https://github.com/dbukenberger/HexahedralLattice
Tip revision: 991ca6893ac1feec28f491429111e0fbdcefccc0 authored by dbukenberger on 20 November 2024, 07:08:57 UTC
Update requirements.txt
Update requirements.txt
Tip revision: 991ca68
FemObject.py
from femUtil import *
# FEM constants
youngs_modulus = 1000.0
poisson_ratio = 0.3
pLambda, pMu = lame_parameters(youngs_modulus, poisson_ratio)
C = linear_stress(pLambda, pMu)
class FemObject:
def __init__(self, inputFile = None, loadResult = False):
if inputFile is None:
return
self.materialized = False
self.inputFile = inputFile
self.fixFuns = []
self.flxFuns = []
self.frcVecs = []
self.funData = []
if '.stress' in inputFile:
self.fromStressFile(inputFile)
return
with open(self.inputFile, 'r') as fh:
for line in fh.readlines():
line = line.strip().split(' ')
if '#' in line:
continue
if line[0] == 'file':
self.meshFile = os.path.dirname(self.inputFile) + '/' + line[1]
continue
if line[0] == 'type':
self.mType = line[1]
continue
if line[1] == 'd':
d = int(line[2])
if '-' in line[2]:
fData = (-d, float(line[-1]))
f = lambda vs, fIdx, tol = eps: vs[:,self.funData[fIdx][0]] <= (self.funData[fIdx][1] + tol)
else:
fData = (d, float(line[-1]))
f = lambda vs, fIdx, tol = eps: vs[:,self.funData[fIdx][0]] >= (self.funData[fIdx][1] - tol)
elif line[1] == 'r':
fData = (np.float32(line[2:-1]), float(line[-1]))
f = lambda vs, fIdx, tol = eps: norm(vs - self.funData[fIdx][0]) < self.funData[fIdx][1] + tol
if line[0] == 'fix':
self.fixFuns.append(f)
self.funData.append(fData)
elif line[0] == 'flx':
self.flxFuns.append(f)
self.funData.append(fData)
elif line[0] == 'vec':
self.frcVecs.append(np.float32(line[1:]))
self.frcVecs = np.float32(self.frcVecs)
self.nDim = 2 if self.mType in ['tri', 'quad'] else 3
if loadResult:
if self.nDim == 2:
self.meshFile = self.inputFile.replace('.frc', '.ply')
self.mType = 'quad'
if self.nDim == 3:
self.meshFile = self.inputFile.replace('.frc', '.mesh')
self.mType = 'hex'
if not os.path.exists(self.meshFile):
print('Result does not yet exist.')
vmsPath = self.meshFile.split('.')[0] + '.vms'
if os.path.exists(self.meshFile.split('.')[0] + '.vms'):
self.vmStress = np.loadtxt(vmsPath)
self.mTypeInit = self.mType
if self.mType in ['tri', 'quad']:
if '.obj' in self.meshFile:
vs, self.ts = loadObjFile(self.meshFile)
else:
vs, self.ts = loadPlyFile(self.meshFile)
self.verts = vs[:,:-1]
if self.mType == 'tri':
self.meshInit = fem.MeshTri(self.verts.T, self.ts.T)
self.eType = fem.ElementTriP1()
elif self.mType == 'quad':
self.meshInit = fem.MeshQuad(self.verts.T, self.ts.T)
self.eType = fem.ElementQuad1()
elif self.mType == 'tet':
self.meshInit = fem.MeshTet.load(self.meshFile)
self.eType = fem.ElementTetP1()
elif self.mType == 'hex':
self.meshInit = fem.MeshHex.load(self.meshFile)
self.eType = fem.ElementHex1()
self.setupFEM()
def fromStressFile(self, filePath):
self.verts, self.ts, self.vIdxsFlx, self.forceVecs, self.vIdxsFix, self.vmStress, self.pStress, self.pStressE, self.sMats = loadStressFile(filePath)
self.nDim = self.verts.shape[1]
if self.nDim == 2:
if self.ts.shape[1] == 3:
self.mType = 'tri'
self.meshInit = fem.MeshTri(self.verts.T, self.ts.T)
self.eType = fem.ElementTriP1()
else:
self.mType = 'quad'
self.meshInit = fem.MeshQuad(self.verts.T, self.ts.T)
self.eType = fem.ElementQuad1()
else:
if self.ts.shape[1] == 4:
self.mType = 'tet'
self.meshInit = fem.MeshTet(self.verts.T, self.ts.T)
self.eType = fem.ElementTetP1()
else:
self.mType = 'hex'
self.meshInit = fem.MeshHex(self.verts.T, self.ts.T)
self.eType = fem.ElementHex1()
self.mTypeInit = self.mType
self.setupFEM()
fVecs = np.zeros((self.nVerts, self.nDim), np.float32)
fVecs[self.vIdxsFlx] = self.forceVecs
self.f = fVecs.ravel()
def setupFEM(self):
self.sf = norm(self.meshInit.doflocs.max(axis=1)-self.meshInit.doflocs.min(axis=1)) / 1000
self.nVerts = len(self.meshInit.doflocs.T)
self.nElems = len(self.meshInit.t.T)
print("#v % 6d, #e % 6d"%(self.nVerts, self.nElems))
vs = self.meshInit.doflocs.T
es = self.meshInit.edges.T if self.nDim == 3 else facesToEdges(self.meshInit.t.T)
self.mel = norm(vs[es[:,0]] - vs[es[:,1]]).mean()
self.eVector = fem.ElementVector(self.eType)
self.basis = fem.Basis(self.meshInit, self.eVector, fem.MappingIsoparametric(self.meshInit, self.eType), 0)
self.K = fem.asm(linear_elasticity(pLambda, pMu), self.basis)
if self.nDim == 2:
tris = self.ts if self.mType == 'tri' else facesToTris(self.ts)
self.volInit = computeTriangleAreas(self.verts[tris], False).sum()
else:
verts = self.meshInit.doflocs.T
if self.mType == 'tet':
tets = self.meshInit.t.T
else:
hexas = self.meshInit.t.T
tets = np.vstack([hexaToTetras(hexa) for hexa in hexOrderDg2BT(hexas)])
self.volInit = computeTetraVolumes(verts[tets]).sum()
self.vol = self.volInit
self.setupBoundaryMasks()
self.setupBoundaryWeights()
def setupBoundaryWeights(self):
self.bWeights = np.zeros(self.nVerts, np.float32)
bElements = self.meshInit.facets.T[self.meshInit.boundary_facets()]
bElements = bElements[np.any(self.boundaryVertMask[bElements], axis=1)]
if self.nDim == 2:
bElementWeights = norm(self.verts[bElements[:,0]] - self.verts[bElements[:,1]]) / 2
elif self.mType == 'tet':
bElementWeights = computeTriangleAreas(self.meshInit.doflocs.T[bElements]) / 3
elif self.mType == 'hex':
bElementWeights = computeTriangleAreas(self.meshInit.doflocs.T[tetrasToFaces(bElements)]).reshape(-1,4).sum(axis=1) / 8
for eIdx, bElement in tqdm(enumerate(bElements), total = len(bElements), ascii=True, desc='boundaryWeights'):
self.bWeights[bElement] += bElementWeights[eIdx]
def materialize(self, alpha = 0.5, walled = False):
self.materialized = [alpha, walled]
if self.mType in ['tri', 'quad']:
self.materializeTriQuad(alpha)
elif self.mType == 'tet':
self.materializeTet(alpha, walled)
elif self.mType == 'hex':
self.materializeHex(alpha, walled)
def materializeOpti(self, alpha = 0.5, walled = False, weights = None):
self.materialized = [alpha, walled]
alpha = abs(alpha)
ws = (self.vmStress/self.vmStress.max()) ** 2 if weights is None else weights
if self.mType in ['tri', 'quad']:
vertsOrig = self.verts
facesOrig = self.ts
edgesOrig = facesToEdges(facesOrig)
self.materializeTriQuad(alpha, False, False)
taus = optimizeTaus(self.volInit * alpha, ws, vertsOrig, [edgesOrig, facesOrig], self.ts, self.mTypeInit)
self.verts = materializeFaceVerts(taus, ws, vertsOrig, edgesOrig, facesOrig, self.mTypeInit)
elif self.mType == 'tet':
vertsOrig = self.meshInit.doflocs.T
edgesOrig = self.meshInit.edges.T
trisOrig = self.meshInit.facets.T
tetsOrig = self.meshInit.t.T
self.materializeTet(alpha, walled, False, False)
taus = optimizeTaus(self.volInit * alpha, ws, vertsOrig, [edgesOrig, trisOrig, tetsOrig], self.ts, self.mTypeInit, walled)
self.verts = materializeTetVerts(taus, ws, vertsOrig, edgesOrig, trisOrig, tetsOrig, self.mTypeInit, walled)
elif self.mType == 'hex':
vertsOrig = self.meshInit.doflocs.T
edgesOrig = self.meshInit.edges.T
quadsOrig = self.meshInit.facets.T
hexasOrig = self.meshInit.t.T
self.materializeHex(alpha, walled, False, False)
taus = optimizeTaus(self.volInit * alpha, ws, vertsOrig, [edgesOrig, quadsOrig, hexasOrig], self.ts, self.mTypeInit, walled)
self.verts = materializeHexVerts(taus, ws, vertsOrig, edgesOrig, quadsOrig, hexasOrig, self.mTypeInit, walled)
self.initMaterializedFEM()
def initMaterializedFEM(self):
if self.mTypeInit in ['tri', 'quad', 'cell']:
self.mType = 'quad'
self.meshInit = fem.MeshQuad(self.verts.T, self.ts.T)
self.eType = fem.ElementQuad1()
self.vol = computeTriangleAreas(self.verts[facesToTris(self.ts)], False).sum()
else:
self.mType = 'hex'
self.meshInit = fem.MeshHex(self.verts.T, self.ts.T)
self.eType = fem.ElementHex1()
hexaTets = np.vstack([hexaToTetras(hexa) for hexa in hexOrderDg2BT(self.ts)])
self.vol = computeTetraVolumes(self.verts[hexaTets]).sum()
self.SJs = self.evalScaledJacobians()
if self.SJs.max() < 0:
self.ts = self.ts[:,::-1]
self.SJs *= -1
self.nVerts = len(self.meshInit.doflocs.T)
self.nElems = len(self.meshInit.t.T)
print('nV: %d, nE: %d'%(self.nVerts, self.nElems))
st = time()
self.eVector = fem.ElementVector(self.eType)
self.basis = fem.Basis(self.meshInit, self.eVector, fem.MappingIsoparametric(self.meshInit, self.eType), 0)
print('basis', time() - st)
st = time()
self.K = fem.asm(linear_elasticity(pLambda, pMu), self.basis)
print('K', time() - st)
st = time()
self.setupBoundaryWeights()
print('weights', time() - st)
def materializeTriQuad(self, alpha = 0.5, withVerts = True, withFEM = True):
tris = self.ts if self.mType == 'tri' else facesToTris(self.ts)
self.volInit = computeTriangleAreas(self.verts[tris], False).sum()
verts = self.meshInit.doflocs.T
faces = self.cs if self.mTypeInit == 'cell' else self.ts
edges = facesToEdges(faces)
if withVerts:
if self.mType == 'tri':
tau = (1 - np.sqrt(1 - alpha)) / 3
if self.mType == 'quad':
tau = (1 - np.sqrt(1 - alpha)) / 2
self.verts = materializeFaceVerts(None, tau, verts, edges, faces, self.mType)
boundaryVertMask = flatten([[self.boundaryVertMask[edge].all()] * 2 for edge in edges])
es = np.repeat(edges, 2, axis=0)
es[1::2] = edges[:,::-1]
edgeHashs = cantorPiV(es, False)
quads = []
idxOffset = 0
for fIdx, face in enumerate(faces):
m = len(face)
for vIdx in range(m):
heCL = cantorPiO(face[vIdx], face[(vIdx+1)%m])
heCR = cantorPiO(face[vIdx], face[(vIdx-1)%m])
vCLidx = np.where(edgeHashs == heCL)[0][0] + len(verts)
vCRidx = np.where(edgeHashs == heCR)[0][0] + len(verts)
vCIidx = idxOffset + vIdx + len(verts) + len(edges)*2
quads.append([face[vIdx], vCLidx, vCIidx, vCRidx]) # corner
heLC = cantorPiO(face[(vIdx+1)%m], face[vIdx])
vLCidx = np.where(edgeHashs == heLC)[0][0] + len(verts)
vLIidx = idxOffset + (vIdx+1)%m + len(verts) + len(edges)*2
quads.append([vCLidx, vLCidx, vLIidx, vCIidx]) # edge
idxOffset += m
boundaryVertMask += [False] * m
self.ts = np.vstack(quads)
self.boundaryVertMask = np.concatenate([self.boundaryVertMask, boundaryVertMask])
if withFEM:
self.initMaterializedFEM()
def materializeTet(self, alpha = 0.5, walled = False, withVerts = True, withFEM = True):
def tetToEdges(tet):
return np.int64(np.transpose([tet[[0,0,0,1,2,3]], tet[[1,2,3,2,3,1]]]))
def tetToFaces(tet):
return np.int64(tet[[[0,2,3], [0,3,1], [0,1,2], [1,3,2]]])
verts = self.meshInit.doflocs.T
edges = self.meshInit.edges.T
faces = self.meshInit.facets.T
tets = self.meshInit.t.T
self.volInit = computeTetraVolumes(verts[tets]).sum()
if walled:
tau = (1 - (1 - alpha)**(1/3)) / 4
numEdgeVerts = 3
numFaceVerts = 7
numCellVerts = 14
else:
taus = {0.25: 0.0943680425, 0.5: 0.1448414, 0.75: 0.195888335}
if alpha in taus.keys(): # exact values
tau = taus[alpha]
else: # approximation with magic numbers
p = np.sqrt(42)/5 + 2 # 3.29615807
q = -np.pi/2 - 1 - 2**(1/3)/2 + np.sqrt(6)/2 + 3*np.sqrt(2)/2 # 0.14528211
tau = np.arcsin(alpha*2-1)/(p*np.pi)+q
numEdgeVerts = 2
numFaceVerts = 3
numCellVerts = 4
if withVerts:
self.verts = materializeTetVerts(None, tau, verts, edges, faces, tets, self.mType, walled)
boundaryVertMask = []
eHashs = cantorPiV(np.int64(edges))
ePos = {}
for i, (e, eHash) in enumerate(zip(edges, eHashs)):
for j, vIdx in enumerate(e):
ePos[(eHash, vIdx)] = numEdgeVerts*i + j
if walled:
ePos[(eHash, None)] = numEdgeVerts*i + 2
boundaryVertMask += [self.boundaryVertMask[e].all()] * numEdgeVerts
fHashs = cantorPiKV(np.int64(faces))
fPos = {}
for i, (fc, fHash) in enumerate(zip(faces, fHashs)):
for j, vIdx in enumerate(fc):
fPos[(fHash, (vIdx+1))] = numFaceVerts*i + j
if walled:
fPos[(fHash, -(vIdx+1))] = numFaceVerts*i + j + 3
if walled:
fPos[(fHash, None)] = numFaceVerts*i + 6
boundaryVertMask += [self.boundaryVertMask[fc].all()] * numFaceVerts
newHexas = []
for tIdx, vIdxs in tqdm(enumerate(tets), total = tets.shape[0], ascii=True, desc='materializing'):
tEdges = tetToEdges(vIdxs)
tEdgesHashs = cantorPiV(tEdges)
eIdxs = []
for edge, eHash in zip(tEdges, tEdgesHashs):
eIdxs += [ePos[(eHash, vIdx)] for vIdx in edge]
if walled:
eIdxs += [ePos[(eHash, None)]]
eIdxs = np.int32(eIdxs) + len(verts)
tFaces = tetToFaces(vIdxs)
tFacesHashs = cantorPiKV(tFaces)
fIdxs = []
for face, fHash in zip(tFaces, tFacesHashs):
fIdxs += [fPos[(fHash, (vIdx+1))] for vIdx in face]
if walled:
fIdxs += [fPos[(fHash, -(vIdx+1))] for vIdx in face]
fIdxs += [fPos[(fHash, None)]]
fIdxs = np.int32(fIdxs) + len(verts) + len(edges) * numEdgeVerts
cIdxs = np.arange(numCellVerts) + tIdx*numCellVerts + len(verts) + len(edges)*numEdgeVerts + len(faces)*numFaceVerts
# corners
if walled:
newHexas += [[vIdxs[0], eIdxs[0], eIdxs[6], eIdxs[3], fIdxs[7], fIdxs[14], fIdxs[0], cIdxs[0]]]
newHexas += [[eIdxs[1], vIdxs[1], fIdxs[9], fIdxs[15], eIdxs[16], eIdxs[9], cIdxs[1], fIdxs[21]]]
newHexas += [[eIdxs[4], fIdxs[16], fIdxs[1], vIdxs[2], cIdxs[2], eIdxs[10], eIdxs[12], fIdxs[23]]]
newHexas += [[fIdxs[2], cIdxs[3], eIdxs[7], eIdxs[13], fIdxs[8], fIdxs[22], vIdxs[3], eIdxs[15]]]
else:
newHexas += [[vIdxs[0], eIdxs[0], eIdxs[4], eIdxs[2], fIdxs[3], fIdxs[6], fIdxs[0], cIdxs[0]]]
newHexas += [[eIdxs[1], vIdxs[1], fIdxs[5], fIdxs[7], eIdxs[11], eIdxs[6], cIdxs[1], fIdxs[9]]]
newHexas += [[eIdxs[3], fIdxs[8], fIdxs[1], vIdxs[2], cIdxs[2], eIdxs[7], eIdxs[8], fIdxs[11]]]
newHexas += [[fIdxs[2], cIdxs[3], eIdxs[5], eIdxs[9], fIdxs[4], fIdxs[10], vIdxs[3], eIdxs[10]]]
# edges
if walled:
newHexas += [[eIdxs[0], eIdxs[2], fIdxs[7], fIdxs[14], fIdxs[11], fIdxs[19], cIdxs[0], cIdxs[4]]]
newHexas += [[eIdxs[2], eIdxs[1], fIdxs[11], fIdxs[19], fIdxs[9], fIdxs[15], cIdxs[4], cIdxs[1]]]
newHexas += [[eIdxs[3], fIdxs[14], fIdxs[0], eIdxs[5], cIdxs[0], fIdxs[18], fIdxs[5], cIdxs[6]]]
newHexas += [[eIdxs[5], fIdxs[18], fIdxs[5], eIdxs[4], cIdxs[6], fIdxs[16], fIdxs[1], cIdxs[2]]]
newHexas += [[eIdxs[6], fIdxs[7], eIdxs[8], fIdxs[0], fIdxs[12], cIdxs[0], fIdxs[4], cIdxs[7]]]
newHexas += [[eIdxs[8], fIdxs[12], eIdxs[7], fIdxs[4], fIdxs[8], cIdxs[7], fIdxs[2], cIdxs[3]]]
newHexas += [[fIdxs[1], cIdxs[2], fIdxs[3], eIdxs[12], cIdxs[9], fIdxs[23], eIdxs[14], fIdxs[24]]]
newHexas += [[fIdxs[3], cIdxs[9], fIdxs[2], eIdxs[14], cIdxs[3], fIdxs[24], eIdxs[13], fIdxs[22]]]
newHexas += [[fIdxs[16], fIdxs[17], cIdxs[2], eIdxs[10], cIdxs[5], eIdxs[11], fIdxs[23], fIdxs[25]]]
newHexas += [[fIdxs[17], fIdxs[15], cIdxs[5], eIdxs[11], cIdxs[1], eIdxs[9], fIdxs[25], fIdxs[21]]]
newHexas += [[fIdxs[9], eIdxs[16], fIdxs[10], cIdxs[1], eIdxs[17], fIdxs[21], cIdxs[8], fIdxs[26]]]
newHexas += [[fIdxs[10], eIdxs[17], fIdxs[8], cIdxs[8], eIdxs[15], fIdxs[26], cIdxs[3], fIdxs[22]]]
else:
newHexas += [[eIdxs[0], eIdxs[1], fIdxs[3], fIdxs[6], fIdxs[5], fIdxs[7], cIdxs[0], cIdxs[1]]]
newHexas += [[eIdxs[2], fIdxs[6], fIdxs[0], eIdxs[3], cIdxs[0], fIdxs[8], fIdxs[1], cIdxs[2]]]
newHexas += [[eIdxs[4], fIdxs[3], eIdxs[5], fIdxs[0], fIdxs[4], cIdxs[0], fIdxs[2], cIdxs[3]]]
newHexas += [[fIdxs[1], cIdxs[2], fIdxs[2], eIdxs[8], cIdxs[3], fIdxs[11], eIdxs[9], fIdxs[10]]]
newHexas += [[fIdxs[8], fIdxs[7], cIdxs[2], eIdxs[7], cIdxs[1], eIdxs[6], fIdxs[11], fIdxs[9]]]
newHexas += [[fIdxs[5], eIdxs[11], fIdxs[4], cIdxs[1], eIdxs[10], fIdxs[9], cIdxs[3], fIdxs[10]]]
# faces
if walled:
newHexas += [[fIdxs[6], cIdxs[11], fIdxs[5], fIdxs[4], cIdxs[6], cIdxs[7], fIdxs[0], cIdxs[0]]]
newHexas += [[fIdxs[6], cIdxs[11], fIdxs[4], fIdxs[3], cIdxs[7], cIdxs[9], fIdxs[2], cIdxs[3]]]
newHexas += [[fIdxs[6], cIdxs[11], fIdxs[3], fIdxs[5], cIdxs[9], cIdxs[6], fIdxs[1], cIdxs[2]]]
newHexas += [[fIdxs[13], cIdxs[12], fIdxs[12], fIdxs[11], cIdxs[7], cIdxs[4], fIdxs[7], cIdxs[0]]]
newHexas += [[fIdxs[13], cIdxs[12], fIdxs[11], fIdxs[10], cIdxs[4], cIdxs[8], fIdxs[9], cIdxs[1]]]
newHexas += [[fIdxs[13], cIdxs[12], fIdxs[10], fIdxs[12], cIdxs[8], cIdxs[7], fIdxs[8], cIdxs[3]]]
newHexas += [[fIdxs[20], cIdxs[13], fIdxs[19], fIdxs[18], cIdxs[4], cIdxs[6], fIdxs[14], cIdxs[0]]]
newHexas += [[fIdxs[20], cIdxs[13], fIdxs[18], fIdxs[17], cIdxs[6], cIdxs[5], fIdxs[16], cIdxs[2]]]
newHexas += [[fIdxs[20], cIdxs[13], fIdxs[17], fIdxs[19], cIdxs[5], cIdxs[4], fIdxs[15], cIdxs[1]]]
newHexas += [[fIdxs[27], cIdxs[10], fIdxs[26], fIdxs[25], cIdxs[8], cIdxs[5], fIdxs[21], cIdxs[1]]]
newHexas += [[fIdxs[27], cIdxs[10], fIdxs[25], fIdxs[24], cIdxs[5], cIdxs[9], fIdxs[23], cIdxs[2]]]
newHexas += [[fIdxs[27], cIdxs[10], fIdxs[24], fIdxs[26], cIdxs[9], cIdxs[8], fIdxs[22], cIdxs[3]]]
boundaryVertMask += [False] * numCellVerts
self.ts = np.int32(newHexas)[:,::-1]
self.boundaryVertMask = np.concatenate([self.boundaryVertMask, boundaryVertMask])
if withFEM:
self.initMaterializedFEM()
def materializeHex(self, alpha = 0.5, walled = False, withVerts = True, withFEM = True):
def hexaToEdges(hexa):
return np.int64(np.transpose([hexa[[0,0,0,1,2,1,3,2,3,4,5,6]], hexa[[1,2,3,4,4,5,5,6,6,7,7,7]]]))
def hexaToFaces(hexa):
return np.int64(hexa[[[0,2,6,3], [0,3,5,1], [0,1,4,2], [6,7,5,3], [2,4,7,6], [1,5,7,4]]])
verts = self.meshInit.doflocs.T
edges = self.meshInit.edges.T
faces = self.meshInit.facets.T
hexas = self.meshInit.t.T
hexaTets = np.vstack([hexaToTetras(hexa) for hexa in hexOrderDg2BT(hexas)])
self.volInit = computeTetraVolumes(verts[hexaTets]).sum()
if withVerts:
if walled:
tau = (1 - (1 - alpha)**(1/3)) / 2
else:
tau = np.arcsin(alpha*2-1)/(2*np.pi)+1/4
self.verts = materializeHexVerts(None, tau, verts, edges, faces, hexas, self.mType, walled)
boundaryVertMask = []
eHashs = cantorPiV(np.int64(edges))
ePos = {}
for i, (e, eHash) in enumerate(zip(edges, eHashs)):
for j, vIdx in enumerate(e):
ePos[(eHash, vIdx)] = 2*i + j
boundaryVertMask += [self.boundaryVertMask[e].all()] * 2
fHashs = cantorPiKV(np.int64(faces))
fPos = {}
for i, (fc, fHash) in enumerate(zip(faces, fHashs)):
for j, vIdx in enumerate(fc):
fPos[(fHash, vIdx)] = 4*i + j
boundaryVertMask += [self.boundaryVertMask[fc].all()] * 4
newHexas = []
for hIdx, vIdxs in tqdm(enumerate(hexas), total = hexas.shape[0], ascii=True, desc='materializing'):
hEdges = hexaToEdges(vIdxs)
hEdgesHashs = cantorPiV(hEdges)
eIdxs = []
for edge, eHash in zip(hEdges, hEdgesHashs):
eIdxs += [ePos[(eHash, vIdx)] for vIdx in edge]
eIdxs = np.int32(eIdxs) + len(verts)
hFaces = hexaToFaces(vIdxs)
hFacesHashs = cantorPiKV(hFaces)
fIdxs = []
for face, fHash in zip(hFaces, hFacesHashs):
fIdxs += [fPos[(fHash, vIdx)] for vIdx in face]
fIdxs = np.int32(fIdxs) + len(verts) + len(edges)*2
cIdxs = np.arange(8) + hIdx*8 + len(verts) + len(edges)*2 + len(faces)*4
# corners
newHexas += [[vIdxs[0], eIdxs[0], eIdxs[2], eIdxs[4], fIdxs[8], fIdxs[4], fIdxs[0], cIdxs[0]]]
newHexas += [[eIdxs[1], vIdxs[1], fIdxs[9], fIdxs[7], eIdxs[6], eIdxs[10], cIdxs[1], fIdxs[20]]]
newHexas += [[eIdxs[3], fIdxs[11], vIdxs[2], fIdxs[1], eIdxs[8], cIdxs[2], eIdxs[14], fIdxs[16]]]
newHexas += [[eIdxs[5], fIdxs[5], fIdxs[3], vIdxs[3], cIdxs[3], eIdxs[12], eIdxs[16], fIdxs[15]]]
newHexas += [[fIdxs[10], eIdxs[7], eIdxs[9], cIdxs[4], vIdxs[4], fIdxs[23], fIdxs[17], eIdxs[18]]]
newHexas += [[fIdxs[6], eIdxs[11], cIdxs[5], eIdxs[13], fIdxs[21], vIdxs[5], fIdxs[14], eIdxs[20]]]
newHexas += [[fIdxs[2], cIdxs[6], eIdxs[15], eIdxs[17], fIdxs[19], fIdxs[12], vIdxs[6], eIdxs[22]]]
newHexas += [[cIdxs[7], fIdxs[22], fIdxs[18], fIdxs[13], eIdxs[19], eIdxs[21], eIdxs[23], vIdxs[7]]]
# edges
newHexas += [[eIdxs[4], fIdxs[4], fIdxs[0], eIdxs[5], cIdxs[0], fIdxs[5], fIdxs[3], cIdxs[3]]]
newHexas += [[eIdxs[2], fIdxs[8], eIdxs[3], fIdxs[0], fIdxs[11], cIdxs[0], fIdxs[1], cIdxs[2]]]
newHexas += [[fIdxs[1], cIdxs[2], eIdxs[14], fIdxs[2], fIdxs[16], cIdxs[6], eIdxs[15], fIdxs[19]]]
newHexas += [[fIdxs[3], cIdxs[3], fIdxs[2], eIdxs[16], cIdxs[6], fIdxs[15], eIdxs[17], fIdxs[12]]]
newHexas += [[eIdxs[0], eIdxs[1], fIdxs[8], fIdxs[4], fIdxs[9], fIdxs[7], cIdxs[0], cIdxs[1]]]
newHexas += [[fIdxs[11], fIdxs[10], eIdxs[8], cIdxs[2], eIdxs[9], cIdxs[4], fIdxs[16], fIdxs[17]]]
newHexas += [[fIdxs[5], fIdxs[6], cIdxs[3], eIdxs[12], cIdxs[5], eIdxs[13], fIdxs[15], fIdxs[14]]]
newHexas += [[cIdxs[6], cIdxs[7], fIdxs[19], fIdxs[12], fIdxs[18], fIdxs[13], eIdxs[22], eIdxs[23]]]
newHexas += [[fIdxs[7], eIdxs[10], cIdxs[1], fIdxs[6], fIdxs[20], eIdxs[11], cIdxs[5], fIdxs[21]]]
newHexas += [[fIdxs[9], eIdxs[6], fIdxs[10], cIdxs[1], eIdxs[7], fIdxs[20], cIdxs[4], fIdxs[23]]]
newHexas += [[cIdxs[4], fIdxs[23], fIdxs[17], cIdxs[7], eIdxs[18], fIdxs[22], fIdxs[18], eIdxs[19]]]
newHexas += [[cIdxs[5], fIdxs[21], cIdxs[7], fIdxs[14], fIdxs[22], eIdxs[20], fIdxs[13], eIdxs[21]]]
# faces
if walled:
newHexas += [[fIdxs[0], cIdxs[0], fIdxs[1], fIdxs[3], cIdxs[2], cIdxs[3], fIdxs[2], cIdxs[6]]]
newHexas += [[fIdxs[8], fIdxs[9], fIdxs[11], cIdxs[0], fIdxs[10], cIdxs[1], cIdxs[2], cIdxs[4]]]
newHexas += [[fIdxs[4], fIdxs[7], cIdxs[0], fIdxs[5], cIdxs[1], fIdxs[6], cIdxs[3], cIdxs[5]]]
newHexas += [[cIdxs[2], cIdxs[4], fIdxs[16], cIdxs[6], fIdxs[17], cIdxs[7], fIdxs[19], fIdxs[18]]]
newHexas += [[cIdxs[3], cIdxs[5], cIdxs[6], fIdxs[15], cIdxs[7], fIdxs[14], fIdxs[12], fIdxs[13]]]
newHexas += [[cIdxs[1], fIdxs[20], cIdxs[4], cIdxs[5], fIdxs[23], fIdxs[21], cIdxs[7], fIdxs[22]]]
# inner block
#newHexas += [[cIdxs[0], cIdxs[1], cIdxs[2], cIdxs[3], cIdxs[4], cIdxs[5], cIdxs[6], cIdxs[7]]]
boundaryVertMask += [False] * 8
self.ts = np.int32(newHexas)
self.boundaryVertMask = np.concatenate([self.boundaryVertMask, boundaryVertMask])
if withFEM:
self.initMaterializedFEM()
def setupBoundaryMasks(self):
self.boundaryVertMask = np.zeros(self.nVerts, dtype=np.bool_)
if self.mType in ['tri', 'quad']:
es = facesToEdges(self.ts if hasattr(self, 'ts') else self.meshInit.t.T, False)
unq, inv, cnt = np.unique(cantorPiKV(es), return_inverse = True, return_counts = True)
self.boundaryEdgeMask = cnt[inv] == 1
self.boundaryVertMask[np.unique(es[self.boundaryEdgeMask].ravel())] = True
if self.mType in ['hex', 'tet']:
ts = self.ts if hasattr(self, 'ts') else self.meshInit.t.T
fcs = tetrasToFaces(ts) if self.mType == 'tet' else hexasToFaces(ts)
unq, inv, cnt = np.unique(cantorPiKV(fcs), return_inverse = True, return_counts = True)
self.boundaryFaceMask = cnt[inv] == 1
self.boundaryVertMask[self.meshInit.boundary_nodes()] = True
def computeCompliance(self, complianceOnly = False):
fVecs = np.zeros((self.nVerts, self.nDim), np.float32)
if not hasattr(self, 'forceVecs'):
vs = self.meshInit.doflocs.T
funIdx = 0
fixMsk = self.boundaryVertMask * 0
for fixFun in self.fixFuns:
msk = fixFun(vs, funIdx, self.mel/1000)
fixMsk = np.bitwise_or(np.bitwise_and(msk, self.boundaryVertMask), fixMsk)
funIdx += 1
self.vIdxsFix = np.where(fixMsk)[0].tolist()
flxMsk = self.boundaryVertMask * 0
flxIdxs = []
for fIdx, flxFun in enumerate(self.flxFuns):
msk = flxFun(vs, funIdx, self.mel/1000)
bMsk = np.bitwise_and(msk, self.boundaryVertMask)
flxMsk = np.bitwise_or(bMsk, flxMsk)
fvIdxs = np.where(bMsk)[0]
flxIdxs.append(fvIdxs)
w = self.bWeights[fvIdxs] #* 0 + 1
fVecs[fvIdxs] = self.frcVecs[fIdx] * w.reshape(-1,1) / w.sum()
funIdx += 1
numVertsPerForce = np.int32(list(map(len, flxIdxs)))
self.vIdxsFlx = np.where(flxMsk)[0].tolist()
else:
fVecs[self.vIdxsFlx] = self.forceVecs
self.f = fVecs.ravel()
print('#fix: %d, #flx: %d'%(len(self.vIdxsFix), len(self.vIdxsFlx)))
if False:
msk = np.ones((self.nVerts, self.nDim), np.bool_)
msk[self.vIdxsFix] = False
self.I = np.where(msk.ravel())[0]
self.cnds = fem.condense(self.K, b = self.f, I = self.I)
else: # same but a bit faster
self.D = (np.tile(np.int32(self.vIdxsFix)*self.nDim,[self.nDim,1]).T + np.arange(self.nDim)).ravel()
self.cnds = fem.condense(self.K, b = self.f, D = self.D)
print('solving...')
if pypardisoFound:
self.u = fem.solve(*self.cnds, solver = solver_pypardiso)
else:
self.u = fem.solve(*self.cnds)
print('done')
self.compliance = np.dot(self.u, self.K.dot(self.u))/2
self.dCols = norm(self.u.reshape(-1,self.nDim))
if complianceOnly:
return self.compliance
# deformed mesh and stresses
self.meshDeformed = self.meshInit.translated(self.u.reshape(-1,self.nDim).T)
self.dg1 = self.basis.with_element(self.eType)
self.u1 = self.basis.interpolate(self.u)
C_sym_grad = C(sym_grad(self.u1))
self.C = np.transpose(C_sym_grad, axes=[2,3,0,1])
if pypardisoFound:
s00 = dg1Project(self.dg1, C_sym_grad[0,0])
s01 = dg1Project(self.dg1, C_sym_grad[0,1])
s11 = dg1Project(self.dg1, C_sym_grad[1,1])
if self.mType in ['tet', 'hex']:
s02 = dg1Project(self.dg1, C_sym_grad[0,2])
s12 = dg1Project(self.dg1, C_sym_grad[1,2])
s22 = dg1Project(self.dg1, C_sym_grad[2,2])
else:
s00 = self.dg1.project(C_sym_grad[0,0])
s01 = self.dg1.project(C_sym_grad[0,1])
s11 = self.dg1.project(C_sym_grad[1,1])
if self.mType in ['tet', 'hex']:
s02 = self.dg1.project(C_sym_grad[0,2])
s12 = self.dg1.project(C_sym_grad[1,2])
s22 = self.dg1.project(C_sym_grad[2,2])
self.sMats = np.zeros((self.nVerts,self.nDim,self.nDim), np.float32)
cts = np.zeros(len(self.sMats))
for tIdx, t in enumerate(self.meshInit.t.T):
self.sMats[t] += self.C[tIdx]
cts[t] += 1
self.sMats /= cts.reshape(-1,1,1)
dets = simpleDets(self.sMats)
self.sMats *= simpleSign(dets.reshape(-1,1,1))
self.pStress = np.zeros_like(self.sMats)
self.pStressE = np.zeros((len(self.pStress), self.nDim), np.float32)
for i, sMat in enumerate(self.sMats):
self.pStress[i], self.pStressE[i] = computePrincipalStress(sMat)
if self.mType in ['tet', 'hex']:
self.vmStress = np.sqrt(((s00-s11)**2 + (s11-s22)**2 + (s22-s00)**2 + 6*(s01**2+s12**2+s02**2))/2)
else:
self.vmStress = np.sqrt(s00**2 + s11**2 - s00*s11 + 3*s01**2)
return self.compliance
def evalScaledJacobians(self, save = False):
verts = self.verts if hasattr(self, 'verts') else self.meshInit.doflocs.T
cells = self.ts if hasattr(self, 'ts') else self.meshInit.t.T
self.SJs = computeJacobians(verts[cells], True)
if save:
mSJs = self.SJs.min(axis=1)
mSJs.sort()
np.savetxt(self.getFileName() + '.msjs', np.transpose([np.linspace(0,1,len(mSJs)), mSJs]), fmt='%.6e')
return self.SJs
def showPs(self): # somehow only works if called before any use of mayavi
if not polyscopeFound or self.nDim < 3:
print('Either polyscope is not installed or model is 2D.')
return
vsInit = self.verts if hasattr(self, 'verts') else self.meshInit.doflocs.T
if self.mType == 'tet':
tetsInit = self.ts if hasattr(self, 'ts') else self.meshInit.t.T
psMeshInit = ps.register_volume_mesh("input_tetInit", vsInit, tets = tetsInit, enabled=True)
else:
hexasInit = self.meshInit.t.T[:,[0,3,6,2,1,5,7,4]]
psMeshInit = ps.register_volume_mesh("input_hexInit", vsInit, hexes = hexasInit, enabled=True)
if hasattr(self, 'vmStress'):
psMeshInit.add_scalar_quantity("vMises", self.vmStress, enabled=True)
psMeshInit.add_scalar_quantity("icdf", icdf(self.vmStress), enabled=False)
if hasattr(self, 'vStress'):
psMeshInit.add_scalar_quantity("vStress", self.vStress, enabled=False)
if hasattr(self, 'SJs'):
hs = self.ts if hasattr(self, 'ts') else self.meshInit.t.T
mSJs = np.ones(len(vsInit))
np.minimum.at(mSJs, hs.ravel(), self.SJs.ravel())
psMeshInit.add_scalar_quantity("mSJs", mSJs, enabled=False, cmap = 'spectral')
if hasattr(self, 'meshDeformed'):
vsTrans = self.meshDeformed.doflocs.T
if self.mType == 'tet':
psTrans = ps.register_volume_mesh("result_tetDeformed", vsTrans, tets = tetsInit)
else:
psTrans = ps.register_volume_mesh("result_hexDeformed", vsTrans, hexes = hexasInit)
psTrans.add_scalar_quantity("vMovement", norm(self.u.reshape(-1,3)))
psTrans.add_scalar_quantity("vMises", self.vmStress, enabled=True)
psTrans.add_scalar_quantity("icdf", icdf(self.vmStress), enabled=False)
psTrans.add_scalar_quantity("pSe0", normZeroToOne(self.pStressE[:,0]), enabled=False)
psTrans.add_scalar_quantity("pSe1", normZeroToOne(self.pStressE[:,1]), enabled=False)
psTrans.add_scalar_quantity("pSe2", normZeroToOne(self.pStressE[:,2]), enabled=False)
ps.show()
def show(self, showField = True, showVerts = False, showVectors = False, showDeformed = True, showLabels = False):
if self.mType in ['tri', 'quad']:
elementsInit = self.ts if hasattr(self, 'ts') else self.meshInit.t.T
es = facesToEdges(elementsInit)
elif self.mType == 'tet':
elementsInit = self.ts if hasattr(self, 'ts') else self.meshInit.t.T
es = tetsToEdges(elementsInit)
elif self.mType == 'hex':
elementsInit = self.meshInit.t.T[:,[0,3,6,2,1,5,7,4]]
es = hexasToEdges(elementsInit)
eTris = toEdgeTris(es)
verts = self.verts if hasattr(self, 'verts') else self.meshInit.doflocs.T
vsInit = pad2Dto3D(verts) if self.nDim == 2 else verts
x,y,z = vsInit.T
scals = icdf(self.vmStress) ** 0.5 if hasattr(self, 'vmStress') else np.zeros_like(x)
# init wireframe
if self.nDim == 2:
self.mPlot = mlab.triangular_mesh(x, y, z, facesToTris(elementsInit), representation = 'surface', scalars = scals)
self.mPlot = mlab.triangular_mesh(x, y, z, eTris, representation = 'mesh', tube_radius=self.sf*0.1, color = (0,0,0))
else:
self.mPlot = mlab.triangular_mesh(x, y, z, eTris, representation = 'mesh', tube_radius=self.sf*2, scalars = scals)
# deformed wireframe
if showDeformed and hasattr(self, 'meshDeformed'):
vsTrans = self.meshDeformed.doflocs.T if self.mType in ['tet', 'hex'] else pad2Dto3D(self.meshDeformed.doflocs.T)
xt,yt,zt = vsTrans.T
if self.nDim == 2:
self.dPlot = mlab.triangular_mesh(xt, yt, zt, facesToTris(elementsInit), representation = 'surface', scalars = scals)
else:
self.dPlot = mlab.triangular_mesh(xt, yt, zt, eTris, representation = 'mesh', tube_radius = self.sf*2, scalars = scals)
# verts
if showVerts:
s = np.ones_like(x)
self.vPlot = mlab.quiver3d(x, y, z, s, s, s, scalars = scals, scale_factor = 0.05, mode='sphere')
self.vPlot.glyph.color_mode = 'color_by_scalar'
self.vPlot.glyph.glyph_source.glyph_position = 'center'
# labels
if showLabels: # very slow, impractical for large models
mlab.gcf().scene.disable_render = True # should speedup rendering but has no effect somehow
for vIdx, v in enumerate(vsInit):
mlab.text3d(v[0], v[1], v[2], str(vIdx), scale = (self.sf*10,self.sf*10,self.sf*10))
mlab.gcf().scene.disable_render = False
# deformation vectors
if showVectors and hasattr(self, 'u'):
uVecs = pad2Dto3D(self.u.reshape(-1,self.nDim))
u,v,w = uVecs.T
s = norm(uVecs)
self.uPlot = mlab.quiver3d(x, y, z, u, v, w, scalars = s, scale_factor = 1, mode='arrow')
# stress field
if showField and hasattr(self, 'pStress'):
x,y,z = np.repeat(vsInit.T, self.nDim, axis=1)
pStressScale = 1#np.clip(self.pStressE / np.percentile(self.pStressE, 99, axis=0), 0, 1).reshape(-1,3,1) ** 0.5
pStress = np.vstack(self.pStress * pStressScale)
u,v,w = pStress.T if self.mType in ['tet', 'hex'] else pad2Dto3D(pStress).T
scals = np.tile(np.arange(self.nDim)[::-1], len(vsInit))
self.sPlot = mlab.quiver3d(x, y, z, u, v, w, scalars = scals)
self.sPlot.glyph.color_mode = 'color_by_scalar'
self.sPlot.glyph.glyph_source.glyph_source.glyph_type = 'dash'
self.sPlot.glyph.glyph_source.glyph_position = 'center'
def showForces(self, showLabels = False):
if self.mType in ['tri', 'quad']:
elementsInit = self.meshInit.t.T
es = facesToEdges(elementsInit)
elif self.mType == 'tet':
elementsInit = self.meshInit.t.T
es = tetsToEdges(elementsInit)
elif self.mType == 'hex':
elementsInit = self.meshInit.t.T[:,[0,3,6,2,1,5,7,4]]
es = hexasToEdges(elementsInit)
eTris = toEdgeTris(es)
vsInit = pad2Dto3D(self.meshInit.doflocs.T) if self.nDim == 2 else self.meshInit.doflocs.T
x,y,z = vsInit.T
# edges
self.ePlot = mlab.triangular_mesh(x, y, z, eTris, representation = 'mesh', tube_radius=self.sf/5, color=(0,0,0))
# labels
if showLabels: # very slow, impractical for large models
mlab.gcf().scene.disable_render = True # should speedup rendering but has no effect somehow
for vIdx, v in enumerate(vsInit):
if self.boundaryVertMask[vIdx]:
mlab.text3d(v[0], v[1], v[2], str(vIdx), scale = (self.sf*2.5,self.sf*2.5,self.sf*2.5))
mlab.gcf().scene.disable_render = False
# vertices
scals = np.zeros_like(x)
scals[self.vIdxsFix] = 1
scals[self.vIdxsFlx] = 2
print('nFix: %d, nFlex: %d'%(len(self.vIdxsFix), len(self.vIdxsFlx)))
s = np.ones_like(x)
self.vPlot = mlab.quiver3d(x, y, z, s, s, s, scalars = scals, scale_factor = self.sf*2, mode='sphere')
self.vPlot.glyph.color_mode = 'color_by_scalar'
self.vPlot.glyph.glyph_source.glyph_position = 'center'
# applied forces
if hasattr(self, 'f'):
x,y,z = vsInit[self.vIdxsFlx].T
fVecs = pad2Dto3D(self.f.reshape(-1,self.nDim)) if self.nDim == 2 else self.f.reshape(-1,self.nDim)
u,v,w = fVecs[self.vIdxsFlx].T
self.fPlot = mlab.quiver3d(x, y, z, u, v, w, scale_factor = self.sf*50, mode='arrow')
self.fPlot.glyph.glyph_source.glyph_position = 'tail'
def exportToStress(self, fileName = None):
fileName = self.getFileName(fileName).split('_')[0] + '.stress'
verts = self.verts if hasattr(self, 'verts') else self.meshInit.doflocs.T
cells = self.ts if hasattr(self, 'ts') else self.meshInit.t.T
fixedIdxs = self.vIdxsFix
forceIdxs = self.vIdxsFlx
forceVecs = self.f.reshape(-1, self.nDim)[self.vIdxsFlx]
sMats = np.transpose(self.sMats, axes=[1,2,0])
stress = sMats[[0,1,0],[0,1,1],:].T if self.nDim == 2 else sMats[[0,1,2,1,0,0],[0,1,2,2,2,1],:].T
writeStressFile(fileName, verts, cells, forceIdxs, forceVecs, fixedIdxs, stress)
def exportToMesh(self, fileName = None):
fileName = self.getFileName(fileName) + ('.mesh' if self.nDim == 3 else '.obj')
verts = self.verts if hasattr(self, 'verts') else self.meshInit.doflocs.T
cells = self.ts if hasattr(self, 'ts') else self.meshInit.t.T
if self.nDim == 2:
writeObjFile(fileName, pad2Dto3D(verts), cells)
elif self.mType == 'hex':
writeMeshFile(fileName, verts, hexOrderDg2BT(cells[:,::-1]))
def getFileName(self, fileName = None):
if fileName is None:
fileName = 'data/' + os.path.basename(self.inputFile).split('.')[0]
fileName += '_' + self.mTypeInit
if self.materialized:
fileName += '_' + ('wall' if self.materialized[1] else 'beam')
fileName += ('_%d'%(self.materialized[0]*100)) if self.materialized[0] > 0 else '_tau'
return fileName
if __name__ == "__main__":
#inFile = 'data/bar2D.frc'
#inFile = 'data/spot2D.frc'
#inFile = 'data/bunny2D.frc'
#inFile = 'data/cube.frc'
inFile = 'data/femur.frc'
#inFile = 'data/fertility.frc'
#inFile = 'data/kitten.frc'
#inFile = 'data/spot.frc'
#inFile = 'data/venus.frc'
#inFile = 'data/JEB.frc'
#inFile = 'data/buddhaDown.frc'
#inFile = 'data/buddhaBack.frc'
#inFile = 'data/buddhaBelly.frc'
fObj = FemObject(inFile, False)
#fObj = FemObject(inFile, True)
c0 = fObj.computeCompliance()
print('c0:', c0)
fObj.exportToStress()
"""
fObj.materialize(0.5, False)
#fObj.materializeOpti(0.5, False, weights = icdf(fObj.vmStress)**2)
c1 = fObj.computeCompliance()
print('c1:', c1)
print('c:', c0, c1, c1/c0)
print('v:', fObj.volInit, fObj.vol, fObj.vol/fObj.volInit)
"""
#SJs = fObj.evalScaledJacobians()
#print('msj:', fObj.SJs.min(), fObj.SJs.max(), SJs.mean())
fObj.showPs()
fObj.show(False, showDeformed = False)
#fObj.showForces()
