part.h::32:234:In file included from :
 space_regrid.c:./mhd_struct.h26:error:
32: In file included from :./space.h2::"Invalid choice of MHD variant"36 :
In file included from ./part.h:84:
In file included from ././hydro/SPHENIX/hydro_part.h:34:

./mhd_struct.herror:: 32:2#error "Invalid choice of MHD variant""Invalid choice of MHD variant":
 
 ^error
: "Invalid choice of MHD variant"
#error "Invalid choice of MHD variant"
#error "Invalid choice of MHD variant"
 ^
 ^
In file included from space_first_init.c:26:
In file included from ./space.h:36:
In file included from ./part.h:84:
In file included from ././hydro/SPHENIX/hydro_part.h:34:
./mhd_struct.h:32:2: error: "Invalid choice of MHD variant"
#error "Invalid choice of MHD variant"
 ^
In file included from space_extras.c:26:
In file included from ./space.h:36:
In file included from ./part.h:84:
In file included from ././hydro/SPHENIX/hydro_part.h:34:
./mhd_struct.h:32:2: error: "Invalid choice of MHD variant"
#error "Invalid choice of MHD variant"
 ^
In file included from space_split.c:26:
In file included from ./space.h:36:
In file included from ./part.h:84:
././hydro/SPHENIX/hydro_part.h:83:25: error: field has incomplete type 'struct mhd_xpart_data'
  struct mhd_xpart_data mhd_data;
                        ^
././hydro/SPHENIX/hydro_part.h:83:10In file included from :space_regrid.c:26:
 In file included from ./space.h:note36: :
In file included from forward declaration of 'struct mhd_xpart_data'./part.h:
84:
././hydro/SPHENIX/hydro_part.h:  struct mhd_xpart_data mhd_data;83
:25         ^:
 error: field has incomplete type 'struct mhd_xpart_data'In file included from space_rebuild.c
:26  struct mhd_xpart_data mhd_data;:

In file included from                         ^./space.h
:36:
In file included from ./part.h././hydro/SPHENIX/hydro_part.h::8384::
10: ././hydro/SPHENIX/hydro_part.h:83note:: 25:forward declaration of 'struct mhd_xpart_data' 
error  struct mhd_xpart_data mhd_data;: 
         ^
field has incomplete type 'struct mhd_xpart_data'
  struct mhd_xpart_data mhd_data;
                        ^
././hydro/SPHENIX/hydro_part.h:83././hydro/SPHENIX/hydro_part.h::10219::24 : noteerror: : field has incomplete type 'struct mhd_part_data'forward declaration of 'struct mhd_xpart_data'

  struct mhd_part_data mhd_data;
  struct mhd_xpart_data mhd_data;
                       ^
         ^
././hydro/SPHENIX/hydro_part.h:219:10:././hydro/SPHENIX/hydro_part.h :219:note24: : forward declaration of 'struct mhd_part_data'
error:   struct mhd_part_data mhd_data;
field has incomplete type 'struct mhd_part_data'         ^

  struct mhd_part_data mhd_data;
                       ^
././hydro/SPHENIX/hydro_part.h:219:10: note: forward declaration of 'struct mhd_part_data'
  struct mhd_part_data mhd_data;
         ^
././hydro/SPHENIX/hydro_part.h:219:24: error: field has incomplete type 'struct mhd_part_data'
  struct mhd_part_data mhd_data;
                       ^
././hydro/SPHENIX/hydro_part.h:219:10: note: forward declaration of 'struct mhd_part_data'
  struct mhd_part_data mhd_data;

I can't reproduce this.

Is that from the latest version of this branch? And with autoreconf run in the directory after the pull?

What compiler is this? I don't recognize the error messages.

I'm on Cray (daint@CSCS). Ok. Starting from scratch, i.e, cloning+./autogen.sh+checkout+configure solved the problem. In my previous attempt, I started from an old commit, checkout to fix_GEAR_pressure_floor+configure which I think should have done the job properly. Everything is running smoothly now. I just wait for the end of the test before approving the merge.

approved this merge request

closed

reopened

Once merged, I'll also add this build to our automated test suite so that it won't be allowed to break again.

removed bug label

added bug label

changed the description

marked the checklist item Apply the same API change to the other hydro schemes. as completed

added 2 commits

• 4b022dd3 - Add doxygen strings
• b7bda477 - Remove unused pressure floor functions

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marked the checklist item Add doxygen strings. as completed

marked the checklist item Apply the same API change to the other hydro schemes. as incomplete

added 1 commit

• 6190be83 - Update the pressure floor to work with Gadget-2, Gasoline, and PE SPH

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added 2 commits

• 177b4cdf - Also fix all the other hydro schemes
• 4ede30f7 - Also fix all the other hydro schemes

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added 1 commit

• 58f11f40 - Fix the subgrid models to work with the pressure floor

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marked the checklist item Apply the same API change to the other hydro schemes. as completed

That should now compile with the different hydro schemes and our normal sets of subgrid. Note that I really don't like it. The pressure floor is really invasive. The solution here is really non-generic as it can only be used with GEAR and nothing else.

Thanks ! I'm sorry that this implementation is not satisfactory at all. It is clear that at some point we will abandon this pressure floor. However, from a physical point of view, I think it make quite a lots of sense as long as the ISM turbulence is not properly resolved. Let me know if its better that I use this branch to update the AGORA example.

Well we should definitely merge this in one way or another as the code is currently broken.

We can think of a better/cleaner implementation of the floor later if needed. Or, indeed, not use it in future models. :)

added 1 commit

• 00bca677 - Also fix the QLA cooling

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• 7ae4336d - Also fix gizmo compilation

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• 9d51af70 - Updated gitignore to not consider the Cloudy tables loaded for the GEAR model

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• e09c1b90 - GEAR/AgoraDisk updated.

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@matthieu I've updated the example. Its working with the files being stored in our website which is not appropriate I think. If you move to
http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/AgoraDisk all the files actually stored here: http://obswww.unige.ch/~revaz/SWIFT/AgoraDisk/ I will finalize the example. Note that the directory does not contain only ICs, but also other files like the cooling tables and the chemistry tables. Is it a problem to store that in /ICs/AgoraDisk

added 1 commit

• d051920f - fix a parameter in agora_disk.yml

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Here you go:

• http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/AgoraDisk/snap.MED.hdf5
• http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/AgoraDisk/snap.LOW.hdf5
• http://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/CloudyData_UVB=HM2012.h5
• http://virgodb.cosma.dur.ac.uk/swift-webstorage/FeedbackTables/POPIIsw.h5

added 1 commit

• 46a2f28e - download scripts updated with the new urls

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U just updated the download scripts with the new urls. From my side, everything is fine. The branch can be merged. Many thanks for the hard work.

marked the checklist item Add the higher-res. ICs to the repo. Update run script. as completed

Do we still need the cleanupSwift.py script?

no. I deleted it no ?

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• b56eaf56 - Apply python script formatting script

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added 1 commit

• f2fd2e82 - Removed unwanted script

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added 3 commits

• e166f398 - Update the QLA, QLA-EAGLE, const-du, const-lambda an no-cooling models to make...
• 2a9399e2 - Make the grackle, EAGLE and COLIBRE cooling applyt the pressure floor....
• 23b4c2fc - Fix the unit tests to make use of the pressure floor

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added 1 commit

• 7a00956c - Prevent the code from compiling with pressure floor and any of the EAGLE feedback combinations

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added 1 commit

• 985b5aee - Make git ignore more binary outputs generated by the RTD

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changed the description

added 1 commit

• a4669854 - Fix the cooling test executables to use the new API of the cooling functions...

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That became a monster clean-up operation. But I think I am happy now. I believe it compiles and runs in all the relevant modes.

Thanks ! I'm cleaning up the two others GEAR examples. Could you please copy this file:

https://obswww.unige.ch/~lhausamm/swift/ZoomIC/h050.hdf5 on the official storage: http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/ZoomIn/h050.hdf5 Thanks.

added 2 commits

• 84e91c65 - GEAR/ZoomIn cleaned
• cb1cc94c - Merge branch 'fix_GEAR_pressure_floor' of...

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• 256c86e0 - GEAR/AgoraCosmo example updated

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Are there more changes we need to consider here?

Yes, I need to finalize to fix the third GEAR example.