def testRValNumpyArray():
x = np.arange(0, 1., 0.2)
print((sys.getrefcount(x)))
a = pg.RVector(x)
print(a)
# should return 2 (self & counter) since the counter is not increased
# while conversion
print((sys.getrefcount(x)))
x = np.arange(0, 1., 0.2, dtype=np.float64)
a = pg.RVector(x)
print(('pg.RVector(x):', a))
x = np.array(a)
a = pg.RVector(x)
print(('pg.RVector(array):', a))
a = pg.RVector([0.2, 0.3, 0.4, 0.5, 0.6])
print(('pg.RVector(list[float]):', a))
a = pg.RVector((0.2, 0.3, 0.4, 0.5, 0.6))
print(('pg.RVector(tuple(float,)):', a))
a = pg.RVector(np.arange(0, 1., 0.2))
print(a)
a = pg.RVector(np.arange(10.))
print(a)
print((pg.norm(np.arange(10.))))
def testSlices():
a = pg.RVector(np.arange(10.))
print((a[0:3:1], np.arange(10.)[0:3:1]))
print((np.arange(10.)[0:3:-1]))
try:
print((a[0:3:-1]))
except:
print("oki")
pass
print((a[3:0:-2]))
print((pg.norm(a[0:3:1])))
def testRValNumpyArray():
x = np.arange(0, 1., 0.2 )
print(sys.getrefcount(x))
a=pg.RVector(x)
print(a)
# should return 2 (self & counter) since the counter is not increased while conversion
print(sys.getrefcount(x))
x = np.arange(0, 1., 0.2, dtype=np.float64)
a=pg.RVector(x)
print(a)
a=pg.RVector([0.2, 0.3, 0.4, 0.5])
print(a)
a=pg.RVector(np.arange(0, 1., 0.2 ))
print(a)
a=pg.RVector(np.arange(10.))
print(a)
print(pg.norm(np.arange(10.)))
fop = DCMultiElectrodeModellingC(mesh, data, verbose=True)
print(dir(fop))
print(fop.jacobian())
print(fop.jacobian().rows())
#fop = pb.DCMultiElectrodeModelling(mesh, data)
fop.regionManager().region(1).setBackground(True)
fop.createRefinedForwardMesh(refine=True, pRefine=False)
cData = pb.getComplexData(data)
mag = pg.abs(cData)
phi = -pg.phase(cData)
print(pg.norm(mag-data('rhoa')))
print(pg.norm(phi-data('ip')/1000))
inv = pg.Inversion(pg.cat(mag, phi),
fop,
verbose=True, dosave=True)
dataTrans = pg.trans.TransCumulative()
datRe = pg.trans.TransLog()
datIm = pg.trans.Trans()
dataTrans.add(datRe, data.size())
dataTrans.add(datIm, data.size())
modRe = pg.trans.TransLog()
modIm = pg.trans.TransLog()
def solveStokes_NEEDNAME(mesh,
velBoundary,
preBoundary=[],
viscosity=1,
pre0=None,
vel0=None,
tol=1e-4,
maxIter=1000,
verbose=1):
"""
"""
velocityRelaxation = 0.5
pressureRelaxation = 0.8
pressureCoeff = None
preCNorm = []
divVNorm = []
velBoundaryX = [[marker, vel[0]] for marker, vel in velBoundary]
velBoundaryY = [[marker, vel[1]] for marker, vel in velBoundary]
print(velBoundaryX)
class WS:
pass
wsux = WS()
wsuy = WS()
wsp = WS()
pressure = None
if pre0 is None:
pressure = np.zeros(mesh.cellCount())
else:
pressure = np.array(pre0)
velocity = None
if vel0 is None:
velocity = np.zeros((mesh.cellCount(), mesh.dimension()))
else:
velocity = np.array(vel0)
mesh.createNeighbourInfos()
CtB = mesh.cellToBoundaryInterpolation()
controlVolumes = CtB * mesh.cellSizes()
for i in range(maxIter):
pressureGrad = cellDataToCellGrad(mesh, pressure, CtB)
# __d('vx', pressureGrad[:,0])
velocity[:, 0] = solveFiniteVolume(mesh,
a=viscosity,
f=-pressureGrad[:, 0],
uBoundary=velBoundaryX,
uL=velocity[:, 0],
relax=velocityRelaxation,
ws=wsux)
# for s in wsux.S:
# print(s)
# __d('rhs', wsux.rhs, 1)
# __d('ux', velocity[:,0])
velocity[:, 1] = solveFiniteVolume(mesh,
a=viscosity,
f=-pressureGrad[:, 1],
uBoundary=velBoundaryY,
uL=velocity[:, 1],
relax=velocityRelaxation,
ws=wsuy)
ap = np.array(wsux.ap * mesh.cellSizes())
apF = CtB * ap
uxF = CtB * velocity[:, 0]
uyF = CtB * velocity[:, 1]
applyBoundaryValues(uxF, mesh, velBoundaryX)
applyBoundaryValues(uyF, mesh, velBoundaryY)
pxF = CtB * pressureGrad[:, 0]
pyF = CtB * pressureGrad[:, 1]
pF2 = cellDataToBoundaryGrad(mesh, pressure, pressureGrad)
velXF = uxF + controlVolumes / apF * (pxF - pF2[:, 0])
velYF = uyF + controlVolumes / apF * (pyF - pF2[:, 1])
applyBoundaryValues(velXF, mesh, velBoundaryX)
applyBoundaryValues(velYF, mesh, velBoundaryY)
if pressureCoeff is None:
pressureCoeff = 1. / apF * mesh.boundarySizes() * \
boundaryToCellDistances(mesh)
div = -divergence(mesh, np.vstack([velXF, velYF]).T)
pressureCorrection = solveFiniteVolume(mesh,
a=pressureCoeff,
f=div,
uBoundary=preBoundary,
ws=wsp)
pressure += pressureCorrection * pressureRelaxation
pressureCorrectionGrad = cellDataToCellGrad(mesh, pressureCorrection,
CtB)
velocity[:, 0] -= pressureCorrectionGrad[:, 0] / ap * mesh.cellSizes()
velocity[:, 1] -= pressureCorrectionGrad[:, 1] / ap * mesh.cellSizes()
preCNorm.append(pg.norm(pressureCorrection))
divVNorm.append(pg.norm(div))
# __d('div', div)
# if ( i == 1):
# sd
if verbose:
# print("\rIter: " + str(i) + " div V=" + str(divVNorm[-1]) + " " +
# str(preCNorm[-1]), end='')
print("\r" + str(i) + " div V=" + str(divVNorm[-1]))
if i == maxIter or divVNorm[-1] < tol:
break
if verbose:
print(str(i) + ": " + str(preCNorm[-1]))
return velocity, pressure, preCNorm, divVNorm
fop = DCMultiElectrodeModellingC(mesh, data, verbose=True)
print(dir(fop))
print(fop.jacobian())
print(fop.jacobian().rows())
#fop = pb.DCMultiElectrodeModelling(mesh, data)
fop.regionManager().region(1).setBackground(True)
fop.createRefinedForwardMesh(refine=True, pRefine=False)
cData = pb.getComplexData(data)
mag = pg.abs(cData)
phi = -pg.phase(cData)
print(pg.norm(mag-data('rhoa')))
print(pg.norm(phi-data('ip')/1000))
inv = pg.RInversion(pg.cat(mag, phi),
fop,
verbose=True, dosave=True)
dataTrans = pg.RTransCumulative()
datRe = pg.RTransLog()
datIm = pg.RTrans()
dataTrans.add(datRe, data.size())
dataTrans.add(datIm, data.size())
modRe = pg.RTransLog()
modIm = pg.RTransLog()
def __solveStokes(mesh,
viscosity,
velBoundary=None,
preBoundary=None,
pre0=None,
vel0=None,
tol=1e-4,
maxIter=1000,
verbose=1,
**kwargs):
"""Steady Navier-Stokes solver."""
workspace = pg.solver.WorkSpace()
wsux = pg.solver.WorkSpace()
wsuy = pg.solver.WorkSpace()
wsp = pg.solver.WorkSpace()
# get cache values if given
ws = kwargs.pop('ws', None)
if ws:
workspace = ws
if hasattr(workspace, 'wsux'):
wsux = workspace.wsux
else:
workspace.wsux = wsux
if hasattr(workspace, 'wsuy'):
wsuy = workspace.wsuy
else:
workspace.wsuy = wsuy
if hasattr(workspace, 'wsp'):
wsp = workspace.wsp
else:
workspace.wsp = wsp
velocityRelaxation = kwargs.pop('vRelax', 0.5)
pressureRelaxation = kwargs.pop('pRelax', 0.8)
pressureCoeff = None
preCNorm = []
divVNorm = []
velBoundaryX = []
velBoundaryY = []
if velBoundary is not None:
for marker, vel in velBoundary:
if vel is not None:
if not isinstance(vel[0], str):
velBoundaryX.append([marker, vel[0]])
if not isinstance(vel[1], str):
velBoundaryY.append([marker, vel[1]])
pressure = None
if pre0 is None:
pressure = np.zeros(mesh.cellCount())
else:
pressure = np.array(pre0)
velocity = None
if vel0 is None:
velocity = np.zeros((mesh.cellCount(), mesh.dimension()))
else:
velocity = np.array(vel0)
mesh.createNeighbourInfos()
CtB = mesh.cellToBoundaryInterpolation()
controlVolumes = CtB * mesh.cellSizes()
density = kwargs.pop('density', 1.0)
force = kwargs.pop('f', [0.0, 0.0])
density = pg.solver.parseArgToArray(density, ndof=mesh.cellCount())
forceX = pg.solver.parseArgToArray(force[0], ndof=mesh.cellCount())
forceY = pg.solver.parseArgToArray(force[1], ndof=mesh.cellCount())
for i in range(maxIter):
pressureGrad = cellDataToCellGrad(mesh, pressure, CtB)
# __d('vx', pressureGrad[:,0])
velocity[:, 0] = solveFiniteVolume(mesh,
a=viscosity,
f=-pressureGrad[:, 0] / density +
forceX,
uB=velBoundaryX,
uL=velocity[:, 0],
relax=velocityRelaxation,
ws=wsux)
# for s in wsux.S:
# print(s)
# __d('rhs', wsux.rhs, 1)
# __d('ux', velocity[:,0])
velocity[:, 1] = solveFiniteVolume(mesh,
a=viscosity,
f=-pressureGrad[:, 1] / density +
forceY,
uB=velBoundaryY,
uL=velocity[:, 1],
relax=velocityRelaxation,
ws=wsuy)
ap = np.array(wsux.ap * mesh.cellSizes())
apF = CtB * ap
uxF = CtB * velocity[:, 0]
uyF = CtB * velocity[:, 1]
applyBoundaryValues(uxF, mesh, velBoundaryX)
applyBoundaryValues(uyF, mesh, velBoundaryY)
pxF = CtB * pressureGrad[:, 0]
pyF = CtB * pressureGrad[:, 1]
pF2 = cellDataToBoundaryGrad(mesh, pressure, pressureGrad)
velXF = uxF + controlVolumes / apF * (pxF - pF2[:, 0])
velYF = uyF + controlVolumes / apF * (pyF - pF2[:, 1])
applyBoundaryValues(velXF, mesh, velBoundaryX)
applyBoundaryValues(velYF, mesh, velBoundaryY)
if pressureCoeff is None:
pressureCoeff = 1. / apF * mesh.boundarySizes() * \
_boundaryToCellDistances(mesh)
div = -mesh.divergence(np.vstack([velXF, velYF]).T)
# boundsDirichlet = pg.solver.parseArgToBoundaries(preBoundary, mesh)
# pB = CtB * pressure
# for ix, [boundary, val] in enumerate(boundsDirichlet):
# boundsDirichlet[ix][1] = -(-pg.solver.generateBoundaryValue(boundary,
# val) + pB[boundary.id()])
pressureCorrection = solveFiniteVolume(
mesh,
a=pressureCoeff,
f=div,
uB=preBoundary,
# uB=boundsDirichlet,
ws=wsp)
# print(i, pg.solver.generateBoundaryValue(mesh.boundary(58), val),
# pB[58], boundsDirichlet[-1][1],
# (CtB*pressureCorrection)[58])
pressure += pressureCorrection * pressureRelaxation
pressureCorrectionGrad = cellDataToCellGrad(mesh, pressureCorrection,
CtB)
velocity[:, 0] -= pressureCorrectionGrad[:, 0] / ap * mesh.cellSizes()
velocity[:, 1] -= pressureCorrectionGrad[:, 1] / ap * mesh.cellSizes()
preCNorm.append(pg.norm(pressureCorrection))
divVNorm.append(pg.norm(div))
if workspace:
workspace.div = div
# __d('div', div)
# if ( i == 1):
# sd
convergenceTest = 100
if i > 6:
convergenceTest = (divVNorm[-1] - divVNorm[-2]) + \
(divVNorm[-2] - divVNorm[-3]) + \
(divVNorm[-3] - divVNorm[-4]) + \
(divVNorm[-4] - divVNorm[-5]) + \
(divVNorm[-5] - divVNorm[-6])
convergenceTest /= 5
if verbose:
print("\r" + str(i) + " div V=" + str(divVNorm[-1]) + " ddiv V=" +
str(convergenceTest))
if divVNorm[-1] > 1e6:
print("\r" + str(i) + " div V=" + str(divVNorm[-1]) + " ddiv V=" +
str(convergenceTest))
raise BaseException("Stokes solver seams to diverging")
if i > 2:
if i == maxIter or divVNorm[-1] < tol or \
abs(convergenceTest * divVNorm[-1]) < tol:
break
if verbose:
print(str(i) + ": |pC|" + str(preCNorm[-1]))
return velocity, pressure, preCNorm, divVNorm
def solveStokes(mesh, viscosity, velBoundary, preBoundary=[],
pre0=None, vel0=None,
tol=1e-4, maxIter=1000,
verbose=1, **kwargs):
"""
"""
ws=kwargs.pop('ws', None)
velocityRelaxation = kwargs.pop('vRelax', 0.5)
pressureRelaxation = kwargs.pop('pRelax', 0.8)
pressureCoeff = None
preCNorm = []
divVNorm = []
velBoundaryX = [[marker, vel[0]] for marker, vel in velBoundary]
velBoundaryY = [[marker, vel[1]] for marker, vel in velBoundary]
class WS:
pass
wsux = WS()
wsuy = WS()
wsp = WS()
pressure = None
if pre0 is None:
pressure = np.zeros(mesh.cellCount())
else:
pressure = np.array(pre0)
velocity = None
if vel0 is None:
velocity = np.zeros((mesh.cellCount(), mesh.dimension()))
else:
velocity = np.array(vel0)
mesh.createNeighbourInfos()
CtB = mesh.cellToBoundaryInterpolation()
controlVolumes = CtB * mesh.cellSizes()
for i in range(maxIter):
pressureGrad = cellDataToCellGrad(mesh, pressure, CtB)
# __d('vx', pressureGrad[:,0])
velocity[:, 0] = solveFiniteVolume(mesh,
a=viscosity,
f=-pressureGrad[:, 0],
uB=velBoundaryX,
uL=velocity[:, 0],
relax=velocityRelaxation,
ws=wsux)
# for s in wsux.S:
# print(s)
# __d('rhs', wsux.rhs, 1)
# __d('ux', velocity[:,0])
velocity[:, 1] = solveFiniteVolume(mesh,
a=viscosity,
f=-pressureGrad[:, 1],
uB=velBoundaryY,
uL=velocity[:, 1],
relax=velocityRelaxation,
ws=wsuy)
ap = np.array(wsux.ap * mesh.cellSizes())
apF = CtB * ap
uxF = CtB * velocity[:, 0]
uyF = CtB * velocity[:, 1]
applyBoundaryValues(uxF, mesh, velBoundaryX)
applyBoundaryValues(uyF, mesh, velBoundaryY)
pxF = CtB * pressureGrad[:, 0]
pyF = CtB * pressureGrad[:, 1]
pF2 = cellDataToBoundaryGrad(mesh, pressure, pressureGrad)
velXF = uxF + controlVolumes / apF * (pxF - pF2[:, 0])
velYF = uyF + controlVolumes / apF * (pyF - pF2[:, 1])
applyBoundaryValues(velXF, mesh, velBoundaryX)
applyBoundaryValues(velYF, mesh, velBoundaryY)
if pressureCoeff is None:
pressureCoeff = 1. / apF * mesh.boundarySizes() * \
boundaryToCellDistances(mesh)
# div = -divergence(mesh, np.vstack([velXF, velYF]).T)
div = -mesh.divergence(np.vstack([velXF, velYF]).T)
pressureCorrection = solveFiniteVolume(mesh,
a=pressureCoeff,
f=div,
uB=preBoundary,
ws=wsp)
pressure += pressureCorrection * pressureRelaxation
pressureCorrectionGrad = cellDataToCellGrad(mesh, pressureCorrection,
CtB)
velocity[:, 0] -= pressureCorrectionGrad[:, 0] / ap * mesh.cellSizes()
velocity[:, 1] -= pressureCorrectionGrad[:, 1] / ap * mesh.cellSizes()
preCNorm.append(pg.norm(pressureCorrection))
divVNorm.append(pg.norm(div))
if ws:
ws.div=div
# __d('div', div)
# if ( i == 1):
# sd
convergenceTest = 100
if i > 6:
convergenceTest = (divVNorm[-1] - divVNorm[-2]) + \
(divVNorm[-2] - divVNorm[-3]) + \
(divVNorm[-3] - divVNorm[-4]) + \
(divVNorm[-4] - divVNorm[-5]) + \
(divVNorm[-5] - divVNorm[-6])
convergenceTest /= 5
if verbose:
print("\r" + str(i) + " div V=" + str(divVNorm[-1]) +
" ddiv V=" + str(convergenceTest))
if i == maxIter or divVNorm[-1] < tol or \
abs(convergenceTest * divVNorm[-1]) < tol:
break
if verbose:
print(str(i) + ": " + str(preCNorm[-1]))
return velocity, pressure, preCNorm, divVNorm
def __solveStokes(mesh, viscosity, velBoundary=None, preBoundary=None,
pre0=None, vel0=None,
tol=1e-4, maxIter=1000,
verbose=1, **kwargs):
"""Steady Navier-Stokes solver."""
workspace = pg.solver.WorkSpace()
wsux = pg.solver.WorkSpace()
wsuy = pg.solver.WorkSpace()
wsp = pg.solver.WorkSpace()
# get cache values if given
ws = kwargs.pop('ws', None)
if ws:
workspace = ws
if hasattr(workspace, 'wsux'):
wsux = workspace.wsux
else:
workspace.wsux = wsux
if hasattr(workspace, 'wsuy'):
wsuy = workspace.wsuy
else:
workspace.wsuy = wsuy
if hasattr(workspace, 'wsp'):
wsp = workspace.wsp
else:
workspace.wsp = wsp
velocityRelaxation = kwargs.pop('vRelax', 0.5)
pressureRelaxation = kwargs.pop('pRelax', 0.8)
pressureCoeff = None
preCNorm = []
divVNorm = []
velBoundaryX = []
velBoundaryY = []
if velBoundary is not None:
for marker, vel in velBoundary:
if vel is not None:
if not isinstance(vel[0], str):
velBoundaryX.append([marker, vel[0]])
if not isinstance(vel[1], str):
velBoundaryY.append([marker, vel[1]])
pressure = None
if pre0 is None:
pressure = np.zeros(mesh.cellCount())
else:
pressure = np.array(pre0)
velocity = None
if vel0 is None:
velocity = np.zeros((mesh.cellCount(), mesh.dimension()))
else:
velocity = np.array(vel0)
mesh.createNeighbourInfos()
CtB = mesh.cellToBoundaryInterpolation()
controlVolumes = CtB * mesh.cellSizes()
density = kwargs.pop('density', 1.0)
force = kwargs.pop('f', [0.0, 0.0])
density = pg.solver.parseArgToArray(density, ndof=mesh.cellCount())
forceX = pg.solver.parseArgToArray(force[0], ndof=mesh.cellCount())
forceY = pg.solver.parseArgToArray(force[1], ndof=mesh.cellCount())
for i in range(maxIter):
pressureGrad = cellDataToCellGrad(mesh, pressure, CtB)
# __d('vx', pressureGrad[:,0])
velocity[:, 0] = solveFiniteVolume(
mesh, a=viscosity,
f=-pressureGrad[:, 0] / density + forceX,
uB=velBoundaryX,
uL=velocity[:, 0],
relax=velocityRelaxation,
ws=wsux)
# for s in wsux.S:
# print(s)
# __d('rhs', wsux.rhs, 1)
# __d('ux', velocity[:,0])
velocity[:, 1] = solveFiniteVolume(
mesh, a=viscosity,
f=-pressureGrad[:, 1] / density + forceY,
uB=velBoundaryY,
uL=velocity[:, 1],
relax=velocityRelaxation,
ws=wsuy)
ap = np.array(wsux.ap * mesh.cellSizes())
apF = CtB * ap
uxF = CtB * velocity[:, 0]
uyF = CtB * velocity[:, 1]
applyBoundaryValues(uxF, mesh, velBoundaryX)
applyBoundaryValues(uyF, mesh, velBoundaryY)
pxF = CtB * pressureGrad[:, 0]
pyF = CtB * pressureGrad[:, 1]
pF2 = cellDataToBoundaryGrad(mesh, pressure, pressureGrad)
velXF = uxF + controlVolumes / apF * (pxF - pF2[:, 0])
velYF = uyF + controlVolumes / apF * (pyF - pF2[:, 1])
applyBoundaryValues(velXF, mesh, velBoundaryX)
applyBoundaryValues(velYF, mesh, velBoundaryY)
if pressureCoeff is None:
pressureCoeff = 1. / apF * mesh.boundarySizes() * \
_boundaryToCellDistances(mesh)
div = -mesh.divergence(np.vstack([velXF, velYF]).T)
# boundsDirichlet = pg.solver.parseArgToBoundaries(preBoundary, mesh)
# pB = CtB * pressure
# for ix, [boundary, val] in enumerate(boundsDirichlet):
# boundsDirichlet[ix][1] = -(-pg.solver.generateBoundaryValue(boundary,
# val) + pB[boundary.id()])
pressureCorrection = solveFiniteVolume(mesh,
a=pressureCoeff,
f=div,
uB=preBoundary,
# uB=boundsDirichlet,
ws=wsp)
# print(i, pg.solver.generateBoundaryValue(mesh.boundary(58), val),
# pB[58], boundsDirichlet[-1][1],
# (CtB*pressureCorrection)[58])
pressure += pressureCorrection * pressureRelaxation
pressureCorrectionGrad = cellDataToCellGrad(mesh, pressureCorrection,
CtB)
velocity[:, 0] -= pressureCorrectionGrad[:, 0] / ap * mesh.cellSizes()
velocity[:, 1] -= pressureCorrectionGrad[:, 1] / ap * mesh.cellSizes()
preCNorm.append(pg.norm(pressureCorrection))
divVNorm.append(pg.norm(div))
if workspace:
workspace.div = div
# __d('div', div)
# if ( i == 1):
# sd
convergenceTest = 100
if i > 6:
convergenceTest = (divVNorm[-1] - divVNorm[-2]) + \
(divVNorm[-2] - divVNorm[-3]) + \
(divVNorm[-3] - divVNorm[-4]) + \
(divVNorm[-4] - divVNorm[-5]) + \
(divVNorm[-5] - divVNorm[-6])
convergenceTest /= 5
if verbose:
print("\r" + str(i) + " div V=" + str(divVNorm[-1]) +
" ddiv V=" + str(convergenceTest))
if divVNorm[-1] > 1e6:
print("\r" + str(i) + " div V=" + str(divVNorm[-1]) +
" ddiv V=" + str(convergenceTest))
raise BaseException("Stokes solver seams to diverging")
if i > 2:
if i == maxIter or divVNorm[-1] < tol or \
abs(convergenceTest * divVNorm[-1]) < tol:
break
if verbose:
print(str(i) + ": |pC|" + str(preCNorm[-1]))
return velocity, pressure, preCNorm, divVNorm