def interpolateEscriptData(domain, data):
"""
esys.weipa does not support the function spaces Solution and
ReducedSolution. This function interpolates Data defined on those function
spaces to compatible alternatives.
"""
from esys.escript import Solution, ReducedSolution
from esys.escript import ContinuousFunction, ReducedContinuousFunction
from esys.escript.util import interpolate
new_data={}
for n,d in sorted(list(data.items()), key=lambda x: x[0]):
if not d.isEmpty():
fs=d.getFunctionSpace()
if domain is None:
domain=fs.getDomain()
elif domain != fs.getDomain():
raise ValueError("weipa: All Data must be on the same domain!")
new_data[n]=d
try:
if fs == Solution(domain):
new_data[n]=interpolate(d, ContinuousFunction(domain))
elif domain.getDescription().startswith("speckley"):
new_data[n]=interpolate(d, ContinuousFunction(domain))
elif fs == ReducedSolution(domain):
new_data[n]=interpolate(d, ReducedContinuousFunction(domain))
except RuntimeError as e:
if str(e).startswith("FunctionSpaceException"):
pass
else:
raise e
return domain,new_data
def interpolateEscriptData(domain, data):
"""
esys.weipa does not support the function spaces Solution and
ReducedSolution. This function interpolates Data defined on those function
spaces to compatible alternatives.
"""
from esys.escript import Solution, ReducedSolution
from esys.escript import ContinuousFunction, ReducedContinuousFunction
from esys.escript.util import interpolate
new_data={}
for n,d in sorted(list(data.items()), key=lambda x: x[0]):
if not d.isEmpty():
fs=d.getFunctionSpace()
if domain is None:
domain=fs.getDomain()
elif domain != fs.getDomain():
raise ValueError("weipa: All Data must be on the same domain!")
new_data[n]=d
try:
if fs == Solution(domain):
new_data[n]=interpolate(d, ContinuousFunction(domain))
elif domain.getDescription().startswith("speckley"):
new_data[n]=interpolate(d, ContinuousFunction(domain))
elif fs == ReducedSolution(domain):
new_data[n]=interpolate(d, ReducedContinuousFunction(domain))
except RuntimeError as e:
if str(e).startswith("FunctionSpaceException"):
pass
else:
raise e
return domain,new_data
def solve(self, globalIter=10, solidIter=50):
"""
solve the coupled PDE using fixed-stress split method,
call solveSolid to get displacement
"""
rtol = self.__rtol
x_safe = self.__domain.getX()
k = util.kronecker(self.__domain)
kdr = util.inner(k, util.tensor_mult(self.__S, k)) / 4.
n = self.getEquivalentPorosity()
perm = self.__permeability * n**3 / (1. - n)**2 * k
kf = self.__bulkFluid
dt = self.__dt
self.__ppde.setValue(A=perm,
D=(n / kf + 1. / kdr) / dt,
Y=(n / kf + 1. / kdr) / dt * self.__pgauss -
self.__meanStressRate / kdr)
p_iter_old = self.__ppde.getSolution()
p_iter_gauss = util.interpolate(p_iter_old,
escript.Function(self.__domain))
u_old, D, sig, s, scene = self.solveSolid(p_iter_gauss=p_iter_gauss,
iter_max=solidIter)
converge = False
iterate = 0
while (not converge) and (iterate < globalIter):
iterate += 1
self.__ppde.setValue(Y=n / kf / dt * self.__pgauss +
1. / kdr / dt * p_iter_gauss -
util.trace(D) / dt)
p_iter = self.__ppde.getSolution()
p_err = util.L2(p_iter - p_iter_old) / util.L2(p_iter)
p_iter_old = p_iter
p_iter_gauss = util.interpolate(p_iter,
escript.Function(self.__domain))
u, D, sig, s, scene = self.solveSolid(p_iter_gauss=p_iter_gauss,
iter_max=solidIter)
u_err = util.L2(u - u_old) / util.L2(u)
u_old = u
converge = (u_err <= rtol and p_err <= rtol * .1)
self.__meanStressRate = (util.trace(sig - self.__stress) / 2. -
p_iter_gauss + self.__pgauss) / dt
self.__pore = p_iter_old
self.__pgauss = p_iter_gauss
self.__domain.setX(x_safe + u_old)
self.__strain += D
self.__stress = sig
self.__S = s
self.__scenes = scene
return u_old
def __init__(self,
domain,
pore0=0.,
perm=1.e-5,
kf=2.2e9,
dt=0.001,
ng=1,
useMPI=False,
np=1,
rtol=1.e-2):
"""
initialization of the problem, i.e. model constructor
:param domain: type Domain, domain of the problem
:param pore0: type float, initial pore pressure
:param perm: type float, d^2/(150 mu_f) in KC equation
:param kf: type float, bulk modulus of the fluid
:param dt: type float, time step for calculation
:param ng: type integer, number of Gauss points
:param useMPI: type boolean, use MPI or not
:param np: type integer, number of processors
:param rtol: type float, relevative tolerance for global convergence
"""
self.__domain = domain
self.__upde = LinearPDE(domain,
numEquations=domain.getDim(),
numSolutions=domain.getDim())
self.__ppde = LinearPDE(domain, numEquations=1, numSolutions=1)
# use reduced interpolation for pore pressure
self.__ppde.setReducedOrderOn()
self.__upde.getSolverOptions().setSolverMethod(SolverOptions.DIRECT)
self.__ppde.getSolverOptions().setSolverMethod(SolverOptions.DIRECT)
self.__upde.setSymmetryOn()
self.__ppde.setSymmetryOn()
self.__dt = dt
self.__bulkFluid = kf
self.__numGaussPoints = ng
self.__rtol = rtol
self.__stress = escript.Tensor(0, escript.Function(domain))
self.__S = escript.Tensor4(0, escript.Function(domain))
self.__pool = get_pool(mpi=useMPI, threads=np)
self.__scenes = self.__pool.map(initLoad, range(ng))
st = self.__pool.map(getStressAndTangent2D, self.__scenes)
for i in xrange(ng):
self.__stress.setValueOfDataPoint(i, st[i][0])
self.__S.setValueOfDataPoint(i, st[i][1])
self.__strain = escript.Tensor(0, escript.Function(domain))
self.__pore = escript.Scalar(pore0, escript.ReducedSolution(domain))
self.__pgauss = util.interpolate(pore0, escript.Function(domain))
self.__permeability = perm
self.__meanStressRate = escript.Scalar(0, escript.Function(domain))
self.__r = escript.Vector(
0, escript.Solution(domain)) #Dirichlet BC for u
def solve(self, globalIter=10, solidIter=50):
"""
solve the coupled PDE using fixed-stress split method,
call solveSolid to get displacement
"""
rtol=self.__rtol
x_safe=self.__domain.getX()
k=util.kronecker(self.__domain)
kdr=util.inner(k,util.tensor_mult(self.__S,k))/4.
n=self.getEquivalentPorosity()
perm=self.__permeability*n**3/(1.-n)**2*k
kf=self.__bulkFluid
dt=self.__dt
self.__ppde.setValue(A=perm,D=(n/kf+1./kdr)/dt,Y=(n/kf+1./kdr)/dt*self.__pgauss-self.__meanStressRate/kdr)
p_iter_old=self.__ppde.getSolution()
p_iter_gauss=util.interpolate(p_iter_old,escript.Function(self.__domain))
u_old,D,sig,s,scene=self.solveSolid(p_iter_gauss=p_iter_gauss,iter_max=solidIter)
converge=False
iterate=0
while (not converge) and (iterate<globalIter):
iterate += 1
self.__ppde.setValue(Y=n/kf/dt*self.__pgauss+1./kdr/dt*p_iter_gauss-util.trace(D)/dt)
p_iter=self.__ppde.getSolution()
p_err=util.L2(p_iter-p_iter_old)/util.L2(p_iter)
p_iter_old=p_iter
p_iter_gauss=util.interpolate(p_iter,escript.Function(self.__domain))
u,D,sig,s,scene=self.solveSolid(p_iter_gauss=p_iter_gauss,iter_max=solidIter)
u_err=util.L2(u-u_old)/util.L2(u)
u_old=u
converge=(u_err<=rtol and p_err <= rtol*.1)
self.__meanStressRate=(util.trace(sig-self.__stress)/2.-p_iter_gauss+self.__pgauss)/dt
self.__pore=p_iter_old
self.__pgauss=p_iter_gauss
self.__domain.setX(x_safe+u_old)
self.__strain+=D
self.__stress=sig
self.__S=s
self.__scenes=scene
return u_old
def __init__(self,domain,pore0=0.,perm=1.e-5,kf=2.2e9,dt=0.001,ng=1,useMPI=False,np=1,rtol=1.e-2):
"""
initialization of the problem, i.e. model constructor
:param domain: type Domain, domain of the problem
:param pore0: type float, initial pore pressure
:param perm: type float, d^2/(150 mu_f) in KC equation
:param kf: type float, bulk modulus of the fluid
:param dt: type float, time step for calculation
:param ng: type integer, number of Gauss points
:param useMPI: type boolean, use MPI or not
:param np: type integer, number of processors
:param rtol: type float, relevative tolerance for global convergence
"""
self.__domain=domain
self.__upde=LinearPDE(domain,numEquations=domain.getDim(),numSolutions=domain.getDim())
self.__ppde=LinearPDE(domain,numEquations=1,numSolutions=1)
# use reduced interpolation for pore pressure
self.__ppde.setReducedOrderOn()
try:
self.__upde.getSolverOptions().setSolverMethod(SolverOptions.DIRECT)
self.__ppde.getSolverOptions().setSolverMethod(SolverOptions.DIRECT)
except:
#import time
print("=======================================================================")
print("For better performance compile python-escript with direct solver method")
print("=======================================================================")
input("Press Enter to continue...")
#time.sleep(5)
self.__upde.setSymmetryOn()
self.__ppde.setSymmetryOn()
self.__dt=dt
self.__bulkFluid=kf
self.__numGaussPoints=ng
self.__rtol=rtol
self.__stress=escript.Tensor(0,escript.Function(domain))
self.__S=escript.Tensor4(0,escript.Function(domain))
self.__pool=get_pool(mpi=useMPI,threads=np)
self.__scenes=self.__pool.map(initLoad,list(range(ng)))
st = self.__pool.map(getStressAndTangent2D,self.__scenes)
for i in range(ng):
self.__stress.setValueOfDataPoint(i,st[i][0])
self.__S.setValueOfDataPoint(i,st[i][1])
self.__strain=escript.Tensor(0,escript.Function(domain))
self.__pore=escript.Scalar(pore0,escript.ReducedSolution(domain))
self.__pgauss=util.interpolate(pore0,escript.Function(domain))
self.__permeability=perm
self.__meanStressRate=escript.Scalar(0,escript.Function(domain))
self.__r=escript.Vector(0,escript.Solution(domain)) #Dirichlet BC for u
def saveVoxet(filename, **data):
"""
Writes `Data` objects to a file using the GOCAD Voxet file format as
separate properties on the same grid.
At the moment only Data on a `ripley` domain can be saved in this format.
Note that this function will produce one header file (ending in .vo) and
a separate property file for each `Data` object.
:param filename: name of the output file ('.vo' is added if required)
:type filename: ``str``
:note: All data objects have to be defined on the same ripley domain and
either defined on reduced Function or on a `FunctionSpace` that
allows interpolation to reduced Function.
"""
from esys.escript import ReducedFunction
from esys.escript.util import interpolate
from esys.ripley.ripleycpp import DATATYPE_FLOAT32, BYTEORDER_BIG_ENDIAN
new_data={}
domain=None
for n,d in sorted(data.items(), key=lambda x: x[0]):
if d.isEmpty():
continue
fs=d.getFunctionSpace()
if domain is None:
domain=fs.getDomain()
elif domain != fs.getDomain():
raise ValueError("saveVoxet: All Data must be on the same domain!")
try:
nd=interpolate(d, ReducedFunction(domain))
except:
raise ValueError("saveVoxet: Unable to interpolate all Data to reduced Function!")
new_data[n]=nd
if filename[-3:]=='.vo':
fileprefix=filename[:-3]+"_"
else:
fileprefix=filename+"_"
filename=filename+'.vo'
origin, spacing, NE = domain.getGridParameters()
# Voxet "origin" actually refers to centre of first cell so shift:
origin = tuple([ origin[i] + spacing[i]/2. for i in range(len(origin)) ])
# flip vertical origin
origin=origin[:-1]+(-origin[-1],)
axis_max=NE[:-1]+(-NE[-1],)
midpoint=tuple([n/2 for n in NE])
if domain.getDim() == 2:
origin=origin+(0.,)
spacing=spacing+(1.,)
NE=NE+(1,)
midpoint=midpoint+(0,)
axis_max=axis_max+(0,)
mainvar=list(new_data.keys())[0]
f=open(filename,'w')
f.write("GOCAD Voxet 1\nHEADER {\nname: escriptdata\n")
f.write("sections: 3 1 1 %d 2 1 %d 3 1 %d\n"%midpoint)
f.write("painted: on\nascii: off\n*painted*variable: %s\n}"%mainvar)
f.write("""
GOCAD_ORIGINAL_COORDINATE_SYSTEM
NAME "gocad Local"
AXIS_NAME X Y Z
AXIS_UNIT m m m
ZPOSITIVE Depth
END_ORIGINAL_COORDINATE_SYSTEM\n""")
f.write("AXIS_O %0.2f %0.2f %0.2f\n"%origin)
f.write("AXIS_U %0.2f 0 0\n"%spacing[0])
f.write("AXIS_V 0 %0.2f 0\n"%spacing[1])
f.write("AXIS_W 0 0 %0.2f\n"%spacing[2])
f.write("AXIS_MIN 0 0 0\n")
f.write("AXIS_MAX %d %d %d\n"%axis_max)
f.write("AXIS_N %d %d %d\n"%NE)
f.write("\n")
num=0
for n,d in sorted(new_data.items(), key=lambda x: x[0]):
num=num+1
propfile=fileprefix+n
domain.writeBinaryGrid(d, propfile, BYTEORDER_BIG_ENDIAN, DATATYPE_FLOAT32)
f.write("\nPROPERTY %d %s\n"%(num, n))
f.write("PROPERTY_SUBCLASS %d QUANTITY Float\n"%num)
f.write("PROP_ESIZE %d 4\n"%num)
f.write("PROP_ETYPE %d IEEE\n"%num)
f.write("PROP_FORMAT %d RAW\n"%num)
f.write("PROP_OFFSET %d 0\n"%num)
f.write("PROP_FILE %d %s\n"%(num,propfile))
f.close()
def saveVoxet(filename, **data):
"""
Writes `Data` objects to a file using the GOCAD Voxet file format as
separate properties on the same grid.
At the moment only Data on a `ripley` domain can be saved in this format.
Note that this function will produce one header file (ending in .vo) and
a separate property file for each `Data` object.
:param filename: name of the output file ('.vo' is added if required)
:type filename: ``str``
:note: All data objects have to be defined on the same ripley domain and
either defined on reduced Function or on a `FunctionSpace` that
allows interpolation to reduced Function.
"""
from esys.escript import ReducedFunction
from esys.escript.util import interpolate
from esys.ripley.ripleycpp import DATATYPE_FLOAT32, BYTEORDER_BIG_ENDIAN
new_data={}
domain=None
for n,d in sorted(data.items(), key=lambda x: x[0]):
if d.isEmpty():
continue
fs=d.getFunctionSpace()
if domain is None:
domain=fs.getDomain()
elif domain != fs.getDomain():
raise ValueError("saveVoxet: All Data must be on the same domain!")
try:
nd=interpolate(d, ReducedFunction(domain))
except:
raise ValueError("saveVoxet: Unable to interpolate all Data to reduced Function!")
new_data[n]=nd
if filename[-3:]=='.vo':
fileprefix=filename[:-3]+"_"
else:
fileprefix=filename+"_"
filename=filename+'.vo'
origin, spacing, NE = domain.getGridParameters()
# Voxet "origin" actually refers to centre of first cell so shift:
origin = tuple([ origin[i] + spacing[i]/2. for i in range(len(origin)) ])
# flip vertical origin
origin=origin[:-1]+(-origin[-1],)
axis_max=NE[:-1]+(-NE[-1],)
midpoint=tuple([n/2 for n in NE])
if domain.getDim() == 2:
origin=origin+(0.,)
spacing=spacing+(1.,)
NE=NE+(1,)
midpoint=midpoint+(0,)
axis_max=axis_max+(0,)
mainvar=list(new_data.keys())[0]
f=open(filename,'w')
f.write("GOCAD Voxet 1\nHEADER {\nname: escriptdata\n")
f.write("sections: 3 1 1 %d 2 1 %d 3 1 %d\n"%midpoint)
f.write("painted: on\nascii: off\n*painted*variable: %s\n}"%mainvar)
f.write("""
GOCAD_ORIGINAL_COORDINATE_SYSTEM
NAME "gocad Local"
AXIS_NAME X Y Z
AXIS_UNIT m m m
ZPOSITIVE Depth
END_ORIGINAL_COORDINATE_SYSTEM\n""")
f.write("AXIS_O %0.2f %0.2f %0.2f\n"%origin)
f.write("AXIS_U %0.2f 0 0\n"%spacing[0])
f.write("AXIS_V 0 %0.2f 0\n"%spacing[1])
f.write("AXIS_W 0 0 %0.2f\n"%spacing[2])
f.write("AXIS_MIN 0 0 0\n")
f.write("AXIS_MAX %d %d %d\n"%axis_max)
f.write("AXIS_N %d %d %d\n"%NE)
f.write("\n")
num=0
for n,d in sorted(new_data.items(), key=lambda x: x[0]):
num=num+1
propfile=fileprefix+n
domain.writeBinaryGrid(d, propfile, BYTEORDER_BIG_ENDIAN, DATATYPE_FLOAT32)
f.write("\nPROPERTY %d %s\n"%(num, n))
f.write("PROPERTY_SUBCLASS %d QUANTITY Float\n"%num)
f.write("PROP_ESIZE %d 4\n"%num)
f.write("PROP_ETYPE %d IEEE\n"%num)
f.write("PROP_FORMAT %d RAW\n"%num)
f.write("PROP_OFFSET %d 0\n"%num)
f.write("PROP_FILE %d %s\n"%(num,propfile))
f.close()