Surface fitting updates #4116

kmittal2 · 2024-02-07T00:33:13Z

Misc updates related to surface fitting capability.

PR	Author	Editor	Reviewers	Assignment	Approval	Merge
#4116	@kmittal2	@tzanio	@vladotomov + @tzanio	2/13/24	⌛due 2/27/24	⌛due 3/5/24

PR Checklist

Code builds.
Code passes make style.
Update CHANGELOG:
- Is this a new feature users need to be aware of? New or updated example or miniapp?
- Does it make sense to create a new section in the CHANGELOG to group with other related features?
Update INSTALL:
- Had a new optional library been added? If so, what range of versions of this library are required? (Make sure the external library is compatible with our BSD license, e.g. it is not licensed under GPL!)
- Have the version ranges for any required or optional libraries changed?
- Does make or cmake have a new target?
- Did the requirements or the installation process change? (rare)
Update continuous integration server configurations if necessary (e.g. with new version requirements for each of MFEM's dependencies)
- .github
- .appveyor.yml
Update .gitignore:
- Check if make distclean; git status shows any files that were generated from the source by the project (not an IDE) but we don't want to track in the repository.
- Add new patterns (just for the new files above) and re-run the above test.
New examples:
- All sample runs at the top of the example source file work.
- Update examples/makefile:
  - Add the example code to the appropriate SEQ_EXAMPLES and PAR_EXAMPLES variables.
  - Add any files generated by it to the clean target.
  - Add the example binary and any files generated by it to the top-level .gitignore file.
- Update examples/CMakeLists.txt:
  - Add the example code to the ALL_EXE_SRCS variable.
  - Make sure THIS_TEST_OPTIONS is set correctly for the new example.
- List the new example in doc/CodeDocumentation.dox.
- If new examples directory (e.g.examples/pumi), list it in doc/CodeDocumentation.conf.in
- Companion pull request for documentation in mfem/web repo:
  - Update or add example-specific documentation, see e.g. the src/examples.md.
  - Add the description, labels and screenshots in src/examples.md and src/img.
  - In examples.md, list the example under the appropriate categories, add new categories if necessary.
  - Add a short description of the example in the "Extensive Examples" section of features.md.
New miniapps:
- All sample runs at the top of the miniapp source file work.
- Update top-level makefile and makefile in corresponding miniapp directory.
- Add the miniapp binary and any files generated by it to the top-level .gitignore file.
- Update CMake build system:
  - Update the CMakeLists.txt file in the miniapps directory, if the new miniapp is in a new directory.
  - Add/update the CMakeLists.txt file in the new miniapp directory.
  - Consider adding a new test for the new miniapp.
- List the new miniapp in doc/CodeDocumentation.dox
- If new miniapps directory (e.g.miniapps/nurbs), add it to MINIAPP_SUBDIRS in the makefile.
- If new miniapps directory (e.g.miniapps/nurbs), list it in doc/CodeDocumentation.conf.in
- Companion pull request for documentation in mfem/web repo:
  - Update or add miniapp-specific documentation, see e.g. the src/meshing.md and src/electromagnetics.md files.
  - Add the description, labels and screenshots in src/examples.md and src/img.
  - The miniapps go at the end of the page, and are usually listed only under a specific "Application (PDE)" category.
  - Add a short description of the miniapp in the "Extensive Examples" section of features.md.
New capability:
- All new public, protected, and private classes, methods, data members, and functions have full Doxygen-style documentation in source comments. Documentation should include descriptions of member data, function arguments and return values, template parameters, and prerequisites for calling new functions.
- Pointer arguments and return values must specify whether ownership is being transferred or lent with the call.
- Any new functions should include descriptions of their intended use e.g. for internal use only, user-facing, etc., along with references to example code whenever possible/appropriate.
- Consider adding new sample runs in existing examples to highlight the new capability.
- Consider saving cool simulation pictures with the new capability in the Confluence gallery (LLNL only) or submitting them, via pull request, to the gallery section of the mfem/web repo.
- If this is a major new feature, consider mentioning it in the short summary inside README (rare).
- List major new classes in doc/CodeDocumentation.dox (rare).
Update this checklist, if the new pull request affects it.
Run make unittest to make sure all unit tests pass.
Run the tests in tests/scripts.
(LLNL only) After merging:
- Update internal tests to include the new features.

…ng-updates

tzanio · 2024-02-13T22:40:40Z

This PR is now under review (see the table in the PR description). To help with the review process, please do not force push to the branch.

vladotomov · 2024-03-22T00:49:28Z

fem/gslib.hpp

@@ -290,6 +291,56 @@ class OversetFindPointsGSLIB : public FindPointsGSLIB
   using FindPointsGSLIB::Interpolate;
 };

+/// Class for gather-scatter (gs) operations on Vectors based on corresponding


Can we have the same doxygen style as in the rest of the file?

vladotomov · 2024-03-22T00:49:51Z

fem/gslib.hpp

+/// GSOPGSLIB gs = GSOPGSLIB(MPI_COMM_WORLD);
+/// gs.Setup(a);
+/// gs.GOP(v, GSOpType::Min);
+/// would return:


return into v?

vladotomov · 2024-03-22T00:52:08Z

fem/gslib.hpp

+   virtual ~GSOPGSLIB();
+
+   // Same ids get grouped together. id == 0 does not participate.
+   virtual void Setup(Array<long long> &ids);


Needs better doxygen (can include see class description).

vladotomov · 2024-03-22T00:52:13Z

fem/gslib.hpp

+
+   // supported operation types
+   enum GSOpType {ADD, MUL, MIN, MAX};
+   virtual void GSOP(Vector &senddata, GSOpType op);


Needs better doxygen (can include see class description).

vladotomov · 2024-03-22T00:52:32Z

fem/gslib.hpp

+   enum GSOpType {ADD, MUL, MIN, MAX};
+   virtual void GSOP(Vector &senddata, GSOpType op);
+
+   virtual void FreeData();


What data, when should this be called?

vladotomov · 2024-03-22T00:58:36Z

fem/tmop.cpp

   delete surf_fit_gf;
-   surf_fit_gf = new GridFunction(s0);
+   ParGridFunction *surf_fit_gf_dummy = new ParGridFunction(s0);
+   surf_fit_gf = surf_fit_gf_dummy;


Why is this change?

vladotomov · 2024-03-22T01:00:00Z

fem/tmop.cpp

@@ -3004,33 +3012,180 @@ void TMOP_Integrator::EnableSurfaceFitting(const ParGridFunction &s0,
   surf_fit_eval->SetInitialField
   (*surf_fit_gf->FESpace()->GetMesh()->GetNodes(), *surf_fit_gf);
   surf_fit_gf_bg = false;
+
+   // Unify marker array across processor boundaries


Why would they be different?
Shouldn't this be done by the caller?

vladotomov · 2024-03-22T01:03:37Z

fem/tmop.cpp

+                                                   fec->GetBasisType());
+   ParFiniteElementSpace *fes_grad = new ParFiniteElementSpace
+   (pmesh,
+    fec_grad,


Is this some editor malfunction?

vladotomov · 2024-03-22T01:05:49Z

fem/tmop.cpp

-               surf_fit_gf_energy += sigma_e(s) * sigma_e(s);
+               const IntegrationPoint &ip_s = ir_s.IntPoint(s);
+               Tpr->SetIntPoint(&ip_s);
+               surf_fit_gf_energy += surf_fit_coeff->Eval(*Tpr, ip_s) *


I thought user-provided Coefficients were not part of the normalization. They would get cancelled out and have no effect.

vladotomov · 2024-03-22T01:06:22Z

fem/tmop_tools.hpp

@@ -224,14 +226,26 @@ class TMOPNewtonSolver : public LBFGSSolver
   /// (ii) surface fitting weight.
   virtual void ProcessNewState(const Vector &x) const;

-   /** @name Methods for adaptive surface fitting weight. (Experimental) */
+   /** @name Methods for adaptive surface fitting. These control the behavior of
+       the weight and the termination of the solver. (Experimental) */


Don't you need ///@{ ... ///@} to actually group the functions in the doxygen.

kmittal2 · 2024-03-25T23:06:48Z

After discussion with @vladotomov, I will be breaking this into smaller PRs.

kmittal2 added 4 commits January 16, 2024 11:40

initial commit

49ea7d1

get face neighbors

6e4240f

Merge branch 'master' of https://github.com/mfem/mfem into tmop-fitti…

90a7d8d

…ng-updates

misc

308502e

kmittal2 added mesh WIP Work in Progress labels Feb 7, 2024

kmittal2 added 12 commits February 6, 2024 17:25

minor refactor and change output from line-search

8bcbe04

change pargridfunc to gridfunc

a265c14

move function definition out of mfem_use_mpi

fbad1ae

update miniapp for hr-adaptivity

dc6c9fc

cosmetic changes

5b05a11

refactor line search

014b24a

documentation

30b2702

documentation

1e20639

minor typos

880c5a9

add gslib group communicator

d1b7a59

rename gatther scatter class

769f5fe

documentation

5ef4b1c

kmittal2 added ready-for-review and removed WIP Work in Progress labels Feb 12, 2024

kmittal2 changed the title ~~[WIP] Surface fitting updates~~ Surface fitting updates Feb 12, 2024

tzanio added in-review and removed ready-for-review labels Feb 13, 2024

tzanio assigned tzanio and vladotomov Feb 13, 2024

tzanio requested review from tzanio and vladotomov February 13, 2024 22:40

kmittal2 added 2 commits February 15, 2024 10:53

fix bug where background mesh used without gslib was causing segfault

d9d9ebe

comment out run with background mesh requiring gslib

7197664

kmittal2 and others added 2 commits March 21, 2024 14:45

add metric 0, and minor change to suppress compiler warning

fec5686

minor

f1496b0

vladotomov requested changes Mar 22, 2024

View reviewed changes

kmittal2 and others added 3 commits March 22, 2024 09:26

addressed reviewer comments

b3330c5

another reviewer cocomment

e9bbe9d

minor

54026b1

kmittal2 closed this Mar 25, 2024

kmittal2 mentioned this pull request Mar 26, 2024

Class to enable gather-scatter type operator with gslib #4213

Merged

61 tasks

tzanio removed the in-review label Mar 26, 2024

kmittal2 mentioned this pull request Mar 27, 2024

TMOP+Fitting - enable residual based convergence with adaptive fitting weight #4215

Merged

61 tasks

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Surface fitting updates #4116

Surface fitting updates #4116

kmittal2 commented Feb 7, 2024 •

edited by tzanio

tzanio commented Feb 13, 2024

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kmittal2 commented Mar 25, 2024

Surface fitting updates #4116

Surface fitting updates #4116

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kmittal2 commented Feb 7, 2024 • edited by tzanio

tzanio commented Feb 13, 2024

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kmittal2 commented Mar 25, 2024

kmittal2 commented Feb 7, 2024 •

edited by tzanio