def test_gmsh_generation_3D(self):
domain = Domain.PiecewiseLinearComplexDomain()
cube = st.Cuboid(domain, dim=[2.,2.,2.])
st.assembleDomain(domain)
domain.writeGeo('gmsh_mesh_test_3D', he_max=0.1)
gmsh_cmd = "gmsh {0:s} -v 10 -3 -o {1:s} -format msh".format(domain.geofile+".geo", domain.geofile+".msh")
check_call(gmsh_cmd, shell=True)
MeshTools.msh2simplex(domain.geofile, nd=3)
# cek disabling exact tests due to cross-platform non-reproducibility
# with open('gmsh_mesh_test_3D.node', 'r') as nodefile:
# npt.assert_equal(nodefile.readline(), '7674 3 0 1\n')
# with open('gmsh_mesh_test_3D.edge', 'r') as edgefile:
# npt.assert_equal(edgefile.readline(), '9384 1\n')
# with open('gmsh_mesh_test_3D.face', 'r') as facefile:
# npt.assert_equal(facefile.readline(), '6256 3 1\n')
# with open('gmsh_mesh_test_3D.ele', 'r') as elefile:
# npt.assert_equal(elefile.readline(), '37473 4 1\n')
with open('gmsh_mesh_test_3D.node', 'r') as nodefile:
assert(abs(int(nodefile.readline().split()[0]) - 7674)/7674.0 < .02)
with open('gmsh_mesh_test_3D.edge', 'r') as edgefile:
assert(abs(int(edgefile.readline().split()[0]) - 9384)/9384.0 < .02)
with open('gmsh_mesh_test_3D.face', 'r') as facefile:
assert(abs(int(facefile.readline().split()[0]) - 6256)/6256.0 < .02)
with open('gmsh_mesh_test_3D.ele', 'r') as elefile:
assert(abs(int(elefile.readline().split()[0]) - 37473)/37473.0 < .02)
def test_adaptIBM_adaptMesh(self):
currentPath = os.path.dirname(os.path.abspath(__file__))
runCommand = "cd " + currentPath + "; parun -l5 cylinder_so.py -C 'T=0.01 onlySaveFinalSolution=True genMesh=False usePUMI=True';"
subprocess.check_call(runCommand, shell=True)
#load initial mesh and extract element count
domain = Domain.PUMIDomain(
manager=MeshAdapt.AdaptManager()) #initialize the domain
filePath = bytes(currentPath + '/', 'utf-8')
domain.AdaptManager.PUMIAdapter.loadModelAndMesh(
filePath + b"Reconstructed.dmg", filePath + b"Reconstructed.smb")
mesh = MeshTools.TetrahedralMesh()
mesh.convertFromPUMI(domain,
domain.AdaptManager.PUMIAdapter, [1], [1],
parallel=comm.size() > 1,
dim=2)
nElements_initial = mesh.nElements_global
#load final mesh and extract element count
domain.AdaptManager.PUMIAdapter.loadModelAndMesh(
filePath + b"Reconstructed.dmg", filePath + b"finalMesh.smb")
mesh2 = MeshTools.TetrahedralMesh()
mesh2.convertFromPUMI(domain,
domain.AdaptManager.PUMIAdapter, [1], [1],
parallel=comm.size() > 1,
dim=2)
nElements_final = mesh2.nElements_global
#adapted mesh should have less elements
assert (nElements_final < nElements_initial)
def test_gmsh_generation_3D(self):
domain = Domain.PiecewiseLinearComplexDomain()
cube = st.Cuboid(domain, dim=[2., 2., 2.])
st.assembleDomain(domain)
domain.writeGeo('gmsh_mesh_test_3D', he_max=0.1)
gmsh_cmd = "gmsh {0:s} -v 10 -3 -o {1:s} -format msh".format(
domain.geofile + ".geo", domain.geofile + ".msh")
check_call(gmsh_cmd, shell=True)
MeshTools.msh2simplex(domain.geofile, nd=3)
# cek disabling exact tests due to cross-platform non-reproducibility
# with open('gmsh_mesh_test_3D.node', 'r') as nodefile:
# npt.assert_equal(nodefile.readline(), '7674 3 0 1\n')
# with open('gmsh_mesh_test_3D.edge', 'r') as edgefile:
# npt.assert_equal(edgefile.readline(), '9384 1\n')
# with open('gmsh_mesh_test_3D.face', 'r') as facefile:
# npt.assert_equal(facefile.readline(), '6256 3 1\n')
# with open('gmsh_mesh_test_3D.ele', 'r') as elefile:
# npt.assert_equal(elefile.readline(), '37473 4 1\n')
with open('gmsh_mesh_test_3D.node', 'r') as nodefile:
assert (abs(int(nodefile.readline().split()[0]) - 7674) / 7674.0 <
.02)
with open('gmsh_mesh_test_3D.edge', 'r') as edgefile:
assert (abs(int(edgefile.readline().split()[0]) - 9384) / 9384.0 <
.02)
with open('gmsh_mesh_test_3D.face', 'r') as facefile:
assert (abs(int(facefile.readline().split()[0]) - 6256) / 6256.0 <
.02)
with open('gmsh_mesh_test_3D.ele', 'r') as elefile:
assert (abs(int(elefile.readline().split()[0]) - 37473) / 37473.0 <
.02)
def PUMI_adaptMesh(self,inputString=b""):
"""
Uses a computed error field to construct a size field and adapts
the mesh using SCOREC tools (a.k.a. MeshAdapt)
"""
##
domain = self.domain
if(hasattr(self,"nSolveSteps")):
logEvent("h-adapt mesh by calling AdaptAdaptManager.PUMIAdapter at step %s" % self.nSolveSteps)
if(b"pseudo" in self.domain.AdaptManager.sizeInputs):
logEvent("Testing solution transfer and restart feature of adaptation. No actual mesh adaptation!")
else:
domain.AdaptManager.PUMIAdapter.adaptPUMIMesh(inputString)
logEvent("Converting PUMI mesh to Proteus")
#ibaned: PUMI conversion #2
#TODO: this code is nearly identical to
#PUMI conversion #1, they should be merged
#into a function
if domain.nd == 3:
mesh = MeshTools.TetrahedralMesh()
else:
mesh = MeshTools.TriangularMesh()
mesh.convertFromPUMI(domain,
domain.AdaptManager.PUMIAdapter,
domain.faceList,
domain.regList,
parallel = self.comm.size() > 1,
dim = domain.nd)
self.PUMI_reallocate(mesh)
self.PUMI2Proteus(domain)
def PUMI_reallocate(self, mesh):
p0 = self.pList[0]
n0 = self.nList[0]
if self.TwoPhaseFlow:
nLevels = p0.myTpFlowProblem.general['nLevels']
nLayersOfOverlapForParallel = p0.myTpFlowProblem.general[
'nLayersOfOverlapForParallel']
parallelPartitioningType = MeshTools.MeshParallelPartitioningTypes.element
domain = p0.myTpFlowProblem.domain
domain.MeshOptions.setParallelPartitioningType('element')
else:
nLevels = n0.nLevels
nLayersOfOverlapForParallel = n0.nLayersOfOverlapForParallel
parallelPartitioningType = n0.parallelPartitioningType
domain = p0.domain
logEvent("Generating %i-level mesh from PUMI mesh" % (nLevels, ))
if domain.nd == 3:
mlMesh = MeshTools.MultilevelTetrahedralMesh(
0,
0,
0,
skipInit=True,
nLayersOfOverlap=nLayersOfOverlapForParallel,
parallelPartitioningType=parallelPartitioningType)
if domain.nd == 2:
mlMesh = MeshTools.MultilevelTriangularMesh(
0,
0,
0,
skipInit=True,
nLayersOfOverlap=nLayersOfOverlapForParallel,
parallelPartitioningType=parallelPartitioningType)
if self.comm.size() == 1:
mlMesh.generateFromExistingCoarseMesh(
mesh,
nLevels,
nLayersOfOverlap=nLayersOfOverlapForParallel,
parallelPartitioningType=parallelPartitioningType)
else:
mlMesh.generatePartitionedMeshFromPUMI(
mesh, nLevels, nLayersOfOverlap=nLayersOfOverlapForParallel)
self.mlMesh_nList = []
for p in self.pList:
self.mlMesh_nList.append(mlMesh)
if (domain.PUMIMesh.size_field_config() == "isotropicProteus"):
mlMesh.meshList[0].subdomainMesh.size_field = numpy.ones(
(mlMesh.meshList[0].subdomainMesh.nNodes_global, 1),
'd') * 1.0e-1
if (domain.PUMIMesh.size_field_config() == 'anisotropicProteus'):
mlMesh.meshList[0].subdomainMesh.size_scale = numpy.ones(
(mlMesh.meshList[0].subdomainMesh.nNodes_global, 3), 'd')
mlMesh.meshList[0].subdomainMesh.size_frame = numpy.ones(
(mlMesh.meshList[0].subdomainMesh.nNodes_global, 9), 'd')
#may want to trigger garbage collection here
self.modelListOld = self.modelList
logEvent("Allocating models on new mesh")
self.allocateModels()
def test_c0q1_hex_mesh():
from proteus import MeshTools
xmf_archive_base=os.path.join(os.path.dirname(os.path.abspath(__file__)),
'..','hex_cube_3x3')
heavy_file_base = xmf_archive_base
mesh_info = MeshTools.readMeshXdmf(xmf_archive_base,heavy_file_base)
hex_meshfile_base = 'hexmesh_3x3'
MeshTools.writeHexMesh(mesh_info,hex_meshfile_base,index_base=1)
check_c0q1(test_hexMesh_3x3=True,use_petsc=True, name="_hexMesh_")
def test_c0q1_hex_mesh():
from proteus import MeshTools
xmf_archive_base = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'..', 'hex_cube_3x3')
heavy_file_base = xmf_archive_base
mesh_info = MeshTools.readMeshXdmf(xmf_archive_base, heavy_file_base)
hex_meshfile_base = 'hexmesh_3x3'
MeshTools.writeHexMesh(mesh_info, hex_meshfile_base, index_base=1)
check_c0q1(test_hexMesh_3x3=True, use_petsc=True, name="_hexMesh_")
def build3DMesh(p, nnx, nny, nnz):
return MeshTools.MultilevelTetrahedralMesh(nnx,nny,nnz,
p.domain.x[0], p.domain.x[1], p.domain.x[2],
p.domain.L[0], p.domain.L[1], p.domain.L[2],
refinementLevels=1,
nLayersOfOverlap=0,
parallelPartitioningType=MeshTools.MeshParallelPartitioningTypes.node)
def build1DMesh(p, nnx):
return MeshTools.MultilevelEdgeMesh(nnx, 1, 1,
p.domain.x[0], 0.0, 0.0,
p.domain.L[0], 1.0, 1.0,
refinementLevels=1,
nLayersOfOverlap=0,
parallelPartitioningType=MeshTools.MeshParallelPartitioningTypes.node)
def build2DMesh(p, nnx, nny):
return MeshTools.MultilevelTriangularMesh(nnx,nny,1,
p.domain.x[0], p.domain.x[1], 1.0,
p.domain.L[0], p.domain.L[1], 1.0,
refinementLevels=1,
nLayersOfOverlap=0,
parallelPartitioningType=MeshTools.MeshParallelPartitioningTypes.node)
def test_2DmultiRegion(verbose=0):
"""Test for loading gmsh mesh through PUMI with multiple-regions"""
testDir = os.path.dirname(os.path.abspath(__file__))
Model = testDir + '/TwoQuads.dmg'
Mesh = testDir + '/TwoQuads.smb'
domain = Domain.PUMIDomain(
dim=2, manager=MeshAdapt.AdaptManager()) #initialize the domain
domain.AdaptManager.reconstructedFlag = 0 #this is used to indicate that no mesh reconstruction is being done.
domain.AdaptManager.PUMIAdapter.loadModelAndMesh(bytes(Model, 'utf-8'),
bytes(Mesh, 'utf-8'))
domain.faceList = [[14], [12], [11], [13], [15], [16]]
domain.boundaryLabels = [1, 2, 3, 4, 5, 6]
domain.regList = [[41], [42]]
mesh = MeshTools.TriangularMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
mesh.convertFromPUMI(domain,
domain.AdaptManager.PUMIAdapter,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
ok(mesh.elementMaterialTypes[0] == 1)
ok(mesh.elementMaterialTypes[-1] == 2)
def refine_uniform_from_tetgen(filebase,refinementLevels,index_base=0,EB=False):
from proteus import MeshTools,Archiver
mesh = MeshTools.TetrahedralMesh()
mesh.generateFromTetgenFiles(filebase,index_base,skipGeometricInit=False)
MLMesh = MeshTools.MultilevelTetrahedralMesh(0,0,0,skipInit=True)
MLMesh.generateFromExistingCoarseMesh(mesh,refinementLevels)
MLMesh.meshList[-1].writeTetgenFiles(filebase+'_out',index_base)
ar = Archiver.XdmfArchive('.',filebase+'_out')
import xml.etree.ElementTree as ElementTree
ar.domain = ElementTree.SubElement(ar.tree.getroot(),"Domain")
mesh.writeMeshXdmf(ar,'mesh_coarse'+'_out',init=True,EB=EB,tCount=0)
MLMesh.meshList[-1].writeMeshXdmf(ar,'mesh_fine'+'_out',init=True,EB=EB,tCount=1)
ar.close()
def test_gmsh_generation_2D(self):
domain = Domain.PlanarStraightLineGraphDomain()
domain.vertices = [[0., 0., 0.], [5., 0., 0.], [5., 5., 0.],
[0., 5., 0.]]
domain.segments = [[0, 1], [1, 2], [2, 3], [3, 0]]
domain.facets = [[[0, 1, 2, 3]]]
domain.writeGeo('gmsh_mesh_test_2D', he_max=0.1)
gmsh_cmd = "gmsh {0:s} -v 10 -2 -o {1:s} -format msh".format(
domain.geofile + ".geo", domain.geofile + ".msh")
check_call(gmsh_cmd, shell=True)
MeshTools.msh2simplex(domain.geofile, nd=2)
with open('gmsh_mesh_test_2D.node', 'r') as nodefile:
npt.assert_equal(nodefile.readline(), '3425 2 0 1\n')
with open('gmsh_mesh_test_2D.edge', 'r') as edgefile:
npt.assert_equal(edgefile.readline(), '10072 1\n')
with open('gmsh_mesh_test_2D.ele', 'r') as elefile:
npt.assert_equal(elefile.readline(), '6648 3 1\n')
def PUMI_reallocate(self,mesh):
p0 = self.pList[0]
n0 = self.nList[0]
nLevels = n0.nLevels
nLayersOfOverlapForParallel = n0.nLayersOfOverlapForParallel
parallelPartitioningType = MeshTools.MeshParallelPartitioningTypes.element
domain = p0.domain
domain.MeshOptions.setParallelPartitioningType('element')
logEvent("Generating %i-level mesh from PUMI mesh" % (nLevels,))
if domain.nd == 3:
mlMesh = MeshTools.MultilevelTetrahedralMesh(
0,0,0,skipInit=True,
nLayersOfOverlap=nLayersOfOverlapForParallel,
parallelPartitioningType=parallelPartitioningType)
if domain.nd == 2:
mlMesh = MeshTools.MultilevelTriangularMesh(
0,0,0,skipInit=True,
nLayersOfOverlap=nLayersOfOverlapForParallel,
parallelPartitioningType=parallelPartitioningType)
if self.comm.size()==1:
mlMesh.generateFromExistingCoarseMesh(
mesh,nLevels,
nLayersOfOverlap=nLayersOfOverlapForParallel,
parallelPartitioningType=parallelPartitioningType)
else:
mlMesh.generatePartitionedMeshFromPUMI(
mesh,nLevels,
nLayersOfOverlap=nLayersOfOverlapForParallel)
#need to remove old mlMesh references to ensure the number of mesh entities is properly updated
self.mlMesh_nList.clear()
for p in self.pList:
self.mlMesh_nList.append(mlMesh)
if (b"isotropicProteus" in self.domain.AdaptManager.sizeInputs):
mlMesh.meshList[0].subdomainMesh.size_field = numpy.ones((mlMesh.meshList[0].subdomainMesh.nNodes_global,1),'d')*1.0e-1
if (b'anisotropicProteus' in self.domain.AdaptManager.sizeInputs):
mlMesh.meshList[0].subdomainMesh.size_scale = numpy.ones((mlMesh.meshList[0].subdomainMesh.nNodes_global,3),'d')
mlMesh.meshList[0].subdomainMesh.size_frame = numpy.ones((mlMesh.meshList[0].subdomainMesh.nNodes_global,9),'d')
#may want to trigger garbage collection here
self.modelListOld = self.modelList
logEvent("Allocating models on new mesh")
self.allocateModels()
def test_gmsh_generation_2D(self):
domain = Domain.PlanarStraightLineGraphDomain()
domain.vertices = [[0., 0., 0.],
[5., 0., 0.],
[5., 5., 0.],
[0., 5., 0.]]
domain.segments = [[0, 1], [1, 2], [2, 3], [3, 0]]
domain.facets = [[[0, 1, 2, 3]]]
domain.writeGeo('gmsh_mesh_test_2D', he_max=0.1)
gmsh_cmd = "gmsh {0:s} -v 10 -2 -o {1:s} -format msh".format(domain.geofile+".geo", domain.geofile+".msh")
check_call(gmsh_cmd, shell=True)
MeshTools.msh2simplex(domain.geofile, nd=2)
with open('gmsh_mesh_test_2D.node', 'r') as nodefile:
npt.assert_equal(nodefile.readline(), '3425 2 0 1\n')
with open('gmsh_mesh_test_2D.edge', 'r') as edgefile:
npt.assert_equal(edgefile.readline(), '10072 1\n')
with open('gmsh_mesh_test_2D.ele', 'r') as elefile:
npt.assert_equal(elefile.readline(), '6648 3 1\n')
def hotstartWithPUMI(self):
#Call restart functions
logEvent("Converting PUMI mesh to Proteus")
if self.pList[0].domain.nd == 3:
mesh = MeshTools.TetrahedralMesh()
else:
mesh = MeshTools.TriangularMesh()
mesh.convertFromPUMI(self.pList[0].domain.AdaptManager.PUMIAdapter,
self.pList[0].domain.faceList,
self.pList[0].domain.regList,
parallel = self.comm.size() > 1,
dim = self.pList[0].domain.nd)
if(self.pList[0].domain.checkpointInfo==None):
sys.exit("Need to specify checkpointInfo file in inputs")
else:
self.PUMIcheckpointer.DecodeModel(self.pList[0].domain.checkpointInfo)
self.PUMI_reallocate(mesh) #need to double check if this call is necessaryor if it can be simplified to a shorter call
PUMI2Proteus(self,self.pList[0].domain)
def test_meshLoadPUMI(verbose=0):
"""Test to load serial PUMI model and mesh"""
testDir=os.path.dirname(os.path.abspath(__file__))
cubeMdl=testDir + '/cube.dmg'
cube670p1=testDir + '/cube.smb'
meshAdaptInstance = MeshAdaptPUMI.MeshAdaptPUMI()
meshAdaptInstance.loadModelAndMesh(cubeMdl, cube670p1)
mesh = MeshTools.TetrahedralMesh()
mesh.cmesh = cmeshTools.CMesh()
meshAdaptInstance.constructFromSerialPUMIMesh(mesh.cmesh)
mesh.buildFromC(mesh.cmesh)
eq(mesh.nElements_global,670)
eq(mesh.nNodes_global,190)
eq(mesh.nEdges_global,977)
eq(mesh.nElementBoundaries_global,1458)
def test_parallelLoadPUMI(verbose=0):
"""Test to load parallel PUMI model and mesh"""
comm = Comm.init()
eq(comm.size(),2)
testDir=os.path.dirname(os.path.abspath(__file__))
domain = Domain.PUMIDomain()
Model=testDir+ '/Prism.dmg'
Mesh=testDir + '/Prism.smb'
domain.PUMIMesh=MeshAdaptPUMI.MeshAdaptPUMI()
domain.PUMIMesh.loadModelAndMesh(Model, Mesh)
mesh = MeshTools.TetrahedralMesh()
mesh.cmesh = cmeshTools.CMesh()
mesh.convertFromPUMI(domain.PUMIMesh, domain.faceList, parallel = comm.size() > 1, dim = domain.nd)
eq(mesh.nElements_global,8148)
eq(mesh.nNodes_global,1880)
eq(mesh.nEdges_global,11001)
eq(mesh.nElementBoundaries_global,17270)
def test_meshLoadPUMI(verbose=0):
"""Test to load serial PUMI model and mesh"""
testDir = os.path.dirname(os.path.abspath(__file__))
cubeMdl = testDir + '/cube.dmg'
cube670p1 = testDir + '/cube.smb'
PUMIAdapter = MeshAdaptPUMI.MeshAdapt()
PUMIAdapter.loadModelAndMesh(bytes(cubeMdl, 'utf-8'),
bytes(cube670p1, 'utf-8'))
mesh = MeshTools.TetrahedralMesh()
mesh.cmesh = cmeshTools.CMesh()
PUMIAdapter.constructFromSerialPUMIMesh(mesh.cmesh)
cmeshTools.allocateGeometricInfo_tetrahedron(mesh.cmesh)
cmeshTools.computeGeometricInfo_tetrahedron(mesh.cmesh)
mesh.buildFromC(mesh.cmesh)
eq(mesh.nElements_global, 670)
eq(mesh.nNodes_global, 190)
eq(mesh.nEdges_global, 977)
eq(mesh.nElementBoundaries_global, 1458)
def test_2DparallelLoadPUMI(verbose=0):
"""Test to load 2D parallel PUMI model and mesh"""
comm = Comm.init()
eq(comm.size(), 2)
testDir = os.path.dirname(os.path.abspath(__file__))
domain = Domain.PUMIDomain(dim=2)
Model = testDir + '/Rectangle.dmg'
Mesh = testDir + '/Rectangle.smb'
domain.PUMIMesh = MeshAdaptPUMI.MeshAdaptPUMI()
domain.PUMIMesh.loadModelAndMesh(Model, Mesh)
mesh = MeshTools.TriangularMesh()
mesh.cmesh = cmeshTools.CMesh()
mesh.convertFromPUMI(domain.PUMIMesh,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
eq(mesh.nElements_global, 8)
eq(mesh.nNodes_global, 10)
eq(mesh.nEdges_global, 17)
eq(mesh.nElementBoundaries_global, 17)
def test_2DmultiRegion(verbose=0):
"""Test for loading gmsh mesh through PUMI with multiple-regions"""
testDir = os.path.dirname(os.path.abspath(__file__))
Model = testDir + '/TwoQuads.dmg'
Mesh = testDir + '/TwoQuads.smb'
domain = Domain.PUMIDomain(dim=2) #initialize the domain
domain.PUMIMesh = MeshAdaptPUMI.MeshAdaptPUMI()
domain.PUMIMesh.loadModelAndMesh(Model, Mesh)
domain.faceList = [[14], [12], [11], [13], [15], [16]]
domain.regList = [[41], [42]]
mesh = MeshTools.TriangularMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
mesh.convertFromPUMI(domain.PUMIMesh,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
ok(mesh.elementMaterialTypes[0] == 1)
ok(mesh.elementMaterialTypes[-1] == 2)
def __init__(self, nd, name="defaultDomain", units="m"):
"""
Set dimensions (nd), name string, and units string
"""
if nd not in [1, 2, 3]:
raise RuntimeError("Domain object must have dimension 1,2, or 3")
self.nd = nd
self.name = name
self.units = units
# make default empty list for parameters
self.vertices = []
self.vertexFlags = []
self.segments = []
self.segmentFlags = []
self.facets = [] # necessary in 2D for gmsh
self.facetFlags = []
self.holes = []
self.holes_ind = [] # for gmsh: index of hole (2D: facet; 3D: volume)
self.regions = []
self.regionFlags = []
self.volumes = [] # only for gmsh: loop of facets
# for bounding box
self.x = []
self.L = []
# list of shape instances (from proteus.SpatialTools.py)
self.shape_list = []
# list of boundary conditions
self.bc = []
# list of auxiliaryVariables
self.auxiliaryVariables = []
# needed for gmsh
self.volumes = []
self.boundaryTags = {}
self.BC = {}
self.BCbyFlag = {}
# use_gmsh hack
self.use_gmsh = False
self.MeshOptions = MeshTools.MeshOptions(self)
def test_poiseuilleError(verbose=0):
"""Test for loading gmsh mesh through PUMI, estimating error for
a Poiseuille flow case. The estimated error should be larger than the
exact error in the seminorm"""
testDir = os.path.dirname(os.path.abspath(__file__))
Model = testDir + '/Couette.null'
Mesh = testDir + '/Couette.msh'
domain = Domain.PUMIDomain() #initialize the domain
domain.PUMIMesh = MeshAdaptPUMI.MeshAdaptPUMI(hmax=0.01,
hmin=0.008,
numIter=1,
sfConfig='ERM',
maType='isotropic',
logType='off')
domain.PUMIMesh.loadModelAndMesh(Model, Mesh)
domain.faceList = [[80], [76], [42], [24], [82], [78]]
mesh = MeshTools.TetrahedralMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
nElements_initial = mesh.nElements_global
mesh.convertFromPUMI(domain.PUMIMesh,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
domain.PUMIMesh.transferFieldToPUMI("coordinates", mesh.nodeArray)
rho = numpy.array([998.2, 998.2])
nu = numpy.array([1.004e-6, 1.004e-6])
g = numpy.asarray([0.0, 0.0, 0.0])
deltaT = 1.0 #dummy number
domain.PUMIMesh.transferPropertiesToPUMI(rho, nu, g, deltaT)
#Poiseuille Flow
Ly = 0.2
Lz = 0.05
Re = 100
Umax = Re * nu[0] / Lz
def vOfX(x):
return 4 * Umax / (Lz**2) * (x[2]) * (Lz - x[2])
def dvOfXdz(x):
return 4 * Umax / (Lz**2) * (Lz - 2 * x[2])
#hard code solution
vector = numpy.zeros((mesh.nNodes_global, 3), 'd')
dummy = numpy.zeros(mesh.nNodes_global)
vector[:, 0] = dummy
vector[:, 1] = 4 * Umax / (Lz**2) * (mesh.nodeArray[:, 2]) * (
Lz - mesh.nodeArray[:, 2]) #v-velocity
vector[:, 2] = dummy
domain.PUMIMesh.transferFieldToPUMI("velocity", vector)
scalar = numpy.zeros((mesh.nNodes_global, 1), 'd')
domain.PUMIMesh.transferFieldToPUMI("p", scalar)
scalar[:, 0] = mesh.nodeArray[:, 2]
domain.PUMIMesh.transferFieldToPUMI("phi", scalar)
del scalar
scalar = numpy.zeros((mesh.nNodes_global, 1), 'd') + 1.0
domain.PUMIMesh.transferFieldToPUMI("vof", scalar)
errorTotal = domain.PUMIMesh.get_local_error()
# load the femspace with linear basis and get the quadrature points on a reference element
elementQuadrature = Quadrature.SimplexGaussQuadrature(domain.nd, 3)
ok(mesh.nNodes_element == 4) #confirm all of the elements have 4 nodes
#hard code computation for H1 seminorm; ideally will be reformatted using the classes within proteus
derivativeArrayRef = [[1, 0, 0], [0, 1, 0], [0, 0, 1], [-1, -1, -1]]
error = 0
for eID in range(mesh.nElements_global):
nodes = mesh.elementNodesArray[eID]
coords = []
for i in range(mesh.nNodes_element):
coords.append(mesh.nodeArray[nodes[i]])
J = numpy.matrix([[
coords[0][0] - coords[3][0], coords[1][0] - coords[3][0],
coords[2][0] - coords[3][0]
],
[
coords[0][1] - coords[3][1],
coords[1][1] - coords[3][1],
coords[2][1] - coords[3][1]
],
[
coords[0][2] - coords[3][2],
coords[1][2] - coords[3][2],
coords[2][2] - coords[3][2]
]])
invJ = J.I
detJ = numpy.linalg.det(J)
gradPhi_h = 0
for k in range(len(elementQuadrature.points)):
tempQpt = 0
zCoord = elementQuadrature.points[k][0]*coords[0][2] \
+elementQuadrature.points[k][1]*coords[1][2] \
+elementQuadrature.points[k][2]*coords[2][2] \
+(1-elementQuadrature.points[k][0]-elementQuadrature.points[k][1]-elementQuadrature.points[k][2])*coords[3][2]
for i in range(mesh.nNodes_element):
temp = 0
for j in range(domain.nd):
temp = temp + derivativeArrayRef[i][j] * invJ[j, 2]
tempQpt = tempQpt + vector[nodes[i]][1] * temp
exactgradPhi = dvOfXdz([0, 0, zCoord])
gradPhi_h = gradPhi_h + tempQpt
error = error + (exactgradPhi - gradPhi_h
)**2 * elementQuadrature.weights[k] * abs(detJ)
error = sqrt(error)
ok(error < errorTotal)
def test_2DgmshLoadAndAdapt(verbose=0):
"""Test for loading gmsh mesh through PUMI, estimating error and adapting for
a 2D Couette flow case"""
testDir=os.path.dirname(os.path.abspath(__file__))
Model=testDir + '/Couette2D.null'
Mesh=testDir + '/Couette2D.msh'
domain = Domain.PUMIDomain(dim=2) #initialize the domain
domain.PUMIMesh=MeshAdaptPUMI.MeshAdaptPUMI(hmax=0.01, hmin=0.008, numIter=1,sfConfig=b'ERM',maType=b'isotropic',targetError=1)
domain.PUMIMesh.loadModelAndMesh(bytes(Model,'utf-8'), bytes(Mesh,'utf-8'))
domain.faceList=[[14],[12],[11],[13]]
domain.boundaryLabels=[1,2,3,4]
mesh = MeshTools.TriangularMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
nElements_initial = mesh.nElements_global
mesh.convertFromPUMI(domain,domain.PUMIMesh, domain.faceList,domain.regList, parallel = comm.size() > 1, dim = domain.nd)
domain.PUMIMesh.transferFieldToPUMI(b"coordinates",mesh.nodeArray)
rho = numpy.array([998.2,998.2])
nu = numpy.array([1.004e-6, 1.004e-6])
g = numpy.asarray([0.0,0.0])
deltaT = 1.0 #dummy number
epsFact = 1.0 #dummy number
domain.PUMIMesh.transferPropertiesToPUMI(rho,nu,g,deltaT,epsFact)
#Couette Flow
Lz = 0.05
Uinf = 2e-3
#hard code solution
vector=numpy.zeros((mesh.nNodes_global,3),'d')
dummy = numpy.zeros(mesh.nNodes_global);
vector[:,0] = Uinf*mesh.nodeArray[:,1]/Lz #v-velocity
vector[:,1] = dummy
vector[:,2] = dummy
domain.PUMIMesh.transferFieldToPUMI(b"velocity", vector)
del vector
del dummy
scalar=numpy.zeros((mesh.nNodes_global,1),'d')
domain.PUMIMesh.transferFieldToPUMI(b"p", scalar)
scalar[:,0] = mesh.nodeArray[:,1]
domain.PUMIMesh.transferFieldToPUMI(b"phi", scalar)
del scalar
scalar = numpy.zeros((mesh.nNodes_global,1),'d')+1.0
domain.PUMIMesh.transferFieldToPUMI(b"vof", scalar)
errorTotal=domain.PUMIMesh.get_local_error()
ok(errorTotal<1e-14)
#ok(domain.PUMIMesh.willAdapt(),1)
domain.PUMIMesh.adaptPUMIMesh()
mesh = MeshTools.TriangularMesh()
mesh.convertFromPUMI(domain,domain.PUMIMesh,
domain.faceList,
domain.regList,
parallel = comm.size() > 1,
dim = domain.nd)
nElements_final = mesh.nElements_global
ok(nElements_final>nElements_initial)
facetFlags=facetFlags)
#regions = regions,
#regionFlags = regionFlags,
#holes=holes)
domain.MeshOptions.setParallelPartitioningType('node')
#domain.MeshOptions.use_gmsh=True
domain.boundaryTags = boundaryTags
domain.writePoly("mesh")
domain.writeGeo("mesh",he_max=he)
#domain.writeGeo("mesh",he_max=he)
#domain.writePLY("mesh")
#domain.writeAsymptote("mesh")
#domain.MeshOptions.triangleOptions="VApq1.25q12feena%e" % ((he**3)/6.0,)
gmsh_cmd = "gmsh {0:s} -v 10 -3 -o {1:s} -format msh2".format(domain.geofile+".geo", domain.geofile+".msh")
check_call(gmsh_cmd, shell=True)
mt.msh2simplex("mesh",nd=3)
domain.MeshOptions.genMesh=False
# ****************************** #
# ***** INITIAL CONDITIONS ***** #
# ****************************** #
class zero(object):
def uOfXT(self,x,t):
return 0.
disc_ICs=True
class clsvof_init_cond(object):
def uOfXT(self,x,t):
waterLine_x = 1.22
waterLine_z = 0.55
phi_x = x[0]-waterLine_x
phi_z = x[2]-waterLine_z
def test_gmshLoadAndAdapt(verbose=0):
"""Test for loading gmsh mesh through PUMI, estimating error and adapting for
a Couette flow case"""
testDir = os.path.dirname(os.path.abspath(__file__))
Model = testDir + '/Couette.null'
Mesh = testDir + '/Couette.msh'
domain = Domain.PUMIDomain() #initialize the domain
domain.PUMIMesh = MeshAdaptPUMI.MeshAdaptPUMI(hmax=0.01,
hmin=0.008,
numIter=1,
sfConfig='ERM',
maType='isotropic')
domain.PUMIMesh.loadModelAndMesh(Model, Mesh)
domain.faceList = [[80], [76], [42], [24], [82], [78]]
mesh = MeshTools.TetrahedralMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
nElements_initial = mesh.nElements_global
mesh.convertFromPUMI(domain.PUMIMesh,
domain.faceList,
parallel=comm.size() > 1,
dim=domain.nd)
domain.PUMIMesh.transferFieldToPUMI("coordinates", mesh.nodeArray)
rho = numpy.array([998.2, 998.2])
nu = numpy.array([1.004e-6, 1.004e-6])
g = numpy.asarray([0.0, 0.0, 0.0])
domain.PUMIMesh.transferPropertiesToPUMI(rho, nu, g)
#Couette Flow
Lz = 0.05
Uinf = 2e-3
#hard code solution
vector = numpy.zeros((mesh.nNodes_global, 3), 'd')
dummy = numpy.zeros(mesh.nNodes_global)
vector[:, 0] = dummy
vector[:, 1] = Uinf * mesh.nodeArray[:, 2] / Lz #v-velocity
vector[:, 2] = dummy
domain.PUMIMesh.transferFieldToPUMI("velocity", vector)
del vector
del dummy
scalar = numpy.zeros((mesh.nNodes_global, 1), 'd')
domain.PUMIMesh.transferFieldToPUMI("p", scalar)
scalar[:, 0] = mesh.nodeArray[:, 2]
domain.PUMIMesh.transferFieldToPUMI("phi", scalar)
del scalar
scalar = numpy.zeros((mesh.nNodes_global, 1), 'd') + 1.0
domain.PUMIMesh.transferFieldToPUMI("vof", scalar)
errorTotal = domain.PUMIMesh.get_local_error()
ok(errorTotal < 1e-14)
ok(domain.PUMIMesh.willAdapt(), 1)
domain.PUMIMesh.adaptPUMIMesh()
mesh = MeshTools.TetrahedralMesh()
mesh.convertFromPUMI(domain.PUMIMesh,
domain.faceList,
parallel=comm.size() > 1,
dim=domain.nd)
nElements_final = mesh.nElements_global
ok(nElements_final > nElements_initial)
def test_gmshLoadAndAdapt(verbose=0):
"""Test for loading gmsh mesh through PUMI, estimating error and adapting for
a Couette flow case"""
testDir = os.path.dirname(os.path.abspath(__file__))
Model = testDir + '/Couette.null'
Mesh = testDir + '/Couette.msh'
domain = Domain.PUMIDomain(
manager=MeshAdapt.AdaptManager()) #initialize the domain
domain.AdaptManager.modelDict = {'flow': 0}
domain.AdaptManager.sizeInputs = [b'error_erm']
domain.AdaptManager.adapt = 1
domain.AdaptManager.hmax = 0.01
domain.AdaptManager.hmin = 0.008
domain.AdaptManager.hphi = 0.008
domain.AdaptManager.numIterations = 1
domain.AdaptManager.targetError = 1
domain.AdaptManager.PUMIAdapter.loadModelAndMesh(bytes(Model, 'utf-8'),
bytes(Mesh, 'utf-8'))
domain.AdaptManager.PUMIAdapter.setAdaptProperties(domain.AdaptManager)
domain.faceList = [[80], [76], [42], [24], [82], [78]]
domain.boundaryLabels = [1, 2, 3, 4, 5, 6]
mesh = MeshTools.TetrahedralMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
nElements_initial = mesh.nElements_global
mesh.convertFromPUMI(domain,
domain.AdaptManager.PUMIAdapter,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
domain.AdaptManager.PUMIAdapter.transferFieldToPUMI(
b"coordinates", mesh.nodeArray)
rho = numpy.array([998.2, 998.2])
nu = numpy.array([1.004e-6, 1.004e-6])
g = numpy.asarray([0.0, 0.0, 0.0])
deltaT = 1.0 #dummy number
epsFact = 1.0 #dummy number
domain.AdaptManager.PUMIAdapter.transferPropertiesToPUMI(
rho, nu, g, deltaT, deltaT, deltaT, epsFact)
#Couette Flow
Lz = 0.05
Uinf = 2e-3
#hard code solution
vector = numpy.zeros((mesh.nNodes_global, 3), 'd')
dummy = numpy.zeros(mesh.nNodes_global)
vector[:, 0] = dummy
vector[:, 1] = Uinf * mesh.nodeArray[:, 2] / Lz #v-velocity
vector[:, 2] = dummy
domain.AdaptManager.PUMIAdapter.transferFieldToPUMI(b"velocity", vector)
del vector
del dummy
scalar = numpy.zeros((mesh.nNodes_global, 1), 'd')
domain.AdaptManager.PUMIAdapter.transferFieldToPUMI(b"p", scalar)
scalar[:, 0] = mesh.nodeArray[:, 2]
domain.AdaptManager.PUMIAdapter.transferFieldToPUMI(b"phi", scalar)
del scalar
scalar = numpy.zeros((mesh.nNodes_global, 1), 'd') + 1.0
domain.AdaptManager.PUMIAdapter.transferFieldToPUMI(b"vof", scalar)
errorTotal = domain.AdaptManager.PUMIAdapter.get_local_error()
ok(errorTotal < 1e-14)
#ok(domain.AdaptManager.willAdapt(),1)
domain.AdaptManager.PUMIAdapter.adaptPUMIMesh(b"")
mesh = MeshTools.TetrahedralMesh()
mesh.convertFromPUMI(domain,
domain.AdaptManager.PUMIAdapter,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
nElements_final = mesh.nElements_global
ok(nElements_final > nElements_initial)
midpoint_z_index = (nPoints_z + 1) // 2
assert (nPoints_x + 1) % 2 == 0
assert (nPoints_y + 1) % 2 == 0
assert (nPoints_z + 1) % 2 == 0
dx = 1.0 / (nPoints_x - 1.0)
dy = 1.0 / (nPoints_y - 1.0)
dz = 1.0 / (nPoints_z - 1.0)
x = np.zeros((nPoints_x, nPoints_y, nPoints_z, 3), 'd')
for i in range(nPoints_x):
for j in range(nPoints_y):
for k in range(nPoints_z):
x[i, j, k, 0] = i * dx
x[i, j, k, 1] = j * dy
x[i, j, k, 2] = k * dz
grid = MeshTools.RectangularGrid(500, 1, 1, Lx=1.0)
X = np.array([n.p for n in grid.nodeList])
Xx = np.array([n.p[0] for n in grid.nodeList])
def test_PlaneCouetteFlow():
iwork = np.zeros((1, ), 'i')
rwork = np.zeros((5, ), 'd')
t = 0.0
rwork[0] = 0.1
rwork[1] = dy * (nPoints_y - 1.0)
rwork[2] = 0.0
rwork[3] = 0.0
rwork[4] = 0.0
ux = np.zeros(x.shape[:-1], 'd')
uy = np.zeros(x.shape[:-1], 'd')