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 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 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)
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)