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# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (c) 2003-2020 by The University of Queensland
# http://www.uq.edu.au
#
# Primary Business: Queensland, Australia
# Licensed under the Apache License, version 2.0
# http://www.apache.org/licenses/LICENSE-2.0
#
# Development until 2012 by Earth Systems Science Computational Center (ESSCC)
# Development 2012-2013 by School of Earth Sciences
# Development from 2014 by Centre for Geoscience Computing (GeoComp)
# Development from 2019 by School of Earth and Environmental Sciences
#
##############################################################################
from __future__ import print_function, division
__copyright__="""Copyright (c) 2003-2020 by The University of Queensland
http://www.uq.edu.au
Primary Business: Queensland, Australia"""
__license__="""Licensed under the Apache License, version 2.0
http://www.apache.org/licenses/LICENSE-2.0"""
__url__="https://launchpad.net/escript-finley"
"""
:var __author__: name of author
:var __copyright__: copyrights
:var __license__: licence agreement
:var __url__: url entry point on documentation
:var __version__: version
:var __date__: date of the version
"""
from .start import HAVE_SYMBOLS
import numpy
from time import time
from . import linearPDEs as lpe
from . import util
from .escriptcpp import Data
if HAVE_SYMBOLS:
import sympy
import esys.escriptcore.symbolic as symb
__author__="Cihan Altinay, Lutz Gross"
class iteration_steps_maxReached(Exception):
"""
Exception thrown if the maximum number of iteration steps is reached.
"""
pass
class DivergenceDetected(Exception):
"""
Exception thrown if Newton-Raphson did not converge.
"""
pass
class InadmissiblePDEOrdering(Exception):
"""
Exception thrown if the ordering of the PDE equations should be revised.
"""
pass
def concatenateRow(*args):
"""
"""
if len(args)==1:
return args[0]
if len(args)>2:
return concatenateRow(args[0], concatenateRow(*args[1:]))
lshape=util.getShape(args[0])
rshape=util.getShape(args[1])
if len(lshape)==0:
if len(rshape)==0:
shape=(2,)
res=numpy.zeros(shape, dtype=object)
res[0]=args[0]
res[1]=args[1]
elif len(rshape)==1:
shape=(rshape[0]+1,)
res=numpy.zeros(shape, dtype=object)
res[0]=args[0]
res[1:]=args[1]
elif len(lshape)==1:
if len(rshape)==1:
shape=(2,)+lshape
res=numpy.zeros(shape, dtype=object)
res[0]=args[0]
res[1]=args[1]
else:
shape=(rshape[0]+1,)+lshape
res=numpy.zeros(shape, dtype=object)
res[0]=args[0]
res[1:]=args[1]
else:
if len(rshape)==1:
shape=(lshape[0]+1,)+lshape[1:]
res=numpy.zeros(shape, dtype=object)
res[:lshape[0]]=args[0]
res[lshape[0]]=args[1]
else:
shape=(lshape[0]+rshape[0],)+lshape[1:]
res=numpy.zeros(shape, dtype=object)
res[:lshape[0]]=args[0]
res[lshape[0]:]=args[1]
subs=args[0].getDataSubstitutions().copy()
subs.update(args[1].getDataSubstitutions())
dim=args[1].getDim() if args[0].getDim()<0 else args[0].getDim()
return symb.Symbol(res, dim=dim, subs=subs)
class NonlinearPDE(object):
"""
This class is used to define a general nonlinear, steady, second order PDE
for an unknown function *u* on a given domain defined through a `Domain`
object.
For a single PDE having a solution with a single component the nonlinear
PDE is defined in the following form:
*-div(X) + Y = 0*
where *X*,*Y*=f(*u*,*grad(u)*). *div(F)* denotes the divergence of *F* and
*grad(F)* is the spatial derivative of *F*.
The coefficients *X* (rank 1) and *Y* (scalar) have to be specified through
`Symbol` objects.
The following natural boundary conditions are considered:
*n[j]*X[j] + y = 0*
where *n* is the outer normal field. Notice that the coefficient *X*
is defined in the PDE. The coefficient *y* is a scalar `Symbol`.
Constraints for the solution prescribe the value of the solution at certain
locations in the domain. They have the form
*u=r* where *q>0*
*r* and *q* are each scalar where *q* is the characteristic function
defining where the constraint is applied. The constraints override any
other condition set by the PDE or the boundary condition.
For a system of PDEs and a solution with several components, *u* is rank
one, while the PDE coefficient *X* is rank two and *y* is rank one.
The PDE is solved by linearising the coefficients and iteratively solving
the corresponding linear PDE until the error is smaller than a tolerance
or a maximum number of iterations is reached.
Typical usage::
u = Symbol('u', dim=dom.getDim())
p = NonlinearPDE(dom, u)
p.setValue(X=grad(u), Y=1+5*u)
v = p.getSolution(u=0.)
"""
DEBUG0=0 # no debug info
DEBUG1=1 # info on Newton-Raphson solver printed
DEBUG2=2 # in addition info from linear solver is printed
DEBUG3=3 # in addition info on linearization is printed
DEBUG4=4 # in addition info on LinearPDE handling is printed
ORDER=0
def __init__(self, domain, u, debug=DEBUG0):
"""
Initializes a new nonlinear PDE.
:param domain: domain of the PDE
:type domain: `Domain`
:param u: The symbol for the unknown PDE function u.
:type u: `Symbol`
:param debug: level of debug information to be printed
"""
if not HAVE_SYMBOLS:
raise RuntimeError("Trying to instantiate a NonlinearPDE but sympy not available")
self.__COEFFICIENTS = [ "X", "X_reduced", "Y", "Y_reduced", "y", "y_reduced", "y_contact", "y_contact_reduced", "y_dirac"]
self._r=Data()
self._set_coeffs={}
self._unknown=u
self._debug=debug
self._rtol=1e-6
self._atol=0.
self._iteration_steps_max=100
self._omega_min=0.0001
self._quadratic_convergence_limit=0.2
self._simplified_newton_limit=0.1
self.dim = domain.getDim()
if u.getRank()==0:
numEquations=1
else:
numEquations=u.getShape()[0]
numSolutions=numEquations
self._lpde=lpe.LinearPDE(domain,numEquations,numSolutions,self._debug > self.DEBUG4 )
def __str__(self):
"""
Returns the string representation of the PDE
:return: a simple representation of the PDE
:rtype: ``str``
"""
return "<%s %d>"%(self.__class__.__name__, id(self))
def getUnknownSymbol(self):
"""
Returns the symbol of the PDE unknown
:return: the symbol of the PDE unknown
:rtype: `Symbol`
"""
return self._unknown
def trace1(self, text):
"""
Prints the text message if the debug level is greater than DEBUG0
:param text: message to be printed
:type text: ``string``
"""
if self._debug > self.DEBUG0:
print("%s: %s"%(str(self), text))
def trace3(self, text):
"""
Prints the text message if the debug level is greater than DEBUG3
:param text: message to be printed
:type text: ``string``
"""
if self._debug > self.DEBUG2:
print("%s: %s"%(str(self), text))
def getLinearSolverOptions(self):
"""
Returns the options of the linear PDE solver class
"""
return self._lpde.getSolverOptions()
def getLinearPDE(self):
"""
Returns the linear PDE used to calculate the Newton-Raphson update
:rtype: `LinearPDE`
"""
return self._lpde
def setOptions(self, **opts):
"""
Allows setting options for the nonlinear PDE.
The supported options are:
``tolerance``
error tolerance for the Newton method
``iteration_steps_max``
maximum number of Newton iterations
``omega_min``
minimum relaxation factor
``atol``
solution norms less than ``atol`` are assumed to be ``atol``.
This can be useful if one of your solutions is expected to
be zero.
``quadratic_convergence_limit``
if the norm of the Newton-Raphson correction is reduced by
less than ``quadratic_convergence_limit`` between two iteration
steps quadratic convergence is assumed.
``simplified_newton_limit``
if the norm of the defect is reduced by less than
``simplified_newton_limit`` between two iteration steps and
quadratic convergence is detected the iteration switches to the
simplified Newton-Raphson scheme.
"""
for key in opts:
if key=='tolerance':
self._rtol=opts[key]
elif key=='iteration_steps_max':
self._iteration_steps_max=opts[key]
elif key=='omega_min':
self._omega_min=opts[key]
elif key=='atol':
self._atol=opts[key]
elif key=='quadratic_convergence_limit':
self._quadratic_convergence_limit=opts[key]
elif key=='simplified_newton_limit':
self._simplified_newton_limit=opts[key]
else:
raise KeyError("Invalid option '%s'"%key)
def getSolution(self, **subs):
"""
Returns the solution of the PDE.
:param subs: Substitutions for all symbols used in the coefficients
including the initial value for the unknown *u*.
:return: the solution
:rtype: `Data`
"""
# get the initial value for the iteration process
# collect components of unknown in u_syms
u_syms=[]
simple_u=False
for i in numpy.ndindex(self._unknown.getShape()):
u_syms.append(symb.Symbol(self._unknown[i]).atoms(sympy.Symbol).pop().name)
if len(set(u_syms))==1: simple_u=True
e=symb.Evaluator(self._unknown)
for sym in u_syms:
if not sym in subs:
raise KeyError("Initial value for '%s' missing."%sym)
if not isinstance(subs[sym], Data):
subs[sym]=Data(subs[sym], self._lpde.getFunctionSpaceForSolution())
e.subs(**{sym:subs[sym]})
ui=e.evaluate()
# modify ui so it meets the constraints:
q=self._lpde.getCoefficient("q")
if not q.isEmpty():
if hasattr(self, "_r"):
r=self._r
if symb.isSymbol(r):
r=symb.Evaluator(r).evaluate(**subs)
elif not isinstance(r, Data):
r=Data(r, self._lpde.getFunctionSpaceForSolution())
elif r.isEmpty():
r=0
else:
r=0
ui = q * r + (1-q) * ui
# separate symbolic expressions from other coefficients
constants={}
expressions={}
for n, e in sorted(self._set_coeffs.items(), key=lambda x: x[0]):
if symb.isSymbol(e):
expressions[n]=e
else:
constants[n]=e
# set constant PDE values now
self._lpde.setValue(**constants)
self._lpde.getSolverOptions().setAbsoluteTolerance(0.)
self._lpde.getSolverOptions().setVerbosity(self._debug > self.DEBUG1)
#=====================================================================
# perform Newton iterations until error is small enough or
# maximum number of iterations reached
n=0
omega=1. # relaxation factor
use_simplified_Newton=False
defect_norm=None
delta_norm=None
converged=False
#subs[u_sym]=ui
if simple_u:
subs[u_syms[0]]=ui
else:
for i in range(len(u_syms)):
subs[u_syms[i]]=ui[i]
while not converged:
if n > self._iteration_steps_max:
raise iteration_steps_maxReached("maximum number of iteration steps reached, giving up.")
self.trace1(5*"="+" iteration step %d "%n + 5*"=")
# calculate the correction delta_u
if n == 0:
self._updateLinearPDE(expressions, subs, **constants)
defect_norm=self._getDefectNorm(self._lpde.getRightHandSide())
LINTOL=0.1
else:
if not use_simplified_Newton:
self._updateMatrix(expressions, subs)
if q_u is None:
LINTOL = 0.1 * min(qtol/defect_norm)
else:
LINTOL = 0.1 * max( q_u**2, min(qtol/defect_norm) )
LINTOL=max(1e-4,min(LINTOL, 0.1))
#LINTOL=1.e-5
self._lpde.getSolverOptions().setTolerance(LINTOL)
self.trace1("PDE is solved with rel. tolerance = %e"%LINTOL)
delta_u=self._lpde.getSolution()
#check for reduced defect:
omega=min(2*omega, 1.) # raise omega
defect_reduced=False
ui_old=ui
while not defect_reduced:
ui=ui_old-delta_u * omega
if simple_u:
subs[u_syms[0]]=ui
else:
for i in range(len(u_syms)):
subs[u_syms[i]]=ui[i]
self._updateRHS(expressions, subs, **constants)
new_defect_norm=self._getDefectNorm(self._lpde.getRightHandSide())
defect_reduced=False
for i in range(len( new_defect_norm)):
if new_defect_norm[i] < defect_norm[i]: defect_reduced=True
#print new_defect_norm
#q_defect=max(self._getSafeRatio(new_defect_norm, defect_norm))
# if defect_norm==0 and new_defect_norm!=0
# this will be util.DBLE_MAX
#self.trace1("Defect reduction = %e with relaxation factor %e."%(q_defect, omega))
if not defect_reduced:
omega*=0.5
if omega < self._omega_min:
raise DivergenceDetected("Underrelaxtion failed to reduce defect, giving up.")
self.trace1("Defect reduction with relaxation factor %e."%(omega, ))
delta_norm, delta_norm_old = self._getSolutionNorm(delta_u) * omega, delta_norm
defect_norm, defect_norm_old = new_defect_norm, defect_norm
u_norm=self._getSolutionNorm(ui, atol=self._atol)
# set the tolerance on equation level:
qtol=self._getSafeRatio(defect_norm_old * u_norm * self._rtol, delta_norm)
# if defect_norm_old==0 and defect_norm_old!=0 this will be util.DBLE_MAX
# -> the ordering of the equations is not appropriate.
# if defect_norm_old==0 and defect_norm_old==0 this is zero so
# convergence can happen for defect_norm==0 only.
if not max(qtol)<util.DBLE_MAX:
raise InadmissiblePDEOrdering("Review ordering of PDE equations.")
# check stopping criteria
if not delta_norm_old is None:
q_u=max(self._getSafeRatio(delta_norm, delta_norm_old))
# if delta_norm_old==0 and delta_norm!=0
# this will be util.DBLE_MAX
if q_u <= self._quadratic_convergence_limit and not omega<1. :
quadratic_convergence=True
self.trace1("Quadratic convergence detected (rate %e <= %e)"%(q_u, self._quadratic_convergence_limit))
converged = all( [ defect_norm[i] <= qtol[i] for i in range(len(qtol)) ])
else:
self.trace1("No quadratic convergence detected (rate %e > %e, omega=%e)"%(q_u, self._quadratic_convergence_limit,omega ))
quadratic_convergence=False
converged=False
else:
q_u=None
converged=False
quadratic_convergence=False
if self._debug > self.DEBUG0:
for i in range(len(u_norm)):
self.trace1("Component %s: u: %e, du: %e, defect: %e, qtol: %e"%(i, u_norm[i], delta_norm[i], defect_norm[i], qtol[i]))
if converged: self.trace1("Iteration has converged.")
# Can we switch to simplified Newton?
if quadratic_convergence:
q_defect=max(self._getSafeRatio(defect_norm, defect_norm_old))
if q_defect < self._simplified_newton_limit:
use_simplified_Newton=True
self.trace1("Simplified Newton-Raphson is applied (rate %e < %e)."%(q_defect, self._simplified_newton_limit))
n+=1
self.trace1(5*"="+" Newton-Raphson iteration completed after %d steps "%n + 5*"=")
return ui
def _getDefectNorm(self, f):
"""
calculates the norm of the defect ``f``
:param f: defect vector
:type f: `Data` of rank 0 or 1.
:return: component-by-component norm of ``f``
:rtype: ``numpy.array`` of rank 1
:raise ValueError: if shape if ``f`` is incorrect.
"""
# this still needs some work!!!
out=[]
s=f.getShape()
if len(s) == 0:
out.append(util.Lsup(f))
elif len(s) == 1:
for i in range(s[0]):
out.append(util.Lsup(f[i]))
else:
raise ValueError("Illegal shape of defect vector: %s"%s)
return numpy.array(out)
def _getSolutionNorm(self, u, atol=0.):
"""
calculates the norm of the solution ``u``
:param u: solution vector
:type u: `Data` of rank 0 or 1.
:return: component-by-component norm of ``u``
:rtype: ``numpy.array`` of rank 1
:raise ValueError: if shape of ``u`` is incorrect.
"""
out=[]
s=u.getShape()
if len(s) == 0:
out.append(max(util.Lsup(u),atol) )
elif len(s) == 1:
for i in range(s[0]):
out.append(max(util.Lsup(u[i]), atol))
else:
raise ValueError("Illegal shape of solution: %s"%s)
return numpy.array(out)
def _getSafeRatio(self, a , b):
"""
Returns the component-by-component ratio of ''a'' and ''b''
If for a component ``i`` the values ``a[i]`` and ``b[i]`` are both
equal to zero their ratio is set to zero.
If ``b[i]`` equals zero but ``a[i]`` is positive the ratio is set to
`util.DBLE_MAX`.
:param a: numerator
:param b: denominator
:type a: ``numpy.array`` of rank 1 with non-negative entries.
:type b: ``numpy.array`` of rank 1 with non-negative entries.
:return: ratio of ``a`` and ``b``
:rtype: ``numpy.array``
"""
out=0.
if a.shape !=b.shape:
raise ValueError("shapes must match.")
s=a.shape
if len(s) != 1:
raise ValueError("rank one is expected.")
out=numpy.zeros(s)
for i in range(s[0]):
if abs(b[i]) > 0:
out[i]=a[i]/b[i]
elif abs(a[i]) > 0:
out[i] = util.DBLE_MAX
else:
out[i] = 0
return out
def getNumSolutions(self):
"""
Returns the number of the solution components
:rtype: ``int``
"""
s=self._unknown.getShape()
if len(s) > 0:
return s[0]
else:
return 1
def getShapeOfCoefficient(self,name):
"""
Returns the shape of the coefficient ``name``
:param name: name of the coefficient enquired
:type name: ``string``
:return: the shape of the coefficient ``name``
:rtype: ``tuple`` of ``int``
:raise IllegalCoefficient: if ``name`` is not a coefficient of the PDE
"""
numSol=self.getNumSolutions()
dim = self.dim
if name=="X" or name=="X_reduced":
if numSol > 1:
return (numSol,dim)
else:
return (dim,)
elif name=="r" or name == "q" :
if numSol > 1:
return (numSol,)
else:
return ()
elif name=="Y" or name=="Y_reduced":
if numSol > 1:
return (numSol,)
else:
return ()
elif name=="y" or name=="y_reduced":
if numSol > 1:
return (numSol,)
else:
return ()
elif name=="y_contact" or name=="y_contact_reduced":
if numSol > 1:
return (numSol,)
else:
return ()
elif name=="y_dirac":
if numSol > 1:
return (numSol,)
else:
return ()
else:
raise lpe.IllegalCoefficient("Attempt to request unknown coefficient %s"%name)
def createCoefficient(self, name):
"""
Creates a new coefficient ``name`` as Symbol
:param name: name of the coefficient requested
:type name: ``string``
:return: the value of the coefficient
:rtype: `Symbol` or `Data` (for name = "q")
:raise IllegalCoefficient: if ``name`` is not a coefficient of the PDE
"""
if name == "q":
return self._lpde.createCoefficient("q")
else:
s=self.getShapeOfCoefficient(name)
return symb.Symbol(name, s, dim=self.dim)
def getCoefficient(self, name):
"""
Returns the value of the coefficient ``name`` as Symbol
:param name: name of the coefficient requested
:type name: ``string``
:return: the value of the coefficient
:rtype: `Symbol`
:raise IllegalCoefficient: if ``name`` is not a coefficient of the PDE
"""
if name in self._set_coeffs:
return self._set_coeffs[name]
elif name == "r":
if hasattr(self, "_r"):
return self._r
else:
raise lpe.IllegalCoefficient("Attempt to request undefined coefficient %s"%name)
elif name == "q":
return self._lpde.getCoefficient("q")
else:
raise lpe.IllegalCoefficient("Attempt to request undefined coefficient %s"%name)
def setValue(self,**coefficients):
"""
Sets new values to one or more coefficients.
:param coefficients: new values assigned to coefficients
:param coefficients: new values assigned to coefficients
:keyword X: value for coefficient ``X``
:type X: `Symbol` or any type that can be cast to a `Data` object
:keyword Y: value for coefficient ``Y``
:type Y: `Symbol` or any type that can be cast to a `Data` object
:keyword y: value for coefficient ``y``
:type y: `Symbol` or any type that can be cast to a `Data` object
:keyword y_contact: value for coefficient ``y_contact``
:type y_contact: `Symbol` or any type that can be cast to a `Data` object
:keyword y_dirac: value for coefficient ``y_dirac``
:type y_dirac: `Symbol` or any type that can be cast to a `Data` object
:keyword q: mask for location of constraint
:type q: any type that can be cast to a `Data` object
:keyword r: value of solution prescribed by constraint
:type r: `Symbol` or any type that can be cast to a `Data` object
:raise IllegalCoefficient: if an unknown coefficient keyword is used
:raise IllegalCoefficientValue: if a supplied coefficient value has an
invalid shape
"""
u=self._unknown
for name,val in sorted(coefficients.items(), key=lambda x: x[0]):
shape=util.getShape(val)
if not shape == self.getShapeOfCoefficient(name):
raise lpe.IllegalCoefficientValue("%s has shape %s but must have shape %s"%(name, shape, self.getShapeOfCoefficient(name)))
rank=len(shape)
if name == "q":
self._lpde.setValue(q=val)
elif name == "r":
self._r=val
elif name=="X" or name=="X_reduced":
if rank != u.getRank()+1:
raise lpe.IllegalCoefficientValue("%s must have rank %d"%(name,u.getRank()+1))
T0=time()
B,A=symb.getTotalDifferential(val, u, 1)
if name=='X_reduced':
self.trace3("Computing A_reduced, B_reduced took %f seconds."%(time()-T0))
self._set_coeffs['A_reduced']=A
self._set_coeffs['B_reduced']=B
self._set_coeffs['X_reduced']=val
else:
self.trace3("Computing A, B took %f seconds."%(time()-T0))
self._set_coeffs['A']=A
self._set_coeffs['B']=B
self._set_coeffs['X']=val
elif name=="Y" or name=="Y_reduced":
if rank != u.getRank():
raise lpe.IllegalCoefficientValue("%s must have rank %d"%(name,u.getRank()))
T0=time()
D,C=symb.getTotalDifferential(val, u, 1)
if name=='Y_reduced':
self.trace3("Computing C_reduced, D_reduced took %f seconds."%(time()-T0))
self._set_coeffs['C_reduced']=C
self._set_coeffs['D_reduced']=D
self._set_coeffs['Y_reduced']=val
else:
self.trace3("Computing C, D took %f seconds."%(time()-T0))
self._set_coeffs['C']=C
self._set_coeffs['D']=D
self._set_coeffs['Y']=val
elif name in ("y", "y_reduced", "y_contact", "y_contact_reduced", \
"y_dirac"):
y=val
if rank != u.getRank():
raise lpe.IllegalCoefficientValue("%s must have rank %d"%(name,u.getRank()))
if not hasattr(y, 'diff'):
d=numpy.zeros(u.getShape()+u.getShape())
else:
d=y.diff(u)
self._set_coeffs[name]=y
self._set_coeffs['d'+name[1:]]=d
else:
raise lpe.IllegalCoefficient("Attempt to set unknown coefficient %s"%name)
def getSensitivity(self, f, g=None, **subs):
"""
Calculates the sensitivity of the solution of an input factor ``f``
in direction ``g``.
:param f: the input factor to be investigated. ``f`` may be of rank 0
or 1.
:type f: `Symbol`
:param g: the direction(s) of change.
If not present, it is *g=eye(n)* where ``n`` is the number of
components of ``f``.
:type g: ``list`` or single of ``float``, ``numpy.array`` or `Data`.
:param subs: Substitutions for all symbols used in the coefficients
including unknown *u* and the input factor ``f`` to be
investigated
:return: the sensitivity
:rtype: `Data` with shape *u.getShape()+(len(g),)* if *len(g)>1* or
*u.getShape()* if *len(g)==1*
"""
s_f=f.getShape()
if len(s_f) == 0:
len_f=1
elif len(s_f) == 1:
len_f=s_f[0]
else:
raise ValueError("rank of input factor must be zero or one.")
if not g is None:
if len(s_f) == 0:
if not isinstance(g, list): g=[g]
else:
if isinstance(g, list):
if len(g) == 0:
raise ValueError("no direction given.")
if len(getShape(g[0])) == 0: g=[g] # if g[0] is a scalar we assume that the list g is to be interprested a data object
else:
g=[g]
# at this point g is a list of directions:
len_g=len(g)
for g_i in g:
if not getShape(g_i) == s_f:
raise ValueError("shape of direction (=%s) must match rank of input factor (=%s)"%(getShape(g_i) , s_f) )
else:
len_g=len_f
#*** at this point g is a list of direction or None and len_g is the
# number of directions to be investigated.
# now we make sure that the operator in the lpde is set (it is the same
# as for the Newton-Raphson scheme)
# if the solution etc are cached this could be omitted:
constants={}
expressions={}
for n, e in sorted(self._set_coeffs.items(), key=lambda x: x[0]):
if n not in self.__COEFFICIENTS:
if symb.isSymbol(e):
expressions[n]=e
else:
constants[n]=e
self._lpde.setValue(**constants)
self._updateMatrix(self, expressions, subs)
#=====================================================================
self._lpde.getSolverOptions().setAbsoluteTolerance(0.)
self._lpde.getSolverOptions().setTolerance(self._rtol)
self._lpde.getSolverOptions().setVerbosity(self._debug > self.DEBUG1)
#=====================================================================
#
# evaluate the derivatives of X, etc with respect to f:
#
ev=symb.Evaluator()
names=[]
if hasattr(self, "_r"):
if symb.isSymbol(self._r):
names.append('r')
ev.addExpression(self._r.diff(f))
for n in sorted(self._set_coeffs.keys()):
if n in self.__COEFFICIENTS and symb.isSymbol(self._set_coeffs[n]):
if n=="X" or n=="X_reduced":
T0=time()
B,A=symb.getTotalDifferential(self._set_coeffs[n], f, 1)
if n=='X_reduced':
self.trace3("Computing A_reduced, B_reduced took %f seconds."%(time()-T0))
names.append('A_reduced'); ev.addExpression(A)
names.append('B_reduced'); ev.addExpression(B)
else:
self.trace3("Computing A, B took %f seconds."%(time()-T0))
names.append('A'); ev.addExpression(A)
names.append('B'); ev.addExpression(B)
elif n=="Y" or n=="Y_reduced":
T0=time()
D,C=symb.getTotalDifferential(self._set_coeffs[n], f, 1)
if n=='Y_reduced':
self.trace3("Computing C_reduced, D_reduced took %f seconds."%(time()-T0))
names.append('C_reduced'); ev.addExpression(C)
names.append('D_reduced'); ev.addExpression(D)
else:
self.trace3("Computing C, D took %f seconds."%(time()-T0))
names.append('C'); ev.addExpression(C)
names.append('D'); ev.addExpression(D)
elif n in ("y", "y_reduced", "y_contact", "y_contact_reduced", "y_dirac"):
names.append('d'+name[1:]); ev.addExpression(self._set_coeffs[name].diff(f))
relevant_symbols['d'+name[1:]]=self._set_coeffs[name].diff(f)
res=ev.evaluate()
if len(names)==1: res=[res]
self.trace3("RHS expressions evaluated in %f seconds."%(time()-T0))
if self._debug > self.DEBUG2:
for i in range(len(names)):
self.trace3("util.Lsup(%s)=%s"%(names[i],util.Lsup(res[i])))
coeffs_f=dict(zip(names,res))
#
# now we are ready to calculate the right hand side coefficients into
# args by multiplication with g and grad(g).
if len_g >1:
if self.getNumSolutions() == 1:
u_g=Data(0., (len_g,), self._lpde.getFunctionSpaceForSolution())
else:
u_g=Data(0., (self.getNumSolutions(), len_g), self._lpde.getFunctionSpaceForSolution())
for i in range(len_g):
# reset coefficients may be set at previous calls:
args={}
for n in self.__COEFFICIENTS: args[n]=Data()
args['r']=Data()
if g is None: # g_l=delta_{il} and len_f=len_g
for n,v in coeffs_f:
name=None
if len_f > 1:
val=v[:,i]
else:
val=v
if n.startswith("d"):
name='y'+n[1:]
elif n.startswith("D"):
name='Y'+n[1:]
elif n.startswith("r"):
name='r'+n[1:]
if name: args[name]=val
else:
g_i=g[i]
for n,v in coeffs_f:
name=None
if n.startswith("d"):
name = 'y'+n[1:]
val = self.__mm(v, g_i)
elif n.startswith("r"):
name= 'r'
val = self.__mm(v, g_i)
elif n.startswith("D"):
name = 'Y'+n[1:]
val = self.__mm(v, g_i)
elif n.startswith("B") and isinstance(g_i, Data):
name = 'Y'+n[1:]
val = self.__mm(v, grad(g_i))
elif n.startswith("C"):
name = 'X'+n[1:]
val = matrix_multiply(v, g_i)
elif n.startswith("A") and isinstance(g_i, Data):
name = 'X'+n[1:]
val = self.__mm(v, grad(g_i))
if name:
if name in args:
args[name]+=val
else:
args[name]=val
self._lpde.setValue(**args)
u_g_i=self._lpde.getSolution()
if len_g >1:
if self.getNumSolutions() == 1:
u_g[i]=-u_g_i
else:
u_g[:,i]=-u_g_i
else:
u_g=-u_g_i
return u_g
def __mm(self, m, v):
"""
a sligtly crude matrix*matrix multiplication
m is A-coefficient, u is vector, v is grad vector: A_ijkl*v_kl
m is B-coefficient, u is vector, v is vector: B_ijk*v_k
m is C-coefficient, u is vector, v is grad vector: C_ikl*v_kl
m is D-coefficient, u is vector, v is vector: D_ij*v_j
m is A-coefficient, u is scalar, v is grad vector: A_jkl*v_kl
m is B-coefficient, u is scalar, v is vector: B_jk*v_k
m is C-coefficient, u is scalar, v is grad vector: C_kl*v_kl
m is D-coefficient, u is scalar, v is vector: D_j*v_j
m is A-coefficient, u is vector, v is grad scalar: A_ijl*v_l
m is B-coefficient, u is vector, v is scalar: B_ij*v
m is C-coefficient, u is vector, v is grad scalar: C_il*v_l
m is D-coefficient, u is vector, v is scalar: D_i*v
m is A-coefficient, u is scalar, v is grad scalar: A_jl*v_l
m is B-coefficient, u is scalar, v is scalar: B_j*v
m is C-coefficient, u is scalar, v is grad scalar: C_l*v_l
m is D-coefficient, u is scalar, v is scalar: D*v
"""
s_m=getShape(m)
s_v=getShape(v)
# m is B-coefficient, u is vector, v is scalar: B_ij*v
# m is D-coefficient, u is vector, v is scalar: D_i*v
# m is B-coefficient, u is scalar, v is scalar: B_j*v
# m is D-coefficient, u is scalar, v is scalar: D*v
if s_m == () or s_v == ():
return m*v
# m is D-coefficient, u is scalar, v is vector: D_j*v_j
# m is C-coefficient, u is scalar, v is grad scalar: C_l*v_l
if len(s_m) == 1:
return inner(m,v)
# m is D-coefficient, u is vector, v is vector: D_ij*v_j
# m is B-coefficient, u is scalar, v is vector: B_jk*v_k
# m is C-coefficient, u is vector, v is grad scalar: C_il*v_l
# m is A-coefficient, u is scalar, v is grad scalar: A_jl*v_l
if len(s_m) == 2 and len(s_v) == 1:
return matrix_mult(m,v)
# m is C-coefficient, u is scalar, v is grad vector: C_kl*v_kl
if len(s_m) == 2 and len(s_v) == 2:
return inner(m,v)
# m is B-coefficient, u is vector, v is vector: B_ijk*v_k
# m is A-coefficient, u is vector, v is grad scalar: A_ijl*v_l
if len(s_m) == 3 and len(s_v) == 1:
return matrix_mult(m,v)
# m is A-coefficient, u is scalar, v is grad vector: A_jkl*v_kl
# m is C-coefficient, u is vector, v is grad vector: C_ikl*v_kl
if len(s_m) == 3 and len(s_v) == 2:
return tensor_mult(m,v)
# m is A-coefficient, u is vector, v is grad vector: A_ijkl*v_kl
if len(s_m) == 4 and len(s_v) == 2:
return tensor_mult(m,v)
def _updateRHS(self, expressions, subs, **constants):
"""
"""
ev=symb.Evaluator()
names=[]
for name in sorted(expressions):
if name in self.__COEFFICIENTS:
ev.addExpression(expressions[name])
names.append(name)
if len(names)==0:
return
self.trace3("Starting expression evaluation.")
T0=time()
ev.subs(**subs)
res=ev.evaluate()
if len(names)==1: res=[res]
self.trace3("RHS expressions evaluated in %f seconds."%(time()-T0))
if self._debug > self.DEBUG2:
for i in range(len(names)):
self.trace3("util.Lsup(%s)=%s"%(names[i],util.Lsup(res[i])))
args=dict(zip(names,res))
# reset coefficients may be set at previous calls:
for n in self.__COEFFICIENTS:
if not n in args and not n in constants: args[n]=Data()
args=dict(list(args.items())+list(constants.items()))
if not 'r' in args: args['r']=Data()
self._lpde.setValue(**args)
def _updateMatrix(self, expressions, subs):
"""
"""
ev=symb.Evaluator()
names=[]
for name in sorted(expressions):
if not name in self.__COEFFICIENTS:
ev.addExpression(expressions[name])
names.append(name)
if len(names)==0:
return
self.trace3("Starting expression evaluation.")
T0=time()
ev.subs(**subs)
res=ev.evaluate()
if len(names)==1: res=[res]
self.trace3("Matrix expressions evaluated in %f seconds."%(time()-T0))
if self._debug > self.DEBUG2:
for i in range(len(names)):
self.trace3("util.Lsup(%s)=%s"%(names[i],util.Lsup(res[i])))
self._lpde.setValue(**dict(zip(names,res)))
def _updateLinearPDE(self, expressions, subs, **constants):
self._updateMatrix(expressions, subs)
self._updateRHS(expressions, subs, **constants)
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