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, manager=MeshAdapt.AdaptManager()) #initialize the domain
modelDict = {'flow': 0}
domain.AdaptManager.modelDict = modelDict
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 = [[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.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])
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] = Uinf * mesh.nodeArray[:, 1] / Lz #v-velocity
vector[:, 1] = dummy
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[:, 1]
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.TriangularMesh()
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)
regionFlags=regionFlags,
regionConstraints=regionConstraints)
#go ahead and add a boundary tags member
domain.boundaryTags = boundaryTags
domain.writePoly("mesh")
domain.writePLY("mesh")
domain.writeAsymptote("mesh")
domain.MeshOptions.triangleOptions = "VApq30ena%8.8f" % (
(he**2) / 2.0, )
#logEvent("""Mesh generated using: tetgen -%s %s""" % (triangleOptions, domain.polyfile + ".poly"))
if genMesh and usePUMI:
from proteus.MeshAdaptPUMI import MeshAdapt
domain.AdaptManager = MeshAdapt.AdaptManager()
#===============================================================================
# Time stepping
#===============================================================================
T = ct.T
dt_fixed = ct.dt_fixed #0.03
dt_init = ct.dt_fixed #min(0.1*dt_fixed,0.001)
if ct.isHotStart:
dt_init = dt_fixed
runCFL = 0.33
nDTout = int(round(T / dt_fixed))
if dt_init < dt_fixed:
tnList = [0.0, dt_init] + [i * dt_fixed for i in range(1, nDTout + 1)]
else:
tnList = [i * dt_fixed for i in range(0, nDTout + 1)]
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(
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)
#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.AdaptManager.PUMIAdapter.transferFieldToPUMI(b"velocity", vector)
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()
# 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)
if useHex:
nnx=4*Refinement+1
nny=1*Refinement+1
nnz=2*Refinement+1
if quas2D:
nny=2
hex=True
domain = Domain.RectangularDomain(L)
else:
boundaries=['bottom','top','front','back','left','right']
boundaryTags=dict([(key,i+1) for (i,key) in enumerate(boundaries)])
if structured:
nnx=4*Refinement
nny=2*Refinement
else:
domain = Domain.PUMIDomain(manager=MeshAdapt.AdaptManager()) #initialize the domain
#domain.numBC=6 #set number of BCs
# domain.numAdaptSteps=1 #set number of adapt steps (loops)
#Following sets list of face tags of geometric model as mapped from boundary Tags,
#meaning if faceList=[[2,4],[1]] and boundaries=['left','right'], then faces with geometry tags 2 and 4 are set as 'left'
#and face with geometric tag 4 is set as 'right'
#The order of boundaries list is important because the last ones take precendence over the first ones,
#which means that the geometric edge or vertex which lies on 2 or more geometric faces will be set with the boundaries tag of
#the geomtric face which is latter in the order (email: [email protected] for any questions)
domain.faceList=[[41],[46],[42],[44],[45],[43]]
domain.boundaryLabels=[1,2,3,4,5,6]
#read the geometry and mesh
testDir=os.path.dirname(os.path.abspath(__file__))
Model = testDir + '/../Couette.null'
Mesh = testDir + '/../Couette.msh'