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Fixed linting
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Signed-off-by: Umberto Zerbinati <zerbinati@maths.ox.ac.uk>
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Umberto Zerbinati committed Jan 24, 2024
1 parent 9afd9f7 commit 1affe74
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Showing 2 changed files with 24 additions and 24 deletions.
6 changes: 3 additions & 3 deletions Makefile
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
MPI_EXEC = ${PETSC_DIR}/${PETSC_ARCH}/bin/mpiexec
lint:
pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc
pylint --disable=C0412,C0103,C0415,C0321,C3001,E0401,E1101,E0611,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,W0406,W0212,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc/utils
pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1728,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc
pylint --disable=C0412,C0103,C0415,C0321,C3001,E0401,E1101,E0611,R1728,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,W0406,W0212,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc/utils
lint_test:
pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1736,R0401,R0914,R0801,R0902,R1702,R0913,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase tests
pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1728,R1736,R0401,R0914,R0801,R0902,R1702,R0913,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase tests
test:
pytest tests/test_env.py
pytest tests/test_vec.py
Expand Down
42 changes: 21 additions & 21 deletions ngsPETSc/utils/firedrake.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
'''
try:
import firedrake as fd
from firedrake.logging import warning
from firedrake.cython import mgimpl as impl
except ImportError:
fd = None
Expand Down Expand Up @@ -77,7 +78,7 @@ def refineMarkedElements(self, mark):
else:
raise NotImplementedError("No implementation for dimension other than 2 and 3.")

def curveField(self, order, digits=8):
def curveField(self, order, tol=1e-8):
'''
This method returns a curved mesh as a Firedrake function.
Expand All @@ -102,7 +103,6 @@ def curveField(self, order, digits=8):
refPts.append(pt)
V = newFunctionCoordinates.dat.data
refPts = np.array(refPts)
rnd = lambda x: round(x, digits)
if self.geometric_dimension() == 2:
#Mapping to the physical domain
physPts = np.ndarray((len(self.netgen_mesh.Elements2D()),
Expand All @@ -122,10 +122,11 @@ def curveField(self, order, digits=8):
Idx = self.locate_cell(bary)
isInMesh = (0<=Idx<len(cellMap.values)) if Idx is not None else False
if isInMesh:
p = [np.argmin(np.sum((pts - pt)**2, axis=1)) for pt in V[cellMap.values[Idx]][0:refPts.shape[0]]]
p = [np.argmin(np.sum((pts - pt)**2, axis=1))
for pt in V[cellMap.values[Idx]][0:refPts.shape[0]]]
curvedPhysPts[i] = curvedPhysPts[i][p]
res = np.linalg.norm(pts[p]-V[cellMap.values[Idx]][0:refPts.shape[0]])
if res > 1e-8:
if res > tol:
fd.logging.warning("Not able to curve Firedrake element {}".format(Idx))
else:
for j, datIdx in enumerate(cellMap.values[Idx][0:refPts.shape[0]]):
Expand All @@ -150,11 +151,12 @@ def curveField(self, order, digits=8):
Idx = self.locate_cell(bary)
isInMesh = (0<=Idx<len(cellMap.values)) if Idx is not None else False
if isInMesh:
p = [np.argmin(np.sum((pts - pt)**2, axis=1)) for pt in V[cellMap.values[Idx]][0:refPts.shape[0]]]
p = [np.argmin(np.sum((pts - pt)**2, axis=1))
for pt in V[cellMap.values[Idx]][0:refPts.shape[0]]]
curvedPhysPts[i] = curvedPhysPts[i][p]
res = np.linalg.norm(pts[p]-V[cellMap.values[Idx]][0:refPts.shape[0]])
if res > 1e-8:
fd.logging.warning("Not able to curve Firedrake element {}, residual is: {}".format(Idx, res))
if res > tol:
warning("Not able to curve element {}, residual is: {}".format(Idx, res))
else:
for j, datIdx in enumerate(cellMap.values[Idx][0:refPts.shape[0]]):
newFunctionCoordinates.sub(0).dat.data[datIdx] = curvedPhysPts[i][j][0]
Expand Down Expand Up @@ -231,6 +233,9 @@ def createFromTopology(self, topology, name):
setattr(fd.MeshGeometry, "curve_field", curveField)

def snapToNetgenDMPlex(ngmesh, petscPlex):
'''
This function snaps the coordinates of a DMPlex mesh to the coordinates of a Netgen mesh.
'''
if petscPlex.getDimension() == 2:
ngCoordinates = ngmesh.Coordinates()
petscCoordinates = petscPlex.getCoordinatesLocal().getArray().reshape(-1, ngmesh.dim)
Expand All @@ -241,16 +246,9 @@ def snapToNetgenDMPlex(ngmesh, petscPlex):
petscPlexCoordinates.setArray(petscPlexCoordinates)
petscPlex.setCoordinatesLocal(petscPlexCoordinates)
else:
ngCoordinates = ngmesh.Coordinates()
petscCoordinates = petscPlex.getCoordinatesLocal().getArray().reshape(-1, ngmesh.dim)
for i, pt in enumerate(petscCoordinates):
j = np.argmin(np.sum((ngCoordinates - pt)**2, axis=1))
petscCoordinates[i] = ngCoordinates[j]
petscPlexCoordinates = petscPlex.getCoordinatesLocal()
petscPlexCoordinates.setArray(petscPlexCoordinates)
petscPlex.setCoordinatesLocal(petscPlexCoordinates)
raise NotImplementedError("Snapping to Netgen meshes is only implemented for 2D meshes.")

def NetgenHierarchy(ngmesh, levs, order=1, digits=8, comm=fd.COMM_WORLD):
def NetgenHierarchy(ngmesh, levs, order=1, tol=1e-8, comm=fd.COMM_WORLD):
'''
This function creates a Firedrake mesh hierarchy from Netgen/NGSolve meshes.
Expand All @@ -272,13 +270,14 @@ def NetgenHierarchy(ngmesh, levs, order=1, digits=8, comm=fd.COMM_WORLD):
raise RuntimeError("Cannot refine parallel overlapped meshes ")
#We curve the mesh
if order>1:
mesh = fd.Mesh(mesh.curve_field(order=order, digits=digits), distribution_parameters=params, comm=comm)
mesh = fd.Mesh(mesh.curve_field(order=order, tol=tol),
distribution_parameters=params, comm=comm)
meshes += [mesh]
for l in range(levs):
for _ in range(levs):
#Streightening the mesh
ngmesh.Curve(1)
#We refine the netgen mesh uniformly
ngmesh.Refine(adaptive=False)
ngmesh.Refine(adaptive=False)
fd.File("meshes/ng.pvd").write(fd.Mesh(ngmesh))
#We refine the DMPlex mesh uniformly
cdm = meshes[-1].topology_dm
Expand All @@ -295,7 +294,8 @@ def NetgenHierarchy(ngmesh, levs, order=1, digits=8, comm=fd.COMM_WORLD):
mesh.netgen_mesh = ngmesh
#We curve the mesh
if order > 1:
mesh = fd.Mesh(mesh.curve_field(order=order, digits=digits), distribution_parameters=params, comm=comm)
mesh = fd.Mesh(mesh.curve_field(order=order, tol=1e-8),
distribution_parameters=params, comm=comm)
meshes += [mesh]
#We populate the coarse to fine map
lgmaps = []
Expand All @@ -318,4 +318,4 @@ def NetgenHierarchy(ngmesh, levs, order=1, digits=8, comm=fd.COMM_WORLD):
fine_to_coarse_cells = dict((Fraction(i, refinements_per_level), f2c)
for i, f2c in enumerate(fine_to_coarse_cells))
return fd.HierarchyBase(meshes, coarse_to_fine_cells, fine_to_coarse_cells,
refinements_per_level, nested=False)
refinements_per_level, nested=False)

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