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Refactor matrices #721

Merged
merged 41 commits into from Nov 10, 2020
Merged

Refactor matrices #721

merged 41 commits into from Nov 10, 2020

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guyer
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@guyer guyer commented Apr 6, 2020

Needed for interprocess communication when writing parallel meshes (#132), but generally beneficial

@guyer guyer added the matrices label Apr 6, 2020
@guyer guyer requested review from tkphd and wd15 and removed request for wd15 and tkphd April 6, 2020 12:17
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wd15 approved these changes Apr 6, 2020
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You've been busy. Well done. I've added a few optional ways to clean things up.

I ran pylint over pysparseMatrix.py and there is a lot of trailing whitespace and the like. Might want to deal with that since you're making quite a lot of changes to it.

fipy/solvers/__init__.py Outdated Show resolved Hide resolved
fipy/matrices/pysparseMatrix.py Show resolved Hide resolved
fipy/matrices/sparseMatrix.py Show resolved Hide resolved
fipy/matrices/sparseMatrix.py Outdated Show resolved Hide resolved
@guyer guyer mentioned this pull request Apr 7, 2020
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wd15 commented Apr 7, 2020

Sorry about Pylint. I wish I hadn't mentioned it now. The commit history looks like it's torturing you. Maybe rebase after @tkphd is done.

@guyer
Introduce _RowMeshMatrix and _ColMeshMatrix
7298714 
- Enable having parallel, ghosted matrices for things other
  than meshed DoF.
- Refactor conversions between meshes and matrices
- Add alii for sparse matrices associated with meshes
@guyer
Add Compact Sparse Row and List of List matrix properties
e0a1603 
Return local matrix representation as lists or ndarrays
@guyer
Add explict matrix transpose property
0a83625
@guyer
Fix syntax
964b132
@guyer
Fix the fix
c836a17
@guyer
More fixin'
26d3875
@guyer
Check Pysparse transpose only in serial
9cb2987 
Pysparse isn't parallel, but it can be invoked in parallel when
building Trilinos matrices
@guyer
Combine implementations of _getStencil
63943a8
@guyer
Refactor _cellIDsToGlobalIDs
9cd6de8
@guyer
Make pylint happier
1f21948
@guyer
Make pylint happier
3798b51
@guyer
Make pylint happier
e3eea3c
@guyer
Make pylint happier
3033ba0
@guyer
Fix typo
526800e
@guyer
Make pylint happier
2a748ce
@guyer
Remove unused method
f66c8ce
@guyer
Make pylint happier
18e2c7b
@guyer
Move mesh-to-matrix conversion tests to where implemented
fdb9782
@guyer
Pre-allocate PETSc matrix
da4872c
@guyer
Give each processor a row
8d142a8
@guyer
Ping the build
bf2ed8f
@guyer
ping the build
6e026ef
@guyer
Revert "Give each processor a row"
ca242b5 
This reverts commit a864064.
@guyer
Revert "Pre-allocate PETSc matrix"
513757a 
This reverts commit 737a6d0.
@guyer
Skip tests when Gmsh not present
4b12c28
@guyer
Initialize PETSc and document how to pass options
3bd14d4
@guyer
Flush assemble matrix before adding or inserting
217679f 
[Cannot mix add values and insert values](https://lists.mcs.anl.gov/pipermail/petsc-users/2014-September/022873.html)
@guyer
Destroy PETSc matrix when done with it
0c29f4c
@guyer
Only delete matrices that exist
daf459a
@guyer
Introduce better alternatives to setPreallocationNNZ(None)
6dcae25
@guyer
Destroy PETSc vectors when done
f2d6ad6
@guyer
Add methods to destroy PETSc objects
9094ffd
@guyer
Store weak reference to ordering method
09673b0 
Reference cycles can cause deadlock on garbage collection
@guyer
Remove explicit destructors that caused PETSc garbage collection issues
e898fb5
@guyer
Generalize mesh to matrix conversion
221ffd8 
Store weak reference to matrix to prevent reference cycles and
faulty garbage collection in parallel.
@guyer
Import appropriate matrices with importlib
2a51a8b
@guyer
Disable TVTK tests if its prerequisites aren't met
4c16484
@guyer
Import mesh matrices along with solver
5b7b937 
Failure to import desired mesh matrices should provoke fail-over
@guyer
Revert "Disable TVTK tests if its prerequisites aren't met"
b289a7e 
This reverts commit 4c16484.
@guyer guyer mentioned this pull request Nov 6, 2020
Merged
@guyer
Remove hyphens
3946f39 
Just not worth fighting spellchecker
@guyer guyer mentioned this pull request Nov 7, 2020
Merged
@guyer guyer merged commit 3cdaccd into usnistgov:master Nov 10, 2020
@guyer guyer deleted the Refactor_matrices branch November 10, 2020 00:47
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