Account for ghost cells and element shape in preallocation

usnistgov · Dec 1, 2023 · bdaa4b8 · bdaa4b8
1 parent 333df13
commit bdaa4b8
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/fipy/matrices/offsetSparseMatrix.py b/fipy/matrices/offsetSparseMatrix.py
@@ -23,7 +23,7 @@ def __init__(self, mesh, nonZerosPerRow=1, exactNonZeros=False,
                 # can't compare to collections.abc.Iterable because PySparse.
                 before = self.equationIndex
                 after = numberOfEquations - self.equationIndex - 1
-                N = mesh.numberOfCells
+                N = len(nonZerosPerRow)
                 nonZerosPerRow = numerix.concatenate([[0] * N * before,
                                                       nonZerosPerRow,
                                                       [0] * N * after])

diff --git a/fipy/terms/abstractDiffusionTerm.py b/fipy/terms/abstractDiffusionTerm.py
@@ -189,7 +189,8 @@ def __getCoefficientMatrix(self, SparseMatrix, var, coeff):
 ##         print 'id1',id1
 ##         print 'id2',id2
 
-        coefficientMatrix = SparseMatrix(mesh=mesh, nonZerosPerRow=mesh._facesPerCell + 1)
+        facesPerCell = mesh._facesPerCell[..., mesh._localNonOverlappingCellIDs]
+        coefficientMatrix = SparseMatrix(mesh=mesh, nonZerosPerRow=facesPerCell + 1)
         interiorCoeff = numerix.take(coeff, interiorFaces, axis=-1).ravel()
         coefficientMatrix.addAt(interiorCoeff, id1.ravel(), id1.swapaxes(0, 1).ravel())
         coefficientMatrix.addAt(-interiorCoeff, id1.ravel(), id2.swapaxes(0, 1).ravel())

diff --git a/fipy/terms/faceTerm.py b/fipy/terms/faceTerm.py
@@ -140,7 +140,8 @@ def _buildMatrix(self, var, SparseMatrix, boundaryConditions=(), dt=None, transi
         id2 = numerix.take(id2, interiorFaces)
 
         b = numerix.zeros(var.shape, 'd').ravel()
-        L = SparseMatrix(mesh=mesh, nonZerosPerRow=mesh._facesPerCell + 1)
+        facesPerCell = mesh._facesPerCell[..., mesh._localNonOverlappingCellIDs]
+        L = SparseMatrix(mesh=mesh, nonZerosPerRow=facesPerCell + 1)
 
         weight = self._getWeight(var, transientGeomCoeff, diffusionGeomCoeff)