Centre for cylinder & spherical meshes #2256

RemDelaporteMathurin · 2022-10-07T07:29:46Z

This fixes #2248 by adding a centre attribute to CylindricalMesh and SphericalMesh

Usage

mesh = openmc.CylindricalMesh()
mesh.phi_grid = np.linspace(0, 2*np.pi, 21)
mesh.z_grid = np.linspace(-1, 1, 11)
mesh.r_grid = np.linspace(0, 1, 11)

mesh.origin = [0.1, 0.2, 0.3]

RemDelaporteMathurin · 2022-10-07T07:58:56Z

@pshriwise I need to declare centre in mesh.cpp. However as I don't speak C++ (yet?) I don't really know how to do this. Would you mind giving this a look?

src/mesh.cpp

RemDelaporteMathurin · 2022-10-07T11:10:40Z

@pshriwise I need to declare centre in mesh.cpp. However as I don't speak C++ (yet?) I don't really know how to do this. Would you mind giving this a look?

I think I managed to add everything we needed for this in the end 😄

RemDelaporteMathurin · 2022-10-07T12:44:26Z

The tests are failing.

One regression test is failing --> I think we just need to update the gold standard input file.
Some unit tests are failing in tests/unit_tests/test_deplete_activation.py although I'm not certain why: @shimwell do you confirm the default centre for cylindrical and spherical meshes is (0, 0, 0) ?

RemDelaporteMathurin · 2022-10-07T14:15:22Z

I honestly don't understand why these four tests are failing.

When I run the tests with pytest tests/ they fail but when I run pytest tests/unit_tests/test_deplete_activation.py it succeeds...

pshriwise · 2022-10-07T15:00:19Z

@pshriwise I need to declare centre in mesh.cpp. However as I don't speak C++ (yet?) I don't really know how to do this. Would you mind giving this a look?

I think I managed to add everything we needed for this in the end 😄

That's great! I'll take a look first thing on Monday -- I'm off today for a long weekend.

pshriwise

Hi @RemDelaporteMathurin! Thanks for taking this on. 🤩 It's been needed for a while and will be a much-used, much-appreciated upgrade.

A couple of minor comments from me here. Additionally, I'd prefer to use the term origin over centre here to be consistent with our description of a sphere surface. Would you mind updating that attribute name?

include/openmc/mesh.h

src/mesh.cpp

openmc/mesh.py

Co-authored-by: Ethan Peterson <[email protected]>

openmc/mesh.py

Co-authored-by: Ethan Peterson <[email protected]>

eepeterson

@RemDelaporteMathurin and @pshriwise just a few more questions and comments

docs/source/io_formats/statepoint.rst

include/openmc/mesh.h

tests/unit_tests/test_cylindrical_mesh.py

tests/unit_tests/test_spherical_mesh.py

…intermediate class

…shes Add an intermediate `PeriodicStructuredMesh` class to separate the `origin` attribute from `StructuredMesh`

….com/RemDelaporteMathurin/openmc into centre_for_cylinder_spherical_meshes

pshriwise · 2023-03-16T16:28:02Z

I've just attempted to handle the conflicts in mesh.py. I'll keep an eye on CI to make sure that was successful.

Aside from that, I think there's one outstanding comment from @eepeterson remaining. @RemDelaporteMathurin are you up for addressing that one?

RemDelaporteMathurin · 2023-03-16T21:11:57Z

@RemDelaporteMathurin are you up for addressing that one?

Thanks for this Patrick, I don't have the bandwidth right now but I can have a look whenever I have time

paulromano · 2023-03-21T18:52:50Z

@RemDelaporteMathurin I just sent a PR to your fork to address the outstanding request from @eepeterson:
RemDelaporteMathurin#7

Update IO format docs for meshes

RemDelaporteMathurin · 2023-03-23T00:25:16Z

@paulromano @eepeterson @pshriwise I think all the comments have been addressed and the tests pass! 🎸

eepeterson

LGTM, thanks for the work team!

RemDelaporteMathurin added 8 commits October 5, 2022 09:29

marks

facc199

centre attribute to CylindricalMesh and SphericalMesh

2a4c8bb

write to xml

c20b351

setters/getters

81ac9b0

read centre from xml

f0f5e34

added two tests to check centre was written/read to/from xml

5787616

now reads back from xml

16add87

offsets the write_to_vtk coordinates

21200d9

RemDelaporteMathurin added 3 commits October 7, 2022 08:40

centre to centre_

896ae27

test if grid_ is defined in this scope

d194e00

[skip ci] removed test

a104c1f

shimwell reviewed Oct 7, 2022

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src/mesh.cpp Outdated Show resolved Hide resolved

RemDelaporteMathurin added 5 commits October 7, 2022 09:15

attempt #2

bdd13ba

declare variable with auto

e394637

declaring centre_ in C file

61b4f30

removed auto + ;

fc5aa68

correct type for centre_

e1dbe49

RemDelaporteMathurin added 2 commits October 7, 2022 12:53

added centre tag to standard

1ed096f

Merge branch 'develop' into centre_for_cylinder_spherical_meshes

5632a40

pshriwise requested changes Oct 11, 2022

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include/openmc/mesh.h Outdated Show resolved Hide resolved

src/mesh.cpp Outdated Show resolved Hide resolved

RemDelaporteMathurin added 5 commits October 11, 2022 15:24

new type for centre_

94547f7

substract before mapping

15f45bc

array<double, 3> for origin CylindricalMesh

27e3bb4

centre to origin

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origin_ instead of origin

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RemDelaporteMathurin added 3 commits February 27, 2023 16:10

removed check and always offset origin

2f9f500

empty_like instead of copy

c61e735

fixed docstrings for origin

9ca6f1b

eepeterson reviewed Feb 27, 2023

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openmc/mesh.py Outdated Show resolved Hide resolved

[skip ci] Minor refactoring

972e1c1

Co-authored-by: Ethan Peterson <[email protected]>

eepeterson reviewed Feb 27, 2023

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openmc/mesh.py Outdated Show resolved Hide resolved

RemDelaporteMathurin and others added 2 commits February 27, 2023 16:23

Update openmc/mesh.py

308be3f

Co-authored-by: Ethan Peterson <[email protected]>

added grids in statepoint specs

c71c134

eepeterson requested changes Mar 1, 2023

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docs/source/io_formats/statepoint.rst Outdated Show resolved Hide resolved

include/openmc/mesh.h Outdated Show resolved Hide resolved

tests/unit_tests/test_cylindrical_mesh.py Outdated Show resolved Hide resolved

tests/unit_tests/test_spherical_mesh.py Outdated Show resolved Hide resolved

Moving origin data member down into Cylindrical/Spherical mesh using …

5946763

…intermediate class

pshriwise mentioned this pull request Mar 5, 2023

Add an intermediate PeriodicStructuredMesh class to separate the origin attribute from StructuredMesh RemDelaporteMathurin/openmc#6

Merged

pshriwise and others added 6 commits March 4, 2023 23:57

Adding docstring. Updating method name

b02e558

Merge pull request #6 from pshriwise/centre_for_cylinder_spherical_me…

1b29adb

…shes Add an intermediate `PeriodicStructuredMesh` class to separate the `origin` attribute from `StructuredMesh`

Merge branch 'develop' into centre_for_cylinder_spherical_meshes

527f5f7

use get_reshaped_data in tests

ab4237c

Merge branch 'centre_for_cylinder_spherical_meshes' of https://github…

024c51a

….com/RemDelaporteMathurin/openmc into centre_for_cylinder_spherical_meshes

Merge branch 'develop' into centre_for_cylinder_spherical_meshes

2d573c3

Update IO format docs for meshes

bb5f727

paulromano mentioned this pull request Mar 21, 2023

Update IO format docs for meshes RemDelaporteMathurin/openmc#7

Merged

RemDelaporteMathurin added 2 commits March 22, 2023 10:07

Merge pull request #7 from paulromano/pr-2256-docs

a091bee

Update IO format docs for meshes

Merge branch 'develop' into centre_for_cylinder_spherical_meshes

10f2a94

eepeterson approved these changes Mar 23, 2023

View reviewed changes

pshriwise approved these changes Mar 23, 2023

View reviewed changes

eepeterson merged commit 572e765 into openmc-dev:develop Mar 23, 2023

pshriwise mentioned this pull request May 31, 2023

Spherical mesh VTK coordinates bug #2416

Closed

paulromano mentioned this pull request Jun 13, 2023

Several small documentation updates #2558

Merged

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Centre for cylinder & spherical meshes #2256

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Centre for cylinder & spherical meshes #2256

Centre for cylinder & spherical meshes #2256

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