def help(args=None):
import sys, shlex
# program name
try:
prog = sys.argv[0]
except Exception:
prog = getattr(sys, 'executable', 'python')
# arguments
if args is None:
args = sys.argv[1:]
elif isinstance(args, str):
args = shlex.split(args)
else:
args = [str(a) for a in args]
# import and initialize
import petsc4py
petsc4py.init([prog, '-help'] + args)
from petsc4py import PETSc
# help dispatcher
COMM = PETSc.COMM_SELF
if 'vec' in args:
vec = PETSc.Vec().create(comm=COMM)
vec.setSizes(0)
vec.setFromOptions()
vec.destroy()
if 'mat' in args:
mat = PETSc.Mat().create(comm=COMM)
mat.setSizes([0, 0])
mat.setFromOptions()
mat.destroy()
if 'pc' in args:
pc = PETSc.PC().create(comm=COMM)
pc.setFromOptions()
pc.destroy()
if 'ksp' in args:
ksp = PETSc.KSP().create(comm=COMM)
ksp.setFromOptions()
ksp.destroy()
if 'snes' in args:
snes = PETSc.SNES().create(comm=COMM)
snes.setFromOptions()
snes.destroy()
if 'ts' in args:
ts = PETSc.TS().create(comm=COMM)
ts.setFromOptions()
ts.destroy()
if 'tao' in args:
tao = PETSc.TAO().create(comm=COMM)
tao.setFromOptions()
tao.destroy()
if 'dmda' in args:
dmda = PETSc.DMDA().create(comm=COMM)
dmda.setFromOptions()
dmda.destroy()
if 'dmplex' in args:
dmplex = PETSc.DMPlex().create(comm=COMM)
dmplex.setFromOptions()
dmplex.destroy()
def generateDMPlex(self, dh, dim=1):
coords, cone, dl = self.generateBody(dh)
self.__dl = dl
self.__L = self.getLong()
self.__dom = PETSc.DMPlex().createFromCellList(dim, cone, coords)
self.setUpDimensions()
points = self.getTotalNodes()
ind = [
poi * 2 + dof for poi in range(points)
for dof in range(len(self.__vel))
]
self.__velVec = PETSc.Vec().createMPI(
((points * len(self.__vel), None)))
self.__velVec.setValues(ind, np.tile(self.__vel, points))
self.__velVec.assemble()
class TestPlex_2D_P3(BaseTestPlex_2D, unittest.TestCase):
DOFS = [1, 2, 1]
class TestPlex_3D_P3(BaseTestPlex_3D, unittest.TestCase):
DOFS = [1, 2, 1, 0]
class TestPlex_3D_P4(BaseTestPlex_3D, unittest.TestCase):
DOFS = [1, 3, 3, 1]
import sys
try:
raise PETSc.Error
PETSc.DMPlex().createBoxMesh(1, comm=PETSc.COMM_SELF).destroy()
except PETSc.Error:
pass
else:
class TestPlex_2D_Box(BaseTestPlex_2D, unittest.TestCase):
def setUp(self):
self.plex = PETSc.DMPlex().createBoxMesh(self.DIM)
class TestPlex_2D_Boundary(BaseTestPlex_2D, unittest.TestCase):
def setUp(self):
boundary = PETSc.DMPlex().create(self.COMM)
boundary.createSquareBoundary([0., 0.], [1., 1.], [2, 2])
boundary.setDimension(self.DIM - 1)
self.plex = PETSc.DMPlex().generate(boundary)
[1.0, 0.0],
[0.0, 0.5],
[0.5, 0.5],
[1.0, 0.5],
[0.0, 1.0],
[0.5, 1.0],
[1.0, 1.0]], dtype=float)
cells = np.asarray([[0,1,4,3],
[1,2,5,4],
[3,4,7,6],
[4,5,8,7]], dtype=PETSc.IntType)
else:
coords = np.zeros((0, 2), dtype=float)
cells = np.zeros((0, 4), dtype=PETSc.IntType)
plex = PETSc.DMPlex().createFromCellList(dim, cells, coords, comm=PETSc.COMM_WORLD)
pStart, pEnd = plex.getChart()
plex.view()
print("pStart, pEnd: ", pStart, pEnd)
# Create section with 1 field with 1 DoF per vertex, edge amd cell
numComp = 1
# Start with an empty vector
numDof = [0] * 3
# Field defined on vertexes
numDof[0] = 1
# Field defined on edges
numDof[1] = 1
# Field defined on cells
numDof[2] = 1
def _create_DMPlex(self, dim, coords, cells, elev):
"""
Create a PETSc DMPlex object from the mesh attributes
Args:
dim: mesh dimensions
coords: mesh coordinates
cells: cell nodes indices
elev: nodes elevation
"""
t0 = clock()
self.dm = PETSc.DMPlex().createFromCellList(dim,
cells,
coords,
comm=PETSc.COMM_WORLD)
if MPIrank == 0 and self.verbose:
print('Create DMPlex (%0.02f seconds)' % (clock() - t0))
# Create boundary labels
t0 = clock()
label = "boundary"
self._set_DMPlex_boundary_points(label)
# label coarse DM in case it is ever needed again
self.dm.createLabel("coarse")
pStart, pEnd = self.dm.getDepthStratum(0)
for pt in range(pStart, pEnd):
self.dm.setLabelValue("coarse", pt, 1)
# Define one DoF on the nodes
self.dm.setNumFields(1)
origSect = self.dm.createSection(1, [1, 0, 0])
origSect.setFieldName(0, "points")
origSect.setUp()
self.dm.setDefaultSection(origSect)
origVec = self.dm.createGlobalVector()
# Distribute to other processors if any
if MPIsize > 1:
sf = self.dm.distribute(overlap=1)
newSect, newVec = self.dm.distributeField(sf, origSect, origVec)
self.dm.setDefaultSection(newSect)
newSect.destroy()
newVec.destroy()
sf.destroy()
origVec.destroy()
origSect.destroy()
self.hGlobal = self.dm.createGlobalVector()
self.hLocal = self.dm.createLocalVector()
self.sizes = self.hGlobal.getSizes(), self.hGlobal.getSizes()
# Local/Global mapping
self.lgmap_row = self.dm.getLGMap()
l2g = self.lgmap_row.indices.copy()
offproc = l2g < 0
l2g[offproc] = -(l2g[offproc] + 1)
self.lgmap_col = PETSc.LGMap().create(l2g, comm=PETSc.COMM_WORLD)
del l2g
if MPIrank == 0 and self.verbose:
print('Distribute DMPlex (%0.02f seconds)' % (clock() - t0))
# Get natural numbering
t0 = clock()
coords = MPI.COMM_WORLD.bcast(coords, root=0)
elev = MPI.COMM_WORLD.bcast(elev, root=0)
self._naturalNumbering(coords)
self.hLocal.setArray(elev[self.natural2local])
self.dm.localToGlobal(self.hLocal, self.hGlobal)
self.dm.globalToLocal(self.hGlobal, self.hLocal)
if MPIrank == 0 and self.verbose:
print('Distribute field to DMPlex (%0.02f seconds)' %
(clock() - t0))
# Forcing event number
self.rainNb = -1
self.tecNb = -1
return
return ret
# Set metric parameters
h_min = 1.0e-10 # Minimum tolerated metric magnitude ~ cell size
h_max = 1.0e-01 # Maximum tolerated metric magnitude ~ cell size
a_max = 1.0e+05 # Maximum tolerated anisotropy
targetComplexity = 10000.0 # Analogous to number of vertices in adapted mesh
p = 1.0 # Lᵖ normalization order
# Create a uniform mesh
OptDB = PETSc.Options()
dim = OptDB.getInt('dim', 2)
numEdges = 10
simplex = True
plex = PETSc.DMPlex().createBoxMesh([numEdges] * dim, simplex=simplex)
plex.distribute()
plex.view()
viewer = PETSc.Viewer().createVTK('base_mesh.vtk', 'w')
viewer(plex)
# Do four mesh adaptation iterations
for i in range(4):
vStart, vEnd = plex.getDepthStratum(0)
# Create a P1 sensor function
comm = plex.getComm()
fe = PETSc.FE().createLagrange(dim, 1, simplex, 1, -1, comm=comm)
plex.setField(0, fe)
plex.createDS()
f = plex.createLocalVector()
def regenerateDMPlex(self, dh, dim=1):
coords, cone, _ = self.generateBody(dh)
dm = PETSc.DMPlex().createFromCellList(dim, cone, coords)
return dm
