Matter: Port Matter classes (with unit tests) #94

julianakwan · 2025-03-01T00:27:18Z

This PR completes my port of the Matter classes and closes #10 . It includes:

Porting MatterCCZ4
Porting the ScalarField and DefaultPotential classes
Porting the calculation of Weyl4_Re and Weyl4_Im for a Matter class
Porting the calculation of the energy density, the momentum density and the spatial stress energy density for Matter classes
Porting the calculation of the relaxation of chi (I didn't know it was going to be depreciated!)
Unit tests for the above
Renaming NewMatterConstraints to just MatterConstraints.
The removal of the Matter directory from the list of ignored files in .lint_ignore

github-actions · 2025-03-01T00:27:32Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/ChiRelaxation.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/MatterCCZ4RHS.impl.hpp
Source/Matter/MatterConstraints.impl.hpp
Source/Matter/MatterWeyl4.impl.hpp
Source/Matter/ScalarField.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

github-actions · 2025-03-04T15:36:28Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/ChiRelaxation.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/MatterCCZ4RHS.impl.hpp
Source/Matter/MatterConstraints.impl.hpp
Source/Matter/MatterWeyl4.impl.hpp
Source/Matter/ScalarField.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

mirenradia

Thanks for this PR Juliana.

It looks pretty good but I have some comments. I know there are a fair few of them but I think most of them should be easy to resolve and the more complicated ones I will try and look at myself.

For the GRChombo HDF5 files you have generated for the tests, where is the code you used to create them? I couldn't find a relevant branch in the GRChombo repo.

I don't think the Tests/MatterWeyl4Test/GRChomboEMTensorTest.h5 file is needed/used so could you remove it as well?

Would you also be able to fix the commit history by applying the fixups?

Tests/ChiRelaxationTest/ChiRelaxationTest.cpp

Source/Matter/ChiRelaxation.hpp

Source/Matter/ChiRelaxation.impl.hpp

Tests/MatterWeyl4Test/MatterWeyl4Test.cpp

Tests/TestCases.hpp

Source/Matter/ChiRelaxation.hpp

KAClough · 2025-03-07T12:46:47Z

Source/Matter/EMTensor.hpp

+    /// 3 components for the momentum density: m_11, m_22, m_33
+    /// 6 components for the stress energy tensor (symmetric): s_11, s_12 etc.
+    static inline const amrex::Vector<std::string> extra_var_names = {
+        "m_11, m_22, m_33, s_11, s_12, s_13, s_22, s_23, s_33"};


Yes. We have always used Si and Sij but here that naming might be confusing. We could use J instead, so then it would be J1,J2,J3, S11, S12 etc. Maybe let's leave this for the naming tidy up as it would be best to be consistent throughout the code.

KAClough · 2025-03-07T12:49:00Z

Source/Matter/EMTensor.impl.hpp

This would be good. I always found the passing of intervals in the constructor a bit ugly and confusing.

Source/Matter/MatterConstraints.impl.hpp

Source/Matter/MatterConstraints.hpp

Source/Matter/MatterCCZ4RHS.impl.hpp

Source/Matter/MatterWeyl4.impl.hpp

Source/Matter/ScalarField.hpp

github-actions · 2025-03-19T22:20:10Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ChiRelaxation.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

github-actions · 2025-04-09T13:51:58Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ChiRelaxation.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

github-actions · 2025-04-09T14:01:45Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ChiRelaxation.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

github-actions · 2025-04-09T15:13:51Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ChiRelaxation.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

github-actions · 2025-04-09T15:33:11Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

julianakwan · 2025-04-09T16:04:07Z

Hi all - I think I have addressed everyone's comments now (and the lint checks have finally passed). Could you please review this PR again and double check that you are happy with everything?

Main changes are:

ChiRelaxation has been moved to a new branch enhancement/chi_relaxation
Names starting with Matter have been moved to ...WithMatter e.g. MatterCCZ4RHS is now CCZ4RHSWithMatter
Constructor classes involving the Matter object no longer require the Matter object to be passed as an argument because the object is now default constructed from the templated type.
Tests/Common/InitialData.hpp now has a function to initialize test scalar field and conjugate momentum values
I have applied the bugfix from GRChombo to the MovingPunctureGauge. Because it is a matter thing only, it is stored in it's own matter file MovingPunctureGaugeWithMatter.hpp

mirenradia

Thanks for making the changes, Juliana. Just a couple more minor changes.

Source/Matter/EMTensor.hpp

Source/Matter/ConstraintsWithMatter.hpp

Source/Matter/CCZ4RHSWithMatter.hpp

Source/Matter/EMTensor.hpp

Source/Matter/CCZ4RHSWithMatter.hpp

Source/Matter/ConstraintsWithMatter.hpp

Source/Matter/ConstraintsWithMatter.impl.hpp

Source/Matter/Weyl4WithMatter.hpp

Source/Matter/Weyl4WithMatter.impl.hpp

github-actions · 2025-04-15T11:53:49Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

julianakwan · 2025-04-15T12:36:51Z

Hi @mirenradia - I believe I have addressed all your comments now. Can you please take another look at this PR? Thanks!

This commit adds: - a set_up function to add the energy density, momemtum density and spatial stress-energy tensor as components of derive_lst - compute_mf a wrapper to the compute function which is called by AMReX whenever a derived variable needs to be calculated.

This commit will: - introduce a set_up function that adds "Weyl4_Re" and "Weyl4_Im" to the derive_lst for matter classes. - wrap the compute function inside compute_mf which is called by AMReX whenever the derived variable are needed.

This commit will: - introduce a set_up function for adding "Ham", "Mom1", "Mom2", and "Mom3" (or alternatively "Ham" and "Mom" normalized) to the derive_lst - introduce a compute_mf wrapper that will calculate the above whenever required by AMReX.

This commit will: - Call compute_mf to calculate derived varables - Refactor the HDF5 output to be consistent with the other unit tests (and update the relevent HDF5 files).

This commit will: - Pull out the test for rho from the MatterWeyl4 unit test into its own test case - Test the outputted values of rho calculated by EMTensor against values calculated by GRChombo - Test the outputted values of chi calculated by ChiRelaxation against values calculated by GRChombo - Add the GRChombo .h5 files for comparison - Add these two new test cases to the list in TestCases.hpp

This commit will: - Add an #if statement around HDF5 parts so they are not compiled if USE_HDF5=FALSE - Also, fix Lint errors

This commit will: - fix the bug in GRChombo with the gauge calculation in MatterCCZ4

This commit will: - Add the definition of phi and Pi to the common header file - Refactor the tests to use these definitions. I noticed that the BSSN Matter test and the chi relaxation test were using different initial conditions from the other so I had to update the HDF5 file outputs as well.

This commit will also: - Rename G_newton to G_Newton in the BSSN Matter test

This commit will: - Switch ordering of naming convention, so MatterCCZ4RHS becomes CCZ4RHSWithMatter, MatterConstraints becomes ConstraintsWithMatter, MatterWeyl4 becomes Weyl4WithMatter Matter: Remove matter object from constructor I forgot to remove the matter object in the constructor for CCZ4RHSWithMatter!

There is now a separate branch for the ChiRelaxation class

This will update the naming convention of emtensor_t: - The trace of the spatial stress energy tensor is now trS - The spatial stress energy tensor itself is now S - The momentum vector is now j

github-actions · 2025-04-17T12:44:53Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

KAClough

I am happy with this PR, I made two minor suggestions for you to consider @julianakwan but I don't feel strongly about them, so whatever you think! Let's get this merged and do the tidy up!

Source/Matter/MovingPunctureGaugeWithMatter.hpp

Source/Matter/ScalarField.impl.hpp

This will: - Remove the calculations of emtensor and add_matter_rhs without the potential and incorporate them into a single function

github-actions · 2025-04-28T14:28:56Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

This will: - Remove the calculations of emtensor and add_matter_rhs without the potential and incorporate them into a single function

Now the choice of which components are stored is decided by the template parameter em_tensor_parts. The choice is more limited as we now assume that if you want the momentum density, you will also want the energy density and similarly if you want the stress tensor, you want everything else too.

github-actions · 2025-04-29T11:59:21Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

julianakwan · 2025-04-29T12:37:45Z

I have incorporated the changes to the EMTensor class from enhancements/matter_class_mr_suggest with some changes - I would prefer to call it EMTensorOptions rather than EMTensorParts as I think this is clearer. (We could also have EMTensorComputeOptions but this is a bit long). I didn't do the same for the ConstraintsWithMatter class because the Constraints parent class needs to be changed as well (which should be done in another PR).

mirenradia · 2025-04-30T08:34:49Z

I have incorporated the changes to the EMTensor class from enhancements/matter_class_mr_suggest with some changes - I would prefer to call it EMTensorOptions rather than EMTensorParts as I think this is clearer. (We could also have EMTensorComputeOptions but this is a bit long). I didn't do the same for the ConstraintsWithMatter class because the Constraints parent class needs to be changed as well (which should be done in another PR).

I'm fine with this. I think @KAClough suggested EMTensorComponents. I think she also wanted to change the last option from all to allDensities. I'll let her respond but I'm otherwise happy to approve this PR.

KAClough · 2025-04-30T13:52:34Z

I'm happy with EMTensorOptions - I didn't like Parts either. Options is nice as it shows you have options to pick! I would like to make it allDensities, thanks @mirenradia for remembering this. But we can also do that in the tidy up, it is not crucial. Let's merge this!

github-actions · 2025-04-30T15:44:35Z

This PR modifies the following files which are ignored by .lint-ignore:

Source/CCZ4/Weyl4.impl.hpp
Source/Matter/CCZ4RHSWithMatter.impl.hpp
Source/Matter/ConstraintsWithMatter.impl.hpp
Source/Matter/EMTensor.impl.hpp
Source/Matter/ScalarField.impl.hpp
Source/Matter/Weyl4WithMatter.impl.hpp

Please consider removing the corresponding patterns from .lint-ignore so that these files can be linted.

julianakwan added the enhancement New feature or request label Mar 1, 2025

julianakwan requested review from KAClough and mirenradia March 1, 2025 00:27

julianakwan self-assigned this Mar 1, 2025

julianakwan changed the title ~~Enhancement/matter class fix~~ Matter: Port Matter classes (with unit tests) Mar 3, 2025

mirenradia requested changes Mar 6, 2025

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KAClough reviewed Mar 7, 2025

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julianakwan force-pushed the enhancement/matter_class_fix branch from 5e527e5 to 2b7a3ce Compare March 19, 2025 22:19

julianakwan force-pushed the enhancement/matter_class_fix branch 2 times, most recently from 1c36aac to a44ef5d Compare April 9, 2025 13:51

julianakwan force-pushed the enhancement/matter_class_fix branch from 50c4e2b to dcf4ae8 Compare April 9, 2025 15:13

julianakwan requested review from mirenradia and KAClough April 9, 2025 15:46

mirenradia requested changes Apr 14, 2025

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julianakwan force-pushed the enhancement/matter_class_fix branch from da3ee70 to 47a3a61 Compare April 15, 2025 11:53

julianakwan force-pushed the enhancement/matter_class_fix branch from 47a3a61 to 20562ea Compare April 15, 2025 12:14

julianakwan requested a review from mirenradia April 15, 2025 12:36

julianakwan mentioned this pull request Apr 16, 2025

Rename components of emtensor_t for consistency #117

Merged

julianakwan added 2 commits April 17, 2025 11:48

Matter: Port MatterCCZ4 class

70f7c08

Matter: Port Constraints and Weyl4 calculations

f208f0a

julianakwan added 14 commits April 17, 2025 11:52

Tests: Update unit tests to use compute_mf for derived variables

cc963c1

This commit will: - Call compute_mf to calculate derived varables - Refactor the HDF5 output to be consistent with the other unit tests (and update the relevent HDF5 files).

Matter: Rename NewMatterConstraints to MatterConstraints

aa46dff

Tests: Add pre-processor directives to surround HDF5 includes

e38e239

This commit will: - Add an #if statement around HDF5 parts so they are not compiled if USE_HDF5=FALSE - Also, fix Lint errors

Matter: Apply bugfix 234 from GRChombo

883a5a3

This commit will: - fix the bug in GRChombo with the gauge calculation in MatterCCZ4

Matter: Remove matter object from constructor

02be432

This commit will also: - Rename G_newton to G_Newton in the BSSN Matter test

Matter: Move the gauge calculation re:matter to its own file

9cbdb7d

Matter: Remove ChiRelaxation (to enhancement/chi_relaxation)

1815ca8

There is now a separate branch for the ChiRelaxation class

Matter: Change naming of emtensor components to be consistent

8c30fcb

This will update the naming convention of emtensor_t: - The trace of the spatial stress energy tensor is now trS - The spatial stress energy tensor itself is now S - The momentum vector is now j

julianakwan force-pushed the enhancement/matter_class_fix branch from 20562ea to 8c30fcb Compare April 17, 2025 12:44

KAClough reviewed Apr 25, 2025

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Source/Matter/MovingPunctureGaugeWithMatter.hpp Show resolved Hide resolved

Source/Matter/ScalarField.impl.hpp Outdated Show resolved Hide resolved

Matter: Combine calculations with and without potential

1e8be04

This will: - Remove the calculations of emtensor and add_matter_rhs without the potential and incorporate them into a single function

julianakwan and others added 2 commits April 29, 2025 12:53

Matter: Combine calculations with and without potential

74457d7

This will: - Remove the calculations of emtensor and add_matter_rhs without the potential and incorporate them into a single function

mirenradia approved these changes Apr 30, 2025

View reviewed changes

Matter: Change option from all to allDensities

8d1ea32

julianakwan merged commit d632ffe into develop Apr 30, 2025
55 of 56 checks passed

julianakwan deleted the enhancement/matter_class_fix branch April 30, 2025 17:22

Matter: Port Matter classes (with unit tests) #94

Matter: Port Matter classes (with unit tests) #94

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