/[escript]/trunk/escript/py_src/linearPDEs.py
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revision 791 by bcumming, Thu Jul 27 00:37:57 2006 UTC revision 1639 by gross, Mon Jul 14 08:55:25 2008 UTC
# Line 1  Line 1 
1    #
2  # $Id$  # $Id$
3    #
4    #######################################################
5    #
6    #           Copyright 2003-2007 by ACceSS MNRF
7    #       Copyright 2007 by University of Queensland
8    #
9    #                http://esscc.uq.edu.au
10    #        Primary Business: Queensland, Australia
11    #  Licensed under the Open Software License version 3.0
12    #     http://www.opensource.org/licenses/osl-3.0.php
13    #
14    #######################################################
15    #
16    
17  """  """
18  The module provides an interface to define and solve linear partial  The module provides an interface to define and solve linear partial
19  differential equations (PDEs) within L{escript}. L{linearPDEs} does not provide any  differential equations (PDEs) within L{escript}. L{linearPDEs} does not provide any
# Line 19  to define of solve these sepecial PDEs. Line 34  to define of solve these sepecial PDEs.
34  @var __date__: date of the version  @var __date__: date of the version
35  """  """
36    
37    import math
38  import escript  import escript
39  import util  import util
40  import numarray  import numarray
# Line 38  class IllegalCoefficient(ValueError): Line 54  class IllegalCoefficient(ValueError):
54     """     """
55     raised if an illegal coefficient of the general ar particular PDE is requested.     raised if an illegal coefficient of the general ar particular PDE is requested.
56     """     """
57       pass
58    
59  class IllegalCoefficientValue(ValueError):  class IllegalCoefficientValue(ValueError):
60     """     """
61     raised if an incorrect value for a coefficient is used.     raised if an incorrect value for a coefficient is used.
62     """     """
63       pass
64    
65    class IllegalCoefficientFunctionSpace(ValueError):
66       """
67       raised if an incorrect function space for a coefficient is used.
68       """
69    
70  class UndefinedPDEError(ValueError):  class UndefinedPDEError(ValueError):
71     """     """
72     raised if a PDE is not fully defined yet.     raised if a PDE is not fully defined yet.
73     """     """
74       pass
75    
76  class PDECoefficient(object):  class PDECoefficient(object):
77      """      """
# Line 56  class PDECoefficient(object): Line 80  class PDECoefficient(object):
80      @cvar INTERIOR: indicator that coefficient is defined on the interior of the PDE domain      @cvar INTERIOR: indicator that coefficient is defined on the interior of the PDE domain
81      @cvar BOUNDARY: indicator that coefficient is defined on the boundary of the PDE domain      @cvar BOUNDARY: indicator that coefficient is defined on the boundary of the PDE domain
82      @cvar CONTACT: indicator that coefficient is defined on the contact region within the PDE domain      @cvar CONTACT: indicator that coefficient is defined on the contact region within the PDE domain
83        @cvar INTERIOR_REDUCED: indicator that coefficient is defined on the interior of the PDE domain using a reduced integration order
84        @cvar BOUNDARY_REDUCED: indicator that coefficient is defined on the boundary of the PDE domain using a reduced integration order
85        @cvar CONTACT_REDUCED: indicator that coefficient is defined on the contact region within the PDE domain using a reduced integration order
86      @cvar SOLUTION: indicator that coefficient is defined trough a solution of the PDE      @cvar SOLUTION: indicator that coefficient is defined trough a solution of the PDE
87      @cvar REDUCED: indicator that coefficient is defined trough a reduced solution of the PDE      @cvar REDUCED: indicator that coefficient is defined trough a reduced solution of the PDE
88      @cvar BY_EQUATION: indicator that the dimension of the coefficient shape is defined by the number PDE equations      @cvar BY_EQUATION: indicator that the dimension of the coefficient shape is defined by the number PDE equations
# Line 77  class PDECoefficient(object): Line 104  class PDECoefficient(object):
104      OPERATOR=10      OPERATOR=10
105      RIGHTHANDSIDE=11      RIGHTHANDSIDE=11
106      BOTH=12      BOTH=12
107        INTERIOR_REDUCED=13
108        BOUNDARY_REDUCED=14
109        CONTACT_REDUCED=15
110    
111      def __init__(self,where,pattern,altering):      def __init__(self, where, pattern, altering):
112         """         """
113         Initialise a PDE Coefficient type         Initialise a PDE Coefficient type
114    
115         @param where: describes where the coefficient lives         @param where: describes where the coefficient lives
116         @type where: one of L{INTERIOR}, L{BOUNDARY}, L{CONTACT}, L{SOLUTION}, L{REDUCED}         @type where: one of L{INTERIOR}, L{BOUNDARY}, L{CONTACT}, L{SOLUTION}, L{REDUCED},
117                               L{INTERIOR_REDUCED}, L{BOUNDARY_REDUCED}, L{CONTACT_REDUCED}.
118         @param pattern: describes the shape of the coefficient and how the shape is build for a given         @param pattern: describes the shape of the coefficient and how the shape is build for a given
119                spatial dimension and numbers of equation and solution in then PDE. For instance,                spatial dimension and numbers of equation and solution in then PDE. For instance,
120                (L{BY_EQUATION},L{BY_SOLUTION},L{BY_DIM}) descrbes a rank 3 coefficient which                (L{BY_EQUATION},L{BY_SOLUTION},L{BY_DIM}) descrbes a rank 3 coefficient which
# Line 94  class PDECoefficient(object): Line 125  class PDECoefficient(object):
125         @type pattern: C{tuple} of L{BY_EQUATION}, L{BY_SOLUTION}, L{BY_DIM}         @type pattern: C{tuple} of L{BY_EQUATION}, L{BY_SOLUTION}, L{BY_DIM}
126         @param altering: indicates what part of the PDE is altered if the coefficiennt is altered         @param altering: indicates what part of the PDE is altered if the coefficiennt is altered
127         @type altering: one of L{OPERATOR}, L{RIGHTHANDSIDE}, L{BOTH}         @type altering: one of L{OPERATOR}, L{RIGHTHANDSIDE}, L{BOTH}
128           @param reduced: indicates if reduced
129           @type reduced: C{bool}
130         """         """
131         super(PDECoefficient, self).__init__()         super(PDECoefficient, self).__init__()
132         self.what=where         self.what=where
# Line 123  class PDECoefficient(object): Line 155  class PDECoefficient(object):
155         """         """
156         if self.what==self.INTERIOR:         if self.what==self.INTERIOR:
157              return escript.Function(domain)              return escript.Function(domain)
158           elif self.what==self.INTERIOR_REDUCED:
159                return escript.ReducedFunction(domain)
160         elif self.what==self.BOUNDARY:         elif self.what==self.BOUNDARY:
161              return escript.FunctionOnBoundary(domain)              return escript.FunctionOnBoundary(domain)
162           elif self.what==self.BOUNDARY_REDUCED:
163                return escript.ReducedFunctionOnBoundary(domain)
164         elif self.what==self.CONTACT:         elif self.what==self.CONTACT:
165              return escript.FunctionOnContactZero(domain)              return escript.FunctionOnContactZero(domain)
166           elif self.what==self.CONTACT_REDUCED:
167                return escript.ReducedFunctionOnContactZero(domain)
168         elif self.what==self.SOLUTION:         elif self.what==self.SOLUTION:
169              if reducedEquationOrder and reducedSolutionOrder:              if reducedEquationOrder and reducedSolutionOrder:
170                  return escript.ReducedSolution(domain)                  return escript.ReducedSolution(domain)
# Line 161  class PDECoefficient(object): Line 199  class PDECoefficient(object):
199         @param newValue: number of components of the PDE solution         @param newValue: number of components of the PDE solution
200         @type newValue: any object that can be converted into a L{Data<escript.Data>} object with the appropriate shape and L{FunctionSpace<escript.FunctionSpace>}         @type newValue: any object that can be converted into a L{Data<escript.Data>} object with the appropriate shape and L{FunctionSpace<escript.FunctionSpace>}
201         @raise IllegalCoefficientValue: if the shape of the assigned value does not match the shape of the coefficient         @raise IllegalCoefficientValue: if the shape of the assigned value does not match the shape of the coefficient
202           @raise IllegalCoefficientFunctionSpace: if unable to interploate value to appropriate function space
203         """         """
204         if newValue==None:         if newValue==None:
205             newValue=escript.Data()             newValue=escript.Data()
206         elif isinstance(newValue,escript.Data):         elif isinstance(newValue,escript.Data):
207             if not newValue.isEmpty():             if not newValue.isEmpty():
208                try:                if not newValue.getFunctionSpace() == self.getFunctionSpace(domain,reducedEquationOrder,reducedSolutionOrder):
209                   newValue=escript.Data(newValue,self.getFunctionSpace(domain,reducedEquationOrder,reducedSolutionOrder))                  try:
210                except:                    newValue=escript.Data(newValue,self.getFunctionSpace(domain,reducedEquationOrder,reducedSolutionOrder))
211                   raise IllegalCoefficientValue,"Unable to interpolate coefficient to function space %s"%self.getFunctionSpace(domain)                  except:
212                      raise IllegalCoefficientFunctionSpace,"Unable to interpolate coefficient to function space %s"%self.getFunctionSpace(domain)
213         else:         else:
214             newValue=escript.Data(newValue,self.getFunctionSpace(domain,reducedEquationOrder,reducedSolutionOrder))             newValue=escript.Data(newValue,self.getFunctionSpace(domain,reducedEquationOrder,reducedSolutionOrder))
215         if not newValue.isEmpty():         if not newValue.isEmpty():
# Line 313  class LinearPDE(object): Line 353  class LinearPDE(object):
353    
354     For a single PDE with a solution with a single component the linear PDE is defined in the following form:     For a single PDE with a solution with a single component the linear PDE is defined in the following form:
355    
356     M{-grad(A[j,l]*grad(u)[l]+B[j]u)[j]+C[l]*grad(u)[l]+D*u =-grad(X)[j,j]+Y}     M{-(grad(A[j,l]+A_reduced[j,l])*grad(u)[l]+(B[j]+B_reduced[j])u)[j]+(C[l]+C_reduced[l])*grad(u)[l]+(D+D_reduced)=-grad(X+X_reduced)[j,j]+(Y+Y_reduced)}
357    
358    
359     where M{grad(F)} denotes the spatial derivative of M{F}. Einstein's summation convention,     where M{grad(F)} denotes the spatial derivative of M{F}. Einstein's summation convention,
360     ie. summation over indexes appearing twice in a term of a sum is performed, is used.     ie. summation over indexes appearing twice in a term of a sum is performed, is used.
361     The coefficients M{A}, M{B}, M{C}, M{D}, M{X} and M{Y} have to be specified through L{Data<escript.Data>} objects in the     The coefficients M{A}, M{B}, M{C}, M{D}, M{X} and M{Y} have to be specified through L{Data<escript.Data>} objects in the
362     L{Function<escript.Function>} on the PDE or objects that can be converted into such L{Data<escript.Data>} objects.     L{Function<escript.Function>} and the coefficients M{A_reduced}, M{B_reduced}, M{C_reduced}, M{D_reduced}, M{X_reduced} and M{Y_reduced} have to be specified through L{Data<escript.Data>} objects in the
363     M{A} is a rank two, M{B}, M{C} and M{X} are rank one and M{D} and M{Y} are scalar.     L{ReducedFunction<escript.ReducedFunction>}. It is also allowd to use objects that can be converted into
364       such L{Data<escript.Data>} objects. M{A} and M{A_reduced} are rank two, M{B_reduced}, M{C_reduced}, M{X_reduced}
365       M{B_reduced}, M{C_reduced} and M{X_reduced} are rank one and M{D}, M{D_reduced} and M{Y_reduced} are scalar.
366    
367     The following natural boundary conditions are considered:     The following natural boundary conditions are considered:
368    
369     M{n[j]*(A[i,j]*grad(u)[l]+B[j]*u)+d*u=n[j]*X[j]+y}     M{n[j]*((A[i,j]+A_reduced[i,j])*grad(u)[l]+(B+B_reduced)[j]*u)+(d+d_reduced)*u=n[j]*(X[j]+X_reduced[j])+y}
370    
371     where M{n} is the outer normal field calculated by L{getNormal<escript.FunctionSpace.getNormal>} of L{FunctionOnBoundary<escript.FunctionOnBoundary>}.     where M{n} is the outer normal field. Notice that the coefficients M{A}, M{A_reduced}, M{B}, M{B_reduced}, M{X} and M{X_reduced} are defined in the PDE. The coefficients M{d} and M{y} and are each a scalar in the L{FunctionOnBoundary<escript.FunctionOnBoundary>} and the coefficients M{d_reduced} and M{y_reduced} and are each a scalar in the L{ReducedFunctionOnBoundary<escript.ReducedFunctionOnBoundary>}.
    Notice that the coefficients M{A}, M{B} and M{X} are defined in the PDE. The coefficients M{d} and M{y} are  
    each a scalar in the L{FunctionOnBoundary<escript.FunctionOnBoundary>}.  
372    
373    
374     Constraints for the solution prescribing the value of the solution at certain locations in the domain. They have the form     Constraints for the solution prescribing the value of the solution at certain locations in the domain. They have the form
# Line 339  class LinearPDE(object): Line 380  class LinearPDE(object):
380    
381     The PDE is symmetrical if     The PDE is symmetrical if
382    
383     M{A[i,j]=A[j,i]}  and M{B[j]=C[j]}     M{A[i,j]=A[j,i]}  and M{B[j]=C[j]} and M{A_reduced[i,j]=A_reduced[j,i]}  and M{B_reduced[j]=C_reduced[j]}
384    
385     For a system of PDEs and a solution with several components the PDE has the form     For a system of PDEs and a solution with several components the PDE has the form
386    
387     M{-grad(A[i,j,k,l]*grad(u[k])[l]+B[i,j,k]*u[k])[j]+C[i,k,l]*grad(u[k])[l]+D[i,k]*u[k] =-grad(X[i,j])[j]+Y[i] }     M{-grad((A[i,j,k,l]+A_reduced[i,j,k,l])*grad(u[k])[l]+(B[i,j,k]+B_reduced[i,j,k])*u[k])[j]+(C[i,k,l]+C_reduced[i,k,l])*grad(u[k])[l]+(D[i,k]+D_reduced[i,k]*u[k] =-grad(X[i,j]+X_reduced[i,j])[j]+Y[i]+Y_reduced[i] }
388    
389     M{A} is a ramk four, M{B} and M{C} are each a rank three, M{D} and M{X} are each a rank two and M{Y} is a rank one.     M{A} and M{A_reduced} are of rank four, M{B}, M{B_reduced}, M{C} and M{C_reduced} are each of rank three, M{D}, M{D_reduced}, M{X_reduced} and M{X} are each a rank two and M{Y} and M{Y_reduced} are of rank one.
390     The natural boundary conditions take the form:     The natural boundary conditions take the form:
391    
392     M{n[j]*(A[i,j,k,l]*grad(u[k])[l]+B[i,j,k]*u[k])+d[i,k]*u[k]=n[j]*X[i,j]+y[i]}     M{n[j]*((A[i,j,k,l]+A_reduced[i,j,k,l])*grad(u[k])[l]+(B[i,j,k]+B_reduced[i,j,k])*u[k])+(d[i,k]+d_reduced[i,k])*u[k]=n[j]*(X[i,j]+X_reduced[i,j])+y[i]+y_reduced[i]}
393    
394    
395     The coefficient M{d} is a rank two and M{y} is a  rank one both in the L{FunctionOnBoundary<escript.FunctionOnBoundary>}. Constraints take the form     The coefficient M{d} is a rank two and M{y} is a rank one both in the L{FunctionOnBoundary<escript.FunctionOnBoundary>}. Constraints take the form and the coefficients M{d_reduced} is a rank two and M{y_reduced} is a rank one both in the L{ReducedFunctionOnBoundary<escript.ReducedFunctionOnBoundary>}.
396    
397       Constraints take the form
398    
399     M{u[i]=r[i]}  where  M{q[i]>0}     M{u[i]=r[i]}  where  M{q[i]>0}
400    
# Line 361  class LinearPDE(object): Line 403  class LinearPDE(object):
403     The system of PDEs is symmetrical if     The system of PDEs is symmetrical if
404    
405          - M{A[i,j,k,l]=A[k,l,i,j]}          - M{A[i,j,k,l]=A[k,l,i,j]}
406            - M{A_reduced[i,j,k,l]=A_reduced[k,l,i,j]}
407          - M{B[i,j,k]=C[k,i,j]}          - M{B[i,j,k]=C[k,i,j]}
408            - M{B_reduced[i,j,k]=C_reduced[k,i,j]}
409          - M{D[i,k]=D[i,k]}          - M{D[i,k]=D[i,k]}
410            - M{D_reduced[i,k]=D_reduced[i,k]}
411          - M{d[i,k]=d[k,i]}          - M{d[i,k]=d[k,i]}
412            - M{d_reduced[i,k]=d_reduced[k,i]}
413    
414     L{LinearPDE} also supports solution discontinuities over a contact region in the domain. To specify the conditions across the     L{LinearPDE} also supports solution discontinuities over a contact region in the domain. To specify the conditions across the
415     discontinuity we are using the generalised flux M{J} which is in the case of a systems of PDEs and several components of the solution     discontinuity we are using the generalised flux M{J} which is in the case of a systems of PDEs and several components of the solution
416     defined as     defined as
417    
418     M{J[i,j]=A[i,j,k,l]*grad(u[k])[l]+B[i,j,k]*u[k]-X[i,j]}     M{J[i,j]=(A[i,j,k,l]+A_reduced[[i,j,k,l])*grad(u[k])[l]+(B[i,j,k]+B_reduced[i,j,k])*u[k]-X[i,j]-X_reduced[i,j]}
419    
420     For the case of single solution component and single PDE M{J} is defined     For the case of single solution component and single PDE M{J} is defined
421    
422     M{J_{j}=A[i,j]*grad(u)[j]+B[i]*u-X[i]}     M{J_{j}=(A[i,j]+A_reduced[i,j])*grad(u)[j]+(B[i]+B_reduced[i])*u-X[i]-X_reduced[i]}
423    
424     In the context of discontinuities M{n} denotes the normal on the discontinuity pointing from side 0 towards side 1     In the context of discontinuities M{n} denotes the normal on the discontinuity pointing from side 0 towards side 1
425     calculated from L{getNormal<escript.FunctionSpace.getNormal>} of L{FunctionOnContactZero<escript.FunctionOnContactZero>}. For a system of PDEs     calculated from L{getNormal<escript.FunctionSpace.getNormal>} of L{FunctionOnContactZero<escript.FunctionOnContactZero>}. For a system of PDEs
426     the contact condition takes the form     the contact condition takes the form
427    
428     M{n[j]*J0[i,j]=n[j]*J1[i,j]=y_contact[i]- d_contact[i,k]*jump(u)[k]}     M{n[j]*J0[i,j]=n[j]*J1[i,j]=(y_contact[i]+y_contact_reduced[i])- (d_contact[i,k]+d_contact_reduced[i,k])*jump(u)[k]}
429    
430     where M{J0} and M{J1} are the fluxes on side 0 and side 1 of the discontinuity, respectively. M{jump(u)}, which is the difference     where M{J0} and M{J1} are the fluxes on side 0 and side 1 of the discontinuity, respectively. M{jump(u)}, which is the difference
431     of the solution at side 1 and at side 0, denotes the jump of M{u} across discontinuity along the normal calcualted by     of the solution at side 1 and at side 0, denotes the jump of M{u} across discontinuity along the normal calcualted by
432     L{jump<util.jump>}.     L{jump<util.jump>}.
433     The coefficient M{d_contact} is a rank two and M{y_contact} is a rank one both in the L{FunctionOnContactZero<escript.FunctionOnContactZero>} or L{FunctionOnContactOne<escript.FunctionOnContactOne>}.     The coefficient M{d_contact} is a rank two and M{y_contact} is a rank one both in the L{FunctionOnContactZero<escript.FunctionOnContactZero>} or L{FunctionOnContactOne<escript.FunctionOnContactOne>}.
434       The coefficient M{d_contact_reduced} is a rank two and M{y_contact_reduced} is a rank one both in the L{ReducedFunctionOnContactZero<escript.ReducedFunctionOnContactZero>} or L{ReducedFunctionOnContactOne<escript.ReducedFunctionOnContactOne>}.
435     In case of a single PDE and a single component solution the contact condition takes the form     In case of a single PDE and a single component solution the contact condition takes the form
436    
437     M{n[j]*J0_{j}=n[j]*J1_{j}=y_contact-d_contact*jump(u)}     M{n[j]*J0_{j}=n[j]*J1_{j}=(y_contact+y_contact_reduced)-(d_contact+y_contact_reduced)*jump(u)}
438    
439     In this case the the coefficient M{d_contact} and M{y_contact} are eaach scalar     In this case the coefficient M{d_contact} and M{y_contact} are each scalar both in the L{FunctionOnContactZero<escript.FunctionOnContactZero>} or L{FunctionOnContactOne<escript.FunctionOnContactOne>} and the coefficient M{d_contact_reduced} and M{y_contact_reduced} are each scalar both in the L{ReducedFunctionOnContactZero<escript.ReducedFunctionOnContactZero>} or L{ReducedFunctionOnContactOne<escript.ReducedFunctionOnContactOne>}
    both in the L{FunctionOnContactZero<escript.FunctionOnContactZero>} or L{FunctionOnContactOne<escript.FunctionOnContactOne>}.  
440    
441     @cvar DEFAULT: The default method used to solve the system of linear equations     @cvar DEFAULT: The default method used to solve the system of linear equations
442     @cvar DIRECT: The direct solver based on LDU factorization     @cvar DIRECT: The direct solver based on LDU factorization
# Line 413  class LinearPDE(object): Line 459  class LinearPDE(object):
459     @cvar SCSL: SGI SCSL solver library     @cvar SCSL: SGI SCSL solver library
460     @cvar MKL: Intel's MKL solver library     @cvar MKL: Intel's MKL solver library
461     @cvar UMFPACK: the UMFPACK library     @cvar UMFPACK: the UMFPACK library
462       @cvar TRILINOS: the TRILINOS parallel solver class library from Sandia Natl Labs
463     @cvar ITERATIVE: The default iterative solver     @cvar ITERATIVE: The default iterative solver
464     @cvar AMG: algebraic multi grid     @cvar AMG: algebraic multi grid
465     @cvar RILU: recursive ILU     @cvar RILU: recursive ILU
# Line 442  class LinearPDE(object): Line 489  class LinearPDE(object):
489     PASO= 21     PASO= 21
490     AMG= 22     AMG= 22
491     RILU = 23     RILU = 23
492       TRILINOS = 24
493       NONLINEAR_GMRES = 25
494    
495     SMALL_TOLERANCE=1.e-13     SMALL_TOLERANCE=1.e-13
496     __PACKAGE_KEY="package"     __PACKAGE_KEY="package"
# Line 479  class LinearPDE(object): Line 528  class LinearPDE(object):
528         "y"         : PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),         "y"         : PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
529         "d_contact" : PDECoefficient(PDECoefficient.CONTACT,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),         "d_contact" : PDECoefficient(PDECoefficient.CONTACT,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),
530         "y_contact" : PDECoefficient(PDECoefficient.CONTACT,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),         "y_contact" : PDECoefficient(PDECoefficient.CONTACT,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
531           "A_reduced"         : PDECoefficient(PDECoefficient.INTERIOR_REDUCED,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_DIM,PDECoefficient.BY_SOLUTION,PDECoefficient.BY_DIM),PDECoefficient.OPERATOR),
532           "B_reduced"         : PDECoefficient(PDECoefficient.INTERIOR_REDUCED,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_DIM,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),
533           "C_reduced"         : PDECoefficient(PDECoefficient.INTERIOR_REDUCED,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION,PDECoefficient.BY_DIM),PDECoefficient.OPERATOR),
534           "D_reduced"         : PDECoefficient(PDECoefficient.INTERIOR_REDUCED,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),
535           "X_reduced"         : PDECoefficient(PDECoefficient.INTERIOR_REDUCED,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_DIM),PDECoefficient.RIGHTHANDSIDE),
536           "Y_reduced"         : PDECoefficient(PDECoefficient.INTERIOR_REDUCED,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
537           "d_reduced"         : PDECoefficient(PDECoefficient.BOUNDARY_REDUCED,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),
538           "y_reduced"         : PDECoefficient(PDECoefficient.BOUNDARY_REDUCED,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
539           "d_contact_reduced" : PDECoefficient(PDECoefficient.CONTACT_REDUCED,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),
540           "y_contact_reduced" : PDECoefficient(PDECoefficient.CONTACT_REDUCED,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
541         "r"         : PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_SOLUTION,),PDECoefficient.RIGHTHANDSIDE),         "r"         : PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_SOLUTION,),PDECoefficient.RIGHTHANDSIDE),
542         "q"         : PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_SOLUTION,),PDECoefficient.BOTH)}         "q"         : PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_SOLUTION,),PDECoefficient.BOTH)}
543    
# Line 760  class LinearPDE(object): Line 819  class LinearPDE(object):
819                    if util.Lsup(d_contact[i,k]-d_contact[k,i])>tol:                    if util.Lsup(d_contact[i,k]-d_contact[k,i])>tol:
820                        if verbose: print "non-symmetric PDE because d_contact[%d,%d]!=d_contact[%d,%d]"%(i,k,k,i)                        if verbose: print "non-symmetric PDE because d_contact[%d,%d]!=d_contact[%d,%d]"%(i,k,k,i)
821                        out=False                        out=False
822             # and now the reduced coefficients
823             A_reduced=self.getCoefficientOfGeneralPDE("A_reduced")
824             if not A_reduced.isEmpty():
825                tol=util.Lsup(A_reduced)*self.SMALL_TOLERANCE
826                if self.getNumSolutions()>1:
827                   for i in range(self.getNumEquations()):
828                      for j in range(self.getDim()):
829                         for k in range(self.getNumSolutions()):
830                            for l in range(self.getDim()):
831                                if util.Lsup(A_reduced[i,j,k,l]-A_reduced[k,l,i,j])>tol:
832                                   if verbose: print "non-symmetric PDE because A_reduced[%d,%d,%d,%d]!=A_reduced[%d,%d,%d,%d]"%(i,j,k,l,k,l,i,j)
833                                   out=False
834                else:
835                   for j in range(self.getDim()):
836                      for l in range(self.getDim()):
837                         if util.Lsup(A_reduced[j,l]-A_reduced[l,j])>tol:
838                            if verbose: print "non-symmetric PDE because A_reduced[%d,%d]!=A_reduced[%d,%d]"%(j,l,l,j)
839                            out=False
840             B_reduced=self.getCoefficientOfGeneralPDE("B_reduced")
841             C_reduced=self.getCoefficientOfGeneralPDE("C_reduced")
842             if B_reduced.isEmpty() and not C_reduced.isEmpty():
843                if verbose: print "non-symmetric PDE because B_reduced is not present but C_reduced is"
844                out=False
845             elif not B_reduced.isEmpty() and C_reduced.isEmpty():
846                if verbose: print "non-symmetric PDE because C_reduced is not present but B_reduced is"
847                out=False
848             elif not B_reduced.isEmpty() and not C_reduced.isEmpty():
849                tol=(util.Lsup(B_reduced)+util.Lsup(C_reduced))*self.SMALL_TOLERANCE/2.
850                if self.getNumSolutions()>1:
851                   for i in range(self.getNumEquations()):
852                       for j in range(self.getDim()):
853                          for k in range(self.getNumSolutions()):
854                             if util.Lsup(B_reduced[i,j,k]-C_reduced[k,i,j])>tol:
855                                  if verbose: print "non-symmetric PDE because B_reduced[%d,%d,%d]!=C_reduced[%d,%d,%d]"%(i,j,k,k,i,j)
856                                  out=False
857                else:
858                   for j in range(self.getDim()):
859                      if util.Lsup(B_reduced[j]-C_reduced[j])>tol:
860                         if verbose: print "non-symmetric PDE because B_reduced[%d]!=C_reduced[%d]"%(j,j)
861                         out=False
862             if self.getNumSolutions()>1:
863               D_reduced=self.getCoefficientOfGeneralPDE("D_reduced")
864               if not D_reduced.isEmpty():
865                 tol=util.Lsup(D_reduced)*self.SMALL_TOLERANCE
866                 for i in range(self.getNumEquations()):
867                    for k in range(self.getNumSolutions()):
868                      if util.Lsup(D_reduced[i,k]-D_reduced[k,i])>tol:
869                          if verbose: print "non-symmetric PDE because D_reduced[%d,%d]!=D_reduced[%d,%d]"%(i,k,k,i)
870                          out=False
871               d_reduced=self.getCoefficientOfGeneralPDE("d_reduced")
872               if not d_reduced.isEmpty():
873                 tol=util.Lsup(d_reduced)*self.SMALL_TOLERANCE
874                 for i in range(self.getNumEquations()):
875                    for k in range(self.getNumSolutions()):
876                      if util.Lsup(d_reduced[i,k]-d_reduced[k,i])>tol:
877                          if verbose: print "non-symmetric PDE because d_reduced[%d,%d]!=d_reduced[%d,%d]"%(i,k,k,i)
878                          out=False
879               d_contact_reduced=self.getCoefficientOfGeneralPDE("d_contact_reduced")
880               if not d_contact_reduced.isEmpty():
881                 tol=util.Lsup(d_contact_reduced)*self.SMALL_TOLERANCE
882                 for i in range(self.getNumEquations()):
883                    for k in range(self.getNumSolutions()):
884                      if util.Lsup(d_contact_reduced[i,k]-d_contact_reduced[k,i])>tol:
885                          if verbose: print "non-symmetric PDE because d_contact_reduced[%d,%d]!=d_contact_reduced[%d,%d]"%(i,k,k,i)
886                          out=False
887        return out        return out
888    
889     def getSolution(self,**options):     def getSolution(self,**options):
# Line 799  class LinearPDE(object): Line 923  class LinearPDE(object):
923       """       """
924       returns the flux M{J} for a given M{u}       returns the flux M{J} for a given M{u}
925    
926       M{J[i,j]=A[i,j,k,l]*grad(u[k])[l]+B[i,j,k]u[k]-X[i,j]}       M{J[i,j]=(A[i,j,k,l]+A_reduced[A[i,j,k,l]]*grad(u[k])[l]+(B[i,j,k]+B_reduced[i,j,k])u[k]-X[i,j]-X_reduced[i,j]}
927    
928       or       or
929    
930       M{J[j]=A[i,j]*grad(u)[l]+B[j]u-X[j]}       M{J[j]=(A[i,j]+A_reduced[i,j])*grad(u)[l]+(B[j]+B_reduced[j])u-X[j]-X_reduced[j]}
931    
932       @param u: argument in the flux. If u is not present or equals L{None} the current solution is used.       @param u: argument in the flux. If u is not present or equals L{None} the current solution is used.
933       @type u: L{Data<escript.Data>} or None       @type u: L{Data<escript.Data>} or None
# Line 811  class LinearPDE(object): Line 935  class LinearPDE(object):
935       @rtype: L{Data<escript.Data>}       @rtype: L{Data<escript.Data>}
936       """       """
937       if u==None: u=self.getSolution()       if u==None: u=self.getSolution()
938       return util.tensormult(self.getCoefficientOfGeneralPDE("A"),util.grad(u))+util.matrixmult(self.getCoefficientOfGeneralPDE("B"),u)-util.self.getCoefficientOfGeneralPDE("X")       return util.tensormult(self.getCoefficientOfGeneralPDE("A"),util.grad(u,Funtion(self.getDomain))) \
939               +util.matrixmult(self.getCoefficientOfGeneralPDE("B"),u) \
940               -util.self.getCoefficientOfGeneralPDE("X") \
941               +util.tensormult(self.getCoefficientOfGeneralPDE("A_reduced"),util.grad(u,ReducedFuntion(self.getDomain))) \
942               +util.matrixmult(self.getCoefficientOfGeneralPDE("B_reduced"),u) \
943               -util.self.getCoefficientOfGeneralPDE("X_reduced")
944     # =============================================================================     # =============================================================================
945     #   solver settings:     #   solver settings:
946     # =============================================================================     # =============================================================================
# Line 824  class LinearPDE(object): Line 953  class LinearPDE(object):
953         @param preconditioner: sets a new solver method.         @param preconditioner: sets a new solver method.
954         @type preconditioner: one of L{DEFAULT}, L{JACOBI} L{ILU0}, L{ILUT},L{SSOR}, L{RILU}         @type preconditioner: one of L{DEFAULT}, L{JACOBI} L{ILU0}, L{ILUT},L{SSOR}, L{RILU}
955         """         """
956         if solver==None: solve=self.DEFAULT         if solver==None: solver=self.__solver_method
957           if preconditioner==None: preconditioner=self.__preconditioner
958           if solver==None: solver=self.DEFAULT
959         if preconditioner==None: preconditioner=self.DEFAULT         if preconditioner==None: preconditioner=self.DEFAULT
960         if not (solver,preconditioner)==self.getSolverMethod():         if not (solver,preconditioner)==self.getSolverMethod():
961             self.__solver_method=solver             self.__solver_method=solver
# Line 868  class LinearPDE(object): Line 999  class LinearPDE(object):
999         elif p==self.MKL: package= "MKL"         elif p==self.MKL: package= "MKL"
1000         elif p==self.SCSL: package= "SCSL"         elif p==self.SCSL: package= "SCSL"
1001         elif p==self.UMFPACK: package= "UMFPACK"         elif p==self.UMFPACK: package= "UMFPACK"
1002           elif p==self.TRILINOS: package= "TRILINOS"
1003         else : method="unknown"         else : method="unknown"
1004         return "%s solver of %s package"%(method,package)         return "%s solver of %s package"%(method,package)
1005    
# Line 886  class LinearPDE(object): Line 1018  class LinearPDE(object):
1018         sets a new solver package         sets a new solver package
1019    
1020         @param package: sets a new solver method.         @param package: sets a new solver method.
1021         @type package: one of L{DEFAULT}, L{PASO} L{SCSL}, L{MKL}, L{UMFPACK}         @type package: one of L{DEFAULT}, L{PASO} L{SCSL}, L{MKL}, L{UMFPACK}, L{TRILINOS}
1022         """         """
1023         if package==None: package=self.DEFAULT         if package==None: package=self.DEFAULT
1024         if not package==self.getSolverPackage():         if not package==self.getSolverPackage():
# Line 923  class LinearPDE(object): Line 1055  class LinearPDE(object):
1055         @param tol: new tolerance for the solver. If the tol is lower then the current tolerence         @param tol: new tolerance for the solver. If the tol is lower then the current tolerence
1056                     the system will be resolved.                     the system will be resolved.
1057         @type tol: positive C{float}         @type tol: positive C{float}
1058         @raise ValueException: if tolerance is not positive.         @raise ValueError: if tolerance is not positive.
1059         """         """
1060         if not tol>0:         if not tol>0:
1061             raise ValueException,"Tolerance as to be positive"             raise ValueError,"Tolerance as to be positive"
1062         if tol<self.getTolerance(): self.__invalidateSolution()         if tol<self.getTolerance(): self.__invalidateSolution()
1063         self.trace("New tolerance %e"%tol)         self.trace("New tolerance %e"%tol)
1064         self.__tolerance=tol         self.__tolerance=tol
# Line 1207  class LinearPDE(object): Line 1339  class LinearPDE(object):
1339         if self.__righthandside.isEmpty():         if self.__righthandside.isEmpty():
1340             self.__righthandside=self.__getNewRightHandSide()             self.__righthandside=self.__getNewRightHandSide()
1341         else:         else:
1342             self.__righthandside*=0             self.__righthandside.setToZero()
1343             self.trace("Right hand side is reset to zero.")             self.trace("Right hand side is reset to zero.")
1344         return self.__righthandside         return self.__righthandside
1345    
# Line 1257  class LinearPDE(object): Line 1389  class LinearPDE(object):
1389       @return: the value of the coefficient  name       @return: the value of the coefficient  name
1390       @rtype: L{Data<escript.Data>}       @rtype: L{Data<escript.Data>}
1391       @raise IllegalCoefficient: if name is not one of coefficients       @raise IllegalCoefficient: if name is not one of coefficients
1392                    M{A}, M{B}, M{C}, M{D}, M{X}, M{Y}, M{d}, M{y}, M{d_contact}, M{y_contact}, M{r} or M{q}.                    M{A}, M{B}, M{C}, M{D}, M{X}, M{Y}, M{d}, M{y}, M{d_contact}, M{y_contact},
1393                      M{A_reduced}, M{B_reduced}, M{C_reduced}, M{D_reduced}, M{X_reduced}, M{Y_reduced}, M{d_reduced}, M{y_reduced}, M{d_contact_reduced}, M{y_contact_reduced}, M{r} or M{q}.
1394       """       """
1395       if self.hasCoefficientOfGeneralPDE(name):       if self.hasCoefficientOfGeneralPDE(name):
1396          return self.getCoefficient(name)          return self.getCoefficient(name)
# Line 1285  class LinearPDE(object): Line 1418  class LinearPDE(object):
1418       @return: a coefficient name initialized to 0.       @return: a coefficient name initialized to 0.
1419       @rtype: L{Data<escript.Data>}       @rtype: L{Data<escript.Data>}
1420       @raise IllegalCoefficient: if name is not one of coefficients       @raise IllegalCoefficient: if name is not one of coefficients
1421                    M{A}, M{B}, M{C}, M{D}, M{X}, M{Y}, M{d}, M{y}, M{d_contact}, M{y_contact}, M{r} or M{q}.                    M{A}, M{B}, M{C}, M{D}, M{X}, M{Y}, M{d}, M{y}, M{d_contact}, M{y_contact},
1422                      M{A_reduced}, M{B_reduced}, M{C_reduced}, M{D_reduced}, M{X_reduced}, M{Y_reduced}, M{d_reduced}, M{y_reduced}, M{d_contact_reduced}, M{y_contact_reduced}, M{r} or M{q}.
1423       """       """
1424       if self.hasCoefficientOfGeneralPDE(name):       if self.hasCoefficientOfGeneralPDE(name):
1425          return escript.Data(0,self.getShapeOfCoefficientOfGeneralPDE(name),self.getFunctionSpaceForCoefficientOfGeneralPDE(name))          return escript.Data(0,self.getShapeOfCoefficientOfGeneralPDE(name),self.getFunctionSpaceForCoefficientOfGeneralPDE(name))
# Line 1301  class LinearPDE(object): Line 1435  class LinearPDE(object):
1435       @return: the function space to be used for coefficient name       @return: the function space to be used for coefficient name
1436       @rtype: L{FunctionSpace<escript.FunctionSpace>}       @rtype: L{FunctionSpace<escript.FunctionSpace>}
1437       @raise IllegalCoefficient: if name is not one of coefficients       @raise IllegalCoefficient: if name is not one of coefficients
1438                    M{A}, M{B}, M{C}, M{D}, M{X}, M{Y}, M{d}, M{y}, M{d_contact}, M{y_contact}, M{r} or M{q}.                    M{A}, M{B}, M{C}, M{D}, M{X}, M{Y}, M{d}, M{y}, M{d_contact}, M{y_contact},
1439                      M{A_reduced}, M{B_reduced}, M{C_reduced}, M{D_reduced}, M{X_reduced}, M{Y_reduced}, M{d_reduced}, M{y_reduced}, M{d_contact_reduced}, M{y_contact_reduced}, M{r} or M{q}.
1440       """       """
1441       if self.hasCoefficientOfGeneralPDE(name):       if self.hasCoefficientOfGeneralPDE(name):
1442          return self.__COEFFICIENTS_OF_GENEARL_PDE[name].getFunctionSpace(self.getDomain())          return self.__COEFFICIENTS_OF_GENEARL_PDE[name].getFunctionSpace(self.getDomain())
# Line 1317  class LinearPDE(object): Line 1452  class LinearPDE(object):
1452       @return: the shape of the coefficient name       @return: the shape of the coefficient name
1453       @rtype: C{tuple} of C{int}       @rtype: C{tuple} of C{int}
1454       @raise IllegalCoefficient: if name is not one of coefficients       @raise IllegalCoefficient: if name is not one of coefficients
1455                    M{A}, M{B}, M{C}, M{D}, M{X}, M{Y}, M{d}, M{y}, M{d_contact}, M{y_contact}, M{r} or M{q}.                    M{A}, M{B}, M{C}, M{D}, M{X}, M{Y}, M{d}, M{y}, M{d_contact}, M{y_contact},
1456                      M{A_reduced}, M{B_reduced}, M{C_reduced}, M{D_reduced}, M{X_reduced}, M{Y_reduced}, M{d_reduced}, M{y_reduced}, M{d_contact_reduced}, M{y_contact_reduced}, M{r} or M{q}.
1457       """       """
1458       if self.hasCoefficientOfGeneralPDE(name):       if self.hasCoefficientOfGeneralPDE(name):
1459          return self.__COEFFICIENTS_OF_GENEARL_PDE[name].getShape(self.getDomain(),self.getNumEquations(),self.getNumSolutions())          return self.__COEFFICIENTS_OF_GENEARL_PDE[name].getShape(self.getDomain(),self.getNumEquations(),self.getNumSolutions())
# Line 1447  class LinearPDE(object): Line 1583  class LinearPDE(object):
1583        @param coefficients: new values assigned to coefficients        @param coefficients: new values assigned to coefficients
1584        @keyword A: value for coefficient A.        @keyword A: value for coefficient A.
1585        @type A: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.        @type A: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1586          @keyword A_reduced: value for coefficient A_reduced.
1587          @type A_reduced: any type that can be casted to L{Data<escript.Data>} object on L{ReducedFunction<escript.ReducedFunction>}.
1588        @keyword B: value for coefficient B        @keyword B: value for coefficient B
1589        @type B: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.        @type B: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1590          @keyword B_reduced: value for coefficient B_reduced
1591          @type B_reduced: any type that can be casted to L{Data<escript.Data>} object on L{ReducedFunction<escript.ReducedFunction>}.
1592        @keyword C: value for coefficient C        @keyword C: value for coefficient C
1593        @type C: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.        @type C: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1594          @keyword C_reduced: value for coefficient C_reduced
1595          @type C_reduced: any type that can be casted to L{Data<escript.Data>} object on L{ReducedFunction<escript.ReducedFunction>}.
1596        @keyword D: value for coefficient D        @keyword D: value for coefficient D
1597        @type D: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.        @type D: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1598          @keyword D_reduced: value for coefficient D_reduced
1599          @type D_reduced: any type that can be casted to L{Data<escript.Data>} object on L{ReducedFunction<escript.ReducedFunction>}.
1600        @keyword X: value for coefficient X        @keyword X: value for coefficient X
1601        @type X: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.        @type X: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1602          @keyword X_reduced: value for coefficient X_reduced
1603          @type X_reduced: any type that can be casted to L{Data<escript.Data>} object on L{ReducedFunction<escript.ReducedFunction>}.
1604        @keyword Y: value for coefficient Y        @keyword Y: value for coefficient Y
1605        @type Y: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.        @type Y: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1606          @keyword Y_reduced: value for coefficient Y_reduced
1607          @type Y_reduced: any type that can be casted to L{Data<escript.Data>} object on L{ReducedFunction<escript.Function>}.
1608        @keyword d: value for coefficient d        @keyword d: value for coefficient d
1609        @type d: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.        @type d: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
1610          @keyword d_reduced: value for coefficient d_reduced
1611          @type d_reduced: any type that can be casted to L{Data<escript.Data>} object on L{ReducedFunctionOnBoundary<escript.ReducedFunctionOnBoundary>}.
1612        @keyword y: value for coefficient y        @keyword y: value for coefficient y
1613        @type y: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.        @type y: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
1614        @keyword d_contact: value for coefficient d_contact        @keyword d_contact: value for coefficient d_contact
1615        @type d_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>}.        @type d_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>} or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.
1616                         or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.        @keyword d_contact_reduced: value for coefficient d_contact_reduced
1617          @type d_contact_reduced: any type that can be casted to L{Data<escript.Data>} object on L{ReducedFunctionOnContactOne<escript.ReducedFunctionOnContactOne>} or  L{ReducedFunctionOnContactZero<escript.ReducedFunctionOnContactZero>}.
1618        @keyword y_contact: value for coefficient y_contact        @keyword y_contact: value for coefficient y_contact
1619        @type y_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>}.        @type y_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>} or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.
1620                         or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.        @keyword y_contact_reduced: value for coefficient y_contact_reduced
1621          @type y_contact_reduced: any type that can be casted to L{Data<escript.Data>} object on L{ReducedFunctionOnContactOne<escript.FunctionOnContactOne>} or L{ReducedFunctionOnContactZero<escript.FunctionOnContactZero>}.
1622        @keyword r: values prescribed to the solution at the locations of constraints        @keyword r: values prescribed to the solution at the locations of constraints
1623        @type r: any type that can be casted to L{Data<escript.Data>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}        @type r: any type that can be casted to L{Data<escript.Data>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1624                 depending of reduced order is used for the solution.                 depending of reduced order is used for the solution.
# Line 1501  class LinearPDE(object): Line 1653  class LinearPDE(object):
1653        # now we check the shape of the coefficient if numEquations and numSolutions are set:        # now we check the shape of the coefficient if numEquations and numSolutions are set:
1654        for i,d in coefficients.iteritems():        for i,d in coefficients.iteritems():
1655          try:          try:
1656             self.COEFFICIENTS[i].setValue(self.getDomain(),self.getNumEquations(),self.getNumSolutions(),self.reduceEquationOrder(),self.reduceSolutionOrder(),d)             self.COEFFICIENTS[i].setValue(self.getDomain(),
1657                                             self.getNumEquations(),self.getNumSolutions(),
1658                                             self.reduceEquationOrder(),self.reduceSolutionOrder(),d)
1659               self.alteredCoefficient(i)
1660            except IllegalCoefficientFunctionSpace,m:
1661                # if the function space is wrong then we try the reduced version:
1662                i_red=i+"_reduced"
1663                if (not i_red in coefficients.keys()) and i_red in self.COEFFICIENTS.keys():
1664                    try:
1665                        self.COEFFICIENTS[i_red].setValue(self.getDomain(),
1666                                                          self.getNumEquations(),self.getNumSolutions(),
1667                                                          self.reduceEquationOrder(),self.reduceSolutionOrder(),d)
1668                        self.alteredCoefficient(i_red)
1669                    except IllegalCoefficientValue,m:
1670                        raise IllegalCoefficientValue("Coefficient %s:%s"%(i,m))
1671                    except IllegalCoefficientFunctionSpace,m:
1672                        raise IllegalCoefficientFunctionSpace("Coefficient %s:%s"%(i,m))
1673                else:
1674                    raise IllegalCoefficientFunctionSpace("Coefficient %s:%s"%(i,m))
1675          except IllegalCoefficientValue,m:          except IllegalCoefficientValue,m:
1676             raise IllegalCoefficientValue("Coefficient %s:%s"%(i,m))             raise IllegalCoefficientValue("Coefficient %s:%s"%(i,m))
         self.alteredCoefficient(i)  
   
1677        self.__altered_coefficients=True        self.__altered_coefficients=True
1678        # check if the systrem is inhomogeneous:        # check if the systrem is inhomogeneous:
1679        if len(coefficients)>0 and not self.isUsingLumping():        if len(coefficients)>0 and not self.isUsingLumping():
# Line 1532  class LinearPDE(object): Line 1700  class LinearPDE(object):
1700                   if not self.getCoefficientOfGeneralPDE("A").isEmpty():                   if not self.getCoefficientOfGeneralPDE("A").isEmpty():
1701                        raise ValueError,"coefficient A in lumped matrix may not be present."                        raise ValueError,"coefficient A in lumped matrix may not be present."
1702                   if not self.getCoefficientOfGeneralPDE("B").isEmpty():                   if not self.getCoefficientOfGeneralPDE("B").isEmpty():
1703                        raise ValueError,"coefficient A in lumped matrix may not be present."                        raise ValueError,"coefficient B in lumped matrix may not be present."
1704                   if not self.getCoefficientOfGeneralPDE("C").isEmpty():                   if not self.getCoefficientOfGeneralPDE("C").isEmpty():
1705                        raise ValueError,"coefficient A in lumped matrix may not be present."                        raise ValueError,"coefficient C in lumped matrix may not be present."
1706                     if not self.getCoefficientOfGeneralPDE("d_contact").isEmpty():
1707                          raise ValueError,"coefficient d_contact in lumped matrix may not be present."
1708                     if not self.getCoefficientOfGeneralPDE("A_reduced").isEmpty():
1709                          raise ValueError,"coefficient A_reduced in lumped matrix may not be present."
1710                     if not self.getCoefficientOfGeneralPDE("B_reduced").isEmpty():
1711                          raise ValueError,"coefficient B_reduced in lumped matrix may not be present."
1712                     if not self.getCoefficientOfGeneralPDE("C_reduced").isEmpty():
1713                          raise ValueError,"coefficient C_reduced in lumped matrix may not be present."
1714                     if not self.getCoefficientOfGeneralPDE("d_contact_reduced").isEmpty():
1715                          raise ValueError,"coefficient d_contact_reduced in lumped matrix may not be present."
1716                   D=self.getCoefficientOfGeneralPDE("D")                   D=self.getCoefficientOfGeneralPDE("D")
1717                     d=self.getCoefficientOfGeneralPDE("d")
1718                     D_reduced=self.getCoefficientOfGeneralPDE("D_reduced")
1719                     d_reduced=self.getCoefficientOfGeneralPDE("d_reduced")
1720                   if not D.isEmpty():                   if not D.isEmpty():
1721                       if self.getNumSolutions()>1:                       if self.getNumSolutions()>1:
                         #D_times_e=util.matrixmult(D,numarray.ones((self.getNumSolutions(),)))  
1722                          D_times_e=util.matrix_mult(D,numarray.ones((self.getNumSolutions(),)))                          D_times_e=util.matrix_mult(D,numarray.ones((self.getNumSolutions(),)))
1723                       else:                       else:
1724                          D_times_e=D                          D_times_e=D
1725                   else:                   else:
1726                      D_times_e=escript.Data()                      D_times_e=escript.Data()
                  d=self.getCoefficientOfGeneralPDE("d")  
1727                   if not d.isEmpty():                   if not d.isEmpty():
1728                       if self.getNumSolutions()>1:                       if self.getNumSolutions()>1:
                         #d_times_e=util.matrixmult(d,numarray.ones((self.getNumSolutions(),)))  
1729                          d_times_e=util.matrix_mult(d,numarray.ones((self.getNumSolutions(),)))                          d_times_e=util.matrix_mult(d,numarray.ones((self.getNumSolutions(),)))
1730                       else:                       else:
1731                          d_times_e=d                          d_times_e=d
1732                   else:                   else:
1733                      d_times_e=escript.Data()                      d_times_e=escript.Data()
1734                   d_contact=self.getCoefficientOfGeneralPDE("d_contact")        
1735                   if not d_contact.isEmpty():                   if not D_reduced.isEmpty():
1736                         if self.getNumSolutions()>1:
1737                            D_reduced_times_e=util.matrix_mult(D_reduced,numarray.ones((self.getNumSolutions(),)))
1738                         else:
1739                            D_reduced_times_e=D_reduced
1740                     else:
1741                        D_reduced_times_e=escript.Data()
1742                     if not d_reduced.isEmpty():
1743                       if self.getNumSolutions()>1:                       if self.getNumSolutions()>1:
1744                          d_contact_times_e=util.matrixmult(d_contact,numarray.ones((self.getNumSolutions(),)))                          d_reduced_times_e=util.matrix_mult(d_reduced,numarray.ones((self.getNumSolutions(),)))
1745                       else:                       else:
1746                          d_contact_times_e=d_contact                          d_reduced_times_e=d_reduced
1747                   else:                   else:
1748                      d_contact_times_e=escript.Data()                      d_reduced_times_e=escript.Data()
1749        
1750                   self.__operator=self.__getNewRightHandSide()                   self.__operator=self.__getNewRightHandSide()
1751                   self.getDomain().addPDEToRHS(self.__operator, \                   if hasattr(self.getDomain(), "addPDEToLumpedSystem") :
1752                                                escript.Data(), \                      self.getDomain().addPDEToLumpedSystem(self.__operator, D_times_e, d_times_e)
1753                                                D_times_e, \                      self.getDomain().addPDEToLumpedSystem(self.__operator, D_reduced_times_e, d_reduced_times_e)
1754                                                d_times_e,\                   else:
1755                                                d_contact_times_e)                      self.getDomain().addPDEToRHS(self.__operator, \
1756                                                     escript.Data(), \
1757                                                     D_times_e, \
1758                                                     d_times_e,\
1759                                                     escript.Data())
1760                        self.getDomain().addPDEToRHS(self.__operator, \
1761                                                     escript.Data(), \
1762                                                     D_reduced_times_e, \
1763                                                     d_reduced_times_e,\
1764                                                     escript.Data())
1765                   self.__operator=1./self.__operator                   self.__operator=1./self.__operator
1766                   self.trace("New lumped operator has been built.")                   self.trace("New lumped operator has been built.")
1767                   self.__operator_is_Valid=True                   self.__operator_is_Valid=True
# Line 1577  class LinearPDE(object): Line 1771  class LinearPDE(object):
1771                                 self.getCoefficientOfGeneralPDE("Y"),\                                 self.getCoefficientOfGeneralPDE("Y"),\
1772                                 self.getCoefficientOfGeneralPDE("y"),\                                 self.getCoefficientOfGeneralPDE("y"),\
1773                                 self.getCoefficientOfGeneralPDE("y_contact"))                                 self.getCoefficientOfGeneralPDE("y_contact"))
1774                     self.getDomain().addPDEToRHS(self.__righthandside, \
1775                                   self.getCoefficientOfGeneralPDE("X_reduced"), \
1776                                   self.getCoefficientOfGeneralPDE("Y_reduced"),\
1777                                   self.getCoefficientOfGeneralPDE("y_reduced"),\
1778                                   self.getCoefficientOfGeneralPDE("y_contact_reduced"))
1779                   self.trace("New right hand side as been built.")                   self.trace("New right hand side as been built.")
1780                   self.__righthandside_isValid=True                   self.__righthandside_isValid=True
1781            else:            else:
# Line 1592  class LinearPDE(object): Line 1791  class LinearPDE(object):
1791                                 self.getCoefficientOfGeneralPDE("y"), \                                 self.getCoefficientOfGeneralPDE("y"), \
1792                                 self.getCoefficientOfGeneralPDE("d_contact"), \                                 self.getCoefficientOfGeneralPDE("d_contact"), \
1793                                 self.getCoefficientOfGeneralPDE("y_contact"))                                 self.getCoefficientOfGeneralPDE("y_contact"))
1794                     self.getDomain().addPDEToSystem(self.__operator,self.__righthandside, \
1795                                   self.getCoefficientOfGeneralPDE("A_reduced"), \
1796                                   self.getCoefficientOfGeneralPDE("B_reduced"), \
1797                                   self.getCoefficientOfGeneralPDE("C_reduced"), \
1798                                   self.getCoefficientOfGeneralPDE("D_reduced"), \
1799                                   self.getCoefficientOfGeneralPDE("X_reduced"), \
1800                                   self.getCoefficientOfGeneralPDE("Y_reduced"), \
1801                                   self.getCoefficientOfGeneralPDE("d_reduced"), \
1802                                   self.getCoefficientOfGeneralPDE("y_reduced"), \
1803                                   self.getCoefficientOfGeneralPDE("d_contact_reduced"), \
1804                                   self.getCoefficientOfGeneralPDE("y_contact_reduced"))
1805                   self.__applyConstraint()                   self.__applyConstraint()
1806                   self.__righthandside=self.copyConstraint(self.__righthandside)                   self.__righthandside=self.copyConstraint(self.__righthandside)
1807                   self.trace("New system has been built.")                   self.trace("New system has been built.")
# Line 1603  class LinearPDE(object): Line 1813  class LinearPDE(object):
1813                                 self.getCoefficientOfGeneralPDE("Y"),\                                 self.getCoefficientOfGeneralPDE("Y"),\
1814                                 self.getCoefficientOfGeneralPDE("y"),\                                 self.getCoefficientOfGeneralPDE("y"),\
1815                                 self.getCoefficientOfGeneralPDE("y_contact"))                                 self.getCoefficientOfGeneralPDE("y_contact"))
1816                     self.getDomain().addPDEToRHS(self.__righthandside, \
1817                                   self.getCoefficientOfGeneralPDE("X_reduced"), \
1818                                   self.getCoefficientOfGeneralPDE("Y_reduced"),\
1819                                   self.getCoefficientOfGeneralPDE("y_reduced"),\
1820                                   self.getCoefficientOfGeneralPDE("y_contact_reduced"))
1821                   self.__righthandside=self.copyConstraint(self.__righthandside)                   self.__righthandside=self.copyConstraint(self.__righthandside)
1822                   self.trace("New right hand side has been built.")                   self.trace("New right hand side has been built.")
1823                   self.__righthandside_isValid=True                   self.__righthandside_isValid=True
# Line 1618  class LinearPDE(object): Line 1833  class LinearPDE(object):
1833                              escript.Data(),\                              escript.Data(),\
1834                              self.getCoefficientOfGeneralPDE("d_contact"), \                              self.getCoefficientOfGeneralPDE("d_contact"), \
1835                              escript.Data())                              escript.Data())
1836                     self.getDomain().addPDEToSystem(self.__operator,escript.Data(), \
1837                                self.getCoefficientOfGeneralPDE("A_reduced"), \
1838                                self.getCoefficientOfGeneralPDE("B_reduced"), \
1839                                self.getCoefficientOfGeneralPDE("C_reduced"), \
1840                                self.getCoefficientOfGeneralPDE("D_reduced"), \
1841                                escript.Data(), \
1842                                escript.Data(), \
1843                                self.getCoefficientOfGeneralPDE("d_reduced"), \
1844                                escript.Data(),\
1845                                self.getCoefficientOfGeneralPDE("d_contact_reduced"), \
1846                                escript.Data())
1847                   self.__applyConstraint()                   self.__applyConstraint()
1848                   self.trace("New operator has been built.")                   self.trace("New operator has been built.")
1849                   self.__operator_is_Valid=True                   self.__operator_is_Valid=True
# Line 1651  class Poisson(LinearPDE): Line 1877  class Poisson(LinearPDE):
1877       """       """
1878       super(Poisson, self).__init__(domain,1,1,debug)       super(Poisson, self).__init__(domain,1,1,debug)
1879       self.COEFFICIENTS={"f": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),       self.COEFFICIENTS={"f": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1880                            "q": PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH)}                          "f_reduced": PDECoefficient(PDECoefficient.INTERIOR_REDUCED,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1881                            "q": PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH)}
1882       self.setSymmetryOn()       self.setSymmetryOn()
1883    
1884     def setValue(self,**coefficients):     def setValue(self,**coefficients):
# Line 1699  class Poisson(LinearPDE): Line 1926  class Poisson(LinearPDE):
1926           return escript.Data()           return escript.Data()
1927       elif name == "y_contact" :       elif name == "y_contact" :
1928           return escript.Data()           return escript.Data()
1929         elif name == "A_reduced" :
1930             return escript.Data()
1931         elif name == "B_reduced" :
1932             return escript.Data()
1933         elif name == "C_reduced" :
1934             return escript.Data()
1935         elif name == "D_reduced" :
1936             return escript.Data()
1937         elif name == "X_reduced" :
1938             return escript.Data()
1939         elif name == "Y_reduced" :
1940             return self.getCoefficient("f_reduced")
1941         elif name == "d_reduced" :
1942             return escript.Data()
1943         elif name == "y_reduced" :
1944             return escript.Data()
1945         elif name == "d_contact_reduced" :
1946             return escript.Data()
1947         elif name == "y_contact_reduced" :
1948             return escript.Data()
1949       elif name == "r" :       elif name == "r" :
1950           return escript.Data()           return escript.Data()
1951       elif name == "q" :       elif name == "q" :
# Line 1735  class Helmholtz(LinearPDE): Line 1982  class Helmholtz(LinearPDE):
1982       self.COEFFICIENTS={"omega": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.OPERATOR),       self.COEFFICIENTS={"omega": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.OPERATOR),
1983                          "k": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.OPERATOR),                          "k": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.OPERATOR),
1984                          "f": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),                          "f": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1985                            "f_reduced": PDECoefficient(PDECoefficient.INTERIOR_REDUCED,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1986                          "alpha": PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.OPERATOR),                          "alpha": PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.OPERATOR),
1987                          "g": PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),                          "g": PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1988                            "g_reduced": PDECoefficient(PDECoefficient.BOUNDARY_REDUCED,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1989                          "r": PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH),                          "r": PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH),
1990                          "q": PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH)}                          "q": PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH)}
1991       self.setSymmetryOn()       self.setSymmetryOn()
# Line 1798  class Helmholtz(LinearPDE): Line 2047  class Helmholtz(LinearPDE):
2047           return escript.Data()           return escript.Data()
2048       elif name == "y_contact" :       elif name == "y_contact" :
2049           return escript.Data()           return escript.Data()
2050         elif name == "A_reduced" :
2051             return escript.Data()
2052         elif name == "B_reduced" :
2053             return escript.Data()
2054         elif name == "C_reduced" :
2055             return escript.Data()
2056         elif name == "D_reduced" :
2057             return escript.Data()
2058         elif name == "X_reduced" :
2059             return escript.Data()
2060         elif name == "Y_reduced" :
2061             return self.getCoefficient("f_reduced")
2062         elif name == "d_reduced" :
2063             return escript.Data()
2064         elif name == "y_reduced" :
2065            return self.getCoefficient("g_reduced")
2066         elif name == "d_contact_reduced" :
2067             return escript.Data()
2068         elif name == "y_contact_reduced" :
2069             return escript.Data()
2070       elif name == "r" :       elif name == "r" :
2071           return self.getCoefficient("r")           return self.getCoefficient("r")
2072       elif name == "q" :       elif name == "q" :
# Line 1896  class LameEquation(LinearPDE): Line 2165  class LameEquation(LinearPDE):
2165           return escript.Data()           return escript.Data()
2166       elif name == "y_contact" :       elif name == "y_contact" :
2167           return escript.Data()           return escript.Data()
2168         elif name == "A_reduced" :
2169             return escript.Data()
2170         elif name == "B_reduced" :
2171             return escript.Data()
2172         elif name == "C_reduced" :
2173             return escript.Data()
2174         elif name == "D_reduced" :
2175             return escript.Data()
2176         elif name == "X_reduced" :
2177             return escript.Data()
2178         elif name == "Y_reduced" :
2179             return escript.Data()
2180         elif name == "d_reduced" :
2181             return escript.Data()
2182         elif name == "y_reduced" :
2183             return escript.Data()
2184         elif name == "d_contact_reduced" :
2185             return escript.Data()
2186         elif name == "y_contact_reduced" :
2187             return escript.Data()
2188       elif name == "r" :       elif name == "r" :
2189           return self.getCoefficient("r")           return self.getCoefficient("r")
2190       elif name == "q" :       elif name == "q" :
# Line 1903  class LameEquation(LinearPDE): Line 2192  class LameEquation(LinearPDE):
2192       else:       else:
2193          raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name          raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
2194    
2195  class AdvectivePDE(LinearPDE):  def LinearSinglePDE(domain,debug=False):
2196     """     """
2197     In cases of PDEs dominated by the advection terms M{B} and M{C} against the adevctive terms M{A}     defines a single linear PDEs
    up-winding has been used.  The L{AdvectivePDE} class applies SUPG upwinding to the advective terms.  
   
    In the following we set  
   
    M{Z[j]=C[j]-B[j]}  
   
    or  
   
    M{Z[i,k,l]=C[i,k,l]-B[i,l,k]}  
   
    To measure the dominance of the advective terms over the diffusive term M{A} the  
    X{Pelclet number} M{P} is used. It is defined as  
   
    M{P=h|Z|/(2|A|)}  
   
    where M{|.|} denotes the L{length<util.length>} of the arument and M{h} is the local cell size  
    from L{getSize<escript.Domain.getSize>}. Where M{|A|==0} M{P} is M{S{infinity}}.  
   
    From the X{Pelclet number} the stabilization parameters M{S{Xi}} and M{S{Xi}} are calculated:  
   
    M{S{Xi}=S{xi}(P) h/|Z|}  
   
    where M{S{xi}} is a suitable function of the Peclet number.  
   
    In the case of a single PDE the coefficient are up-dated in the following way:  
          - M{A[i,j] S{<-} A[i,j] + S{Xi} * Z[j] * Z[l]}  
          - M{B[j] S{<-} B[j] + S{Xi} * C[j] * D}  
          - M{C[j] S{<-} C[j] + S{Xi} * B[j] * D}  
          - M{X[j] S{<-} X[j] + S{Xi} * Z[j] * Y}  
   
    Similar for the case of a systems of PDEs:  
          - M{A[i,j,k,l] S{<-} A[i,j,k,l]+ S{delta}[p,m] * S{Xi} * Z[p,i,j] * Z[m,k,l]}  
          - M{B[i,j,k] S{<-} B[i,j,k] +  S{delta}[p,m] * S{Xi} * D[p,k] * C[m,i,j]}  
          - M{C[i,k,l] S{<-} C[i,k,l] +  S{delta}[p,m] * S{Xi} * D[p,k] * B[m,l,i]}  
          - M{X[i,j] S{<-} X[i,j] + S{delta}[p,m] * S{Xi}  * Y[p] * Z[m,i,j]}  
   
    where M{S{delta}} is L{kronecker}.  
    Using upwinding in this form, introduces an additonal error which is proprtional to the cell size M{h}  
    but with the intension to stabilize the solution.  
2198    
2199       @param domain: domain of the PDE
2200       @type domain: L{Domain<escript.Domain>}
2201       @param debug: if True debug informations are printed.
2202       @rtype: L{LinearPDE}
2203     """     """
2204     def __init__(self,domain,numEquations=None,numSolutions=None,xi=None,debug=False):     return LinearPDE(domain,numEquations=1,numSolutions=1,debug=debug)
       """  
       creates a linear, steady, second order PDE on a L{Domain<escript.Domain>}  
   
       @param domain: domain of the PDE  
       @type domain: L{Domain<escript.Domain>}  
       @param numEquations: number of equations. If numEquations==None the number of equations  
                            is exracted from the PDE coefficients.  
       @param numSolutions: number of solution components. If  numSolutions==None the number of solution components  
                            is exracted from the PDE coefficients.  
       @param xi: defines a function which returns for any given Preclet number as L{Scalar<escript.Scalar>} object the  
                  M{S{xi}}-value used to define the stabilization parameters. If equal to None, L{ELMAN_RAMAGE} is used.  
       @type xi: callable object which returns a L{Scalar<escript.Scalar>} object.  
       @param debug: if True debug informations are printed.  
       """  
       super(AdvectivePDE, self).__init__(domain,\  
                                          numEquations,numSolutions,debug)  
       if xi==None:  
          self.__xi=AdvectivePDE.ELMAN_RAMAGE  
       else:  
          self.__xi=xi  
       self.__Xi=escript.Data()  
   
    def setValue(self,**coefficients):  
       """  
       sets new values to coefficients  
2205    
2206        @param coefficients: new values assigned to coefficients  def LinearPDESystem(domain,debug=False):
2207        @keyword A: value for coefficient A.     """
2208        @type A: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.     defines a system of linear PDEs
       @keyword B: value for coefficient B  
       @type B: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.  
       @keyword C: value for coefficient C  
       @type C: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.  
       @keyword D: value for coefficient D  
       @type D: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.  
       @keyword X: value for coefficient X  
       @type X: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.  
       @keyword Y: value for coefficient Y  
       @type Y: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.  
       @keyword d: value for coefficient d  
       @type d: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.  
       @keyword y: value for coefficient y  
       @type y: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.  
       @keyword d_contact: value for coefficient d_contact  
       @type d_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>}.  
                        or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.  
       @keyword y_contact: value for coefficient y_contact  
       @type y_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>}.  
                        or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.  
       @keyword r: values prescribed to the solution at the locations of constraints  
       @type r: any type that can be casted to L{Data<escript.Data>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}  
                depending of reduced order is used for the solution.  
       @keyword q: mask for location of constraints  
       @type q: any type that can be casted to L{Data<escript.Data>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}  
                depending of reduced order is used for the representation of the equation.  
       @raise IllegalCoefficient: if an unknown coefficient keyword is used.  
2209    
2210        """     @param domain: domain of the PDE
2211        if "A" in coefficients.keys()   or "B" in coefficients.keys() or "C" in coefficients.keys(): self.__Xi=escript.Data()     @type domain: L{Domain<escript.Domain>}
2212        super(AdvectivePDE, self).setValue(**coefficients)     @param debug: if True debug informations are printed.
2213       @rtype: L{LinearPDE}
2214       """
2215       return LinearPDE(domain,numEquations=domain.getDim(),numSolutions=domain.getDim(),debug=debug)
2216    
2217     def ELMAN_RAMAGE(self,P):  class TransportPDE(object):
2218       """       """
2219       Predefined function to set a values for M{S{xi}} from a Preclet number M{P}.       Warning: This is still a very experimental. The class is still changing!
      This function uses the method suggested by H.C. Elman and A. Ramage, I{SIAM J. Numer. Anal.}, B{40} (2002)  
           - M{S{xi}(P)=0} for M{P<1}  
           - M{S{xi}(P)=(1-1/P)/2} otherwise  
   
      @param P: Preclet number  
      @type P: L{Scalar<escript.Scalar>}  
      @return: up-wind weightimg factor  
      @rtype: L{Scalar<escript.Scalar>}  
      """  
      return util.wherePositive(P-1.)*0.5*(1.-1./(P+1.e-15))  
   
    def SIMPLIFIED_BROOK_HUGHES(self,P):  
      """  
      Predefined function to set a values for M{S{xi}} from a Preclet number M{P}.  
      The original methods is  
   
      M{S{xi}(P)=coth(P)-1/P}  
   
      As the evaluation of M{coth} is expensive we are using the approximation:  
   
          - M{S{xi}(P)=P/3} where M{P<3}  
          - M{S{xi}(P)=1/2} otherwise  
   
      @param P: Preclet number  
      @type P: L{Scalar<escript.Scalar>}  
      @return: up-wind weightimg factor  
      @rtype: L{Scalar<escript.Scalar>}  
      """  
      c=util.whereNegative(P-3.)  
      return P/6.*c+1./2.*(1.-c)  
   
    def HALF(self,P):  
      """  
      Predefined function to set value M{1/2} for M{S{xi}}  
   
      @param P: Preclet number  
      @type P: L{Scalar<escript.Scalar>}  
      @return: up-wind weightimg factor  
      @rtype: L{Scalar<escript.Scalar>}  
      """  
      return escript.Scalar(0.5,P.getFunctionSpace())  
   
    def __getXi(self):  
       if self.__Xi.isEmpty():  
          B=self.getCoefficient("B")  
          C=self.getCoefficient("C")  
          A=self.getCoefficient("A")  
          h=self.getDomain().getSize()  
          self.__Xi=escript.Scalar(0.,self.getFunctionSpaceForCoefficient("A"))  
          if not C.isEmpty() or not B.isEmpty():  
             if not C.isEmpty() and not B.isEmpty():  
                 if self.getNumEquations()>1:  
                    if self.getNumSolutions()>1:  
                       flux2=escript.Scalar(0,self.getFunctionSpaceForCoefficient("A"))  
                       for i in range(self.getNumEquations()):  
                          for k in range(self.getNumSolutions()):  
                             for l in range(self.getDim()): flux2+=(C[i,k,l]-B[i,l,k])**2  
                       length_of_flux=util.sqrt(flux2)  
                       # flux=C-util.reorderComponents(B,[0,2,1])  
                    else:  
                       flux2=escript.Scalar(0,self.getFunctionSpaceForCoefficient("A"))  
                       for i in range(self.getNumEquations()):  
                          for l in range(self.getDim()): flux2+=(C[i,l]-B[i,l])**2  
                       length_of_flux=util.sqrt(flux2)  
                       # flux=C-B  
                 else:  
                    if self.getNumSolutions()>1:  
                       flux2=escript.Scalar(0,self.getFunctionSpaceForCoefficient("A"))  
                       for k in range(self.getNumSolutions()):  
                          for l in range(self.getDim()): flux2+=(C[k,l]-B[l,k])**2  
                       # flux=C-util.reorderComponents(B,[1,0])  
                       length_of_flux=util.sqrt(flux2)  
                    else:  
                       length_of_flux=util.length(C-B)  
             elif C.isEmpty():  
               length_of_flux=util.length(B)  
             else:  
               length_of_flux=util.length(C)  
             flux_max=util.Lsup(length_of_flux)  
             if flux_max>0.:  
               if A.isEmpty():  
                   inv_A=1./self.SMALL_TOLERANCE  
                   peclet_number=escript.Scalar(inv_A,length_of_flux.getFunctionSpace())  
                   xi=self.__xi(self,peclet_number)  
               else:  
                   # length_of_A=util.inner(flux,util.tensormutiply(A,flux))  
                   length_of_A=util.length(A)  
                   A_max=util.Lsup(length_of_A)  
                   if A_max>0:  
                        inv_A=1./(length_of_A+A_max*self.SMALL_TOLERANCE)  
                   else:  
                        inv_A=1./self.SMALL_TOLERANCE  
                   peclet_number=length_of_flux*h/2*inv_A  
                   xi=self.__xi(self,peclet_number)  
               self.__Xi=h*xi/(length_of_flux+flux_max*self.SMALL_TOLERANCE)  
               self.trace("preclet number = %e"%util.Lsup(peclet_number))  
             else:  
               self.__Xi=escript.Scalar(0.,length_of_flux.getFunctionSpace())  
       return self.__Xi  
2220    
2221         Mu_{,t} =-(A_{ij}u_{,j})_j-(B_{j}u)_{,j} + C_{j} u_{,j} + Y_i + X_{i,i}
2222        
2223         u=r where q>0
2224        
2225         all coefficients are constant over time.
2226    
2227         typical usage:
2228    
2229             p=TransportPDE(dom)
2230             p.setValue(M=Scalar(1.,Function(dom),C=Scalar(1.,Function(dom)*[-1.,0.])
2231             p.setInitialSolution(u=exp(-length(dom.getX()-[0.1,0.1])**2)
2232             t=0
2233             dt=0.1
2234             while (t<1.):
2235                  u=p.solve(dt)
2236    
2237         """
2238         def __init__(self,domain,num_equations=1,theta=0.5,useSUPG=False,trace=True):
2239            self.__domain=domain
2240            self.__num_equations=num_equations
2241            self.__useSUPG=useSUPG
2242            self.__trace=trace
2243            self.__theta=theta
2244            self.__matrix_type=0
2245            self.__reduced=True
2246            self.__reassemble=True
2247            if self.__useSUPG:
2248               self.__pde=LinearPDE(domain,numEquations=num_equations,numSolutions=num_equations,debug=trace)
2249               self.__pde.setSymmetryOn()
2250               self.__pde.setReducedOrderOn()
2251            else:
2252               self.__transport_problem=self.__getNewTransportProblem()
2253            self.setTolerance()
2254            self.__M=escript.Data()
2255            self.__A=escript.Data()
2256            self.__B=escript.Data()
2257            self.__C=escript.Data()
2258            self.__D=escript.Data()
2259            self.__X=escript.Data()
2260            self.__Y=escript.Data()
2261            self.__d=escript.Data()
2262            self.__y=escript.Data()
2263            self.__d_contact=escript.Data()
2264            self.__y_contact=escript.Data()
2265            self.__r=escript.Data()
2266            self.__q=escript.Data()
2267    
2268         def trace(self,text):
2269                 if self.__trace: print text
2270         def getSafeTimeStepSize(self):
2271            if self.__useSUPG:
2272                if self.__reassemble:
2273                   h=self.__domain.getSize()
2274                   dt=None
2275                   if not self.__A.isEmpty():
2276                      dt2=util.inf(h**2*self.__M/util.length(self.__A))
2277                      if dt == None:
2278                         dt = dt2
2279                      else:
2280                         dt=1./(1./dt+1./dt2)
2281                   if not self.__B.isEmpty():
2282                      dt2=util.inf(h*self.__M/util.length(self.__B))
2283                      if dt == None:
2284                         dt = dt2
2285                      else:
2286                         dt=1./(1./dt+1./dt2)
2287                   if not  self.__C.isEmpty():
2288                      dt2=util.inf(h*self.__M/util.length(self.__C))
2289                      if dt == None:
2290                         dt = dt2
2291                      else:
2292                         dt=1./(1./dt+1./dt2)
2293                   if not self.__D.isEmpty():
2294                      dt2=util.inf(self.__M/util.length(self.__D))
2295                      if dt == None:
2296                         dt = dt2
2297                      else:
2298                         dt=1./(1./dt+1./dt2)
2299                   self.__dt = dt/2
2300                return self.__dt
2301            else:
2302                return self.__getTransportProblem().getSafeTimeStepSize()
2303         def getDomain(self):
2304            return self.__domain
2305         def getTheta(self):
2306            return self.__theta
2307         def getNumEquations(self):
2308            return self.__num_equations
2309         def setReducedOn(self):
2310              if not self.reduced():
2311                  if self.__useSUPG:
2312                     self.__pde.setReducedOrderOn()
2313                  else:
2314                     self.__transport_problem=self.__getNewTransportProblem()
2315              self.__reduced=True
2316         def setReducedOff(self):
2317              if self.reduced():
2318                  if self.__useSUPG:
2319                     self.__pde.setReducedOrderOff()
2320                  else:
2321                     self.__transport_problem=self.__getNewTransportProblem()
2322              self.__reduced=False
2323         def reduced(self):
2324             return self.__reduced
2325         def getFunctionSpace(self):
2326            if self.reduced():
2327               return escript.ReducedSolution(self.getDomain())
2328            else:
2329               return escript.Solution(self.getDomain())
2330    
2331     def getCoefficientOfGeneralPDE(self,name):       def setTolerance(self,tol=1.e-8):
2332       """          self.__tolerance=tol
2333       return the value of the coefficient name of the general PDE          if self.__useSUPG:
2334                  self.__pde.setTolerance(self.__tolerance)
2335    
2336       @param name: name of the coefficient requested.       def __getNewTransportProblem(self):
2337       @type name: C{string}         """
2338       @return: the value of the coefficient name         returns an instance of a new operator
2339       @rtype: L{Data<escript.Data>}         """
2340       @raise IllegalCoefficient: if name is not one of coefficients         self.trace("New Transport problem is allocated.")
2341                    M{A}, M{B}, M{C}, M{D}, M{X}, M{Y}, M{d}, M{y}, M{d_contact}, M{y_contact}, M{r} or M{q}.         return self.getDomain().newTransportProblem( \
2342       @note: This method is called by the assembling routine to map the Possion equation onto the general PDE.                                 self.getTheta(),
2343       """                                 self.getNumEquations(), \
2344       if not self.getNumEquations() == self.getNumSolutions():                                 self.getFunctionSpace(), \
2345            raise ValueError,"AdvectivePDE expects the number of solution componets and the number of equations to be equal."                                 self.__matrix_type)
2346              
2347       if name == "A" :       def __getNewSolutionVector(self):
2348           A=self.getCoefficient("A")           if self.getNumEquations() ==1 :
2349           B=self.getCoefficient("B")                  out=escript.Data(0.0,(),self.getFunctionSpace())
          C=self.getCoefficient("C")  
          if B.isEmpty() and C.isEmpty():  
             Aout=A  
          else:  
             if A.isEmpty():  
                Aout=self.createCoefficientOfGeneralPDE("A")  
             else:  
                Aout=A[:]  
             Xi=self.__getXi()  
             if self.getNumEquations()>1:  
                 for i in range(self.getNumEquations()):  
                    for j in range(self.getDim()):  
                       for k in range(self.getNumSolutions()):  
                          for l in range(self.getDim()):  
                             if not C.isEmpty() and not B.isEmpty():  
                                # tmp=C-util.reorderComponents(B,[0,2,1])  
                                # Aout=Aout+Xi*util.generalTensorProduct(util.reorder(tmp,[1,2,0]),tmp,offset=1)  
                                for p in range(self.getNumEquations()): Aout[i,j,k,l]+=Xi*(C[p,i,j]-B[p,j,i])*(C[p,k,l]-B[p,l,k])  
                             elif C.isEmpty():  
                                for p in range(self.getNumEquations()): Aout[i,j,k,l]+=Xi*B[p,j,i]*B[p,l,k]  
                                # Aout=Aout+Xi*util.generalTensorProduct(util.reorder(B,[2,1,0]),util.reorder(B,[0,2,1]),offset=1)  
                             else:  
                                for p in range(self.getNumEquations()): Aout[i,j,k,l]+=Xi*C[p,i,j]*C[p,k,l]  
                                # Aout=Aout+Xi*util.generalTensorProduct(util.reorder(C,[1,2,0]),C,offset=1)  
             else:  
                if not C.isEmpty() and not B.isEmpty():  
                    delta=(C-B)  
                    Aout+=util.outer(Xi*delta,delta)  
                elif not B.isEmpty():  
                    Aout+=util.outer(Xi*B,B)  
                elif not C.isEmpty():  
                    Aout+=util.outer(Xi*C,C)  
          return Aout  
      elif name == "B" :  
          # return self.getCoefficient("B")  
          B=self.getCoefficient("B")  
          C=self.getCoefficient("C")  
          D=self.getCoefficient("D")  
          if C.isEmpty() or D.isEmpty():  
             Bout=B  
          else:  
             Xi=self.__getXi()  
             if B.isEmpty():  
                 Bout=self.createCoefficientOfGeneralPDE("B")  
             else:  
                 Bout=B[:]  
             if self.getNumEquations()>1:  
                for k in range(self.getNumSolutions()):  
                   for p in range(self.getNumEquations()):  
                      tmp=Xi*D[p,k]  
                      for i in range(self.getNumEquations()):  
                         for j in range(self.getDim()):  
                            Bout[i,j,k]+=tmp*C[p,i,j]  
                            # Bout=Bout+Xi*util.generalTensorProduct(util.reorder(C,[1,2,0]),D,offset=1)  
             else:  
                Bout+=(Xi*D)*C  
          return Bout  
      elif name == "C" :  
          # return self.getCoefficient("C")  
          B=self.getCoefficient("B")  
          C=self.getCoefficient("C")  
          D=self.getCoefficient("D")  
          if B.isEmpty() or D.isEmpty():  
             Cout=C  
          else:  
             Xi=self.__getXi()  
             if C.isEmpty():  
                 Cout=self.createCoefficientOfGeneralPDE("C")  
             else:  
                 Cout=C[:]  
             if self.getNumEquations()>1:  
                for k in range(self.getNumSolutions()):  
                    for p in range(self.getNumEquations()):  
                       tmp=Xi*D[p,k]  
                       for i in range(self.getNumEquations()):  
                         for l in range(self.getDim()):  
                                  Cout[i,k,l]+=tmp*B[p,l,i]  
                                  # Cout=Cout+Xi*B[p,l,i]*D[p,k]  
             else:  
                Cout+=(Xi*D)*B  
          return Cout  
      elif name == "D" :  
          return self.getCoefficient("D")  
      elif name == "X" :  
          # return self.getCoefficient("X")  
          X=self.getCoefficient("X")  
          Y=self.getCoefficient("Y")  
          B=self.getCoefficient("B")  
          C=self.getCoefficient("C")  
          if Y.isEmpty() or (B.isEmpty() and C.isEmpty()):  
             Xout=X  
2350           else:           else:
2351              if X.isEmpty():                  out=escript.Data(0.0,(self.getNumEquations(),),self.getFunctionSpace())
2352                  Xout=self.createCoefficientOfGeneralPDE("X")           return out
             else:  
                 Xout=X[:]  
             Xi=self.__getXi()  
             if self.getNumEquations()>1:  
                  for p in range(self.getNumEquations()):  
                     tmp=Xi*Y[p]  
                     for i in range(self.getNumEquations()):  
                        for j in range(self.getDim()):  
                           if not C.isEmpty() and not B.isEmpty():  
                              Xout[i,j]+=tmp*(C[p,i,j]-B[p,j,i])  
                              # Xout=X_out+Xi*util.inner(Y,C-util.reorderComponents(B,[0,2,1]),offset=1)  
                           elif C.isEmpty():  
                              Xout[i,j]-=tmp*B[p,j,i]  
                              # Xout=X_out-Xi*util.inner(Y,util.reorderComponents(B,[0,2,1]),offset=1)  
                           else:  
                              Xout[i,j]+=tmp*C[p,i,j]  
                              # Xout=X_out+Xi*util.inner(Y,C,offset=1)  
             else:  
               if not C.isEmpty() and not B.isEmpty():  
                 Xout+=(Xi*Y)*(C-B)  
               elif C.isEmpty():  
                 Xout-=(Xi*Y)*B  
               else:  
                 Xout+=(Xi*Y)*C  
          return Xout  
      elif name == "Y" :  
          return self.getCoefficient("Y")  
      elif name == "d" :  
          return self.getCoefficient("d")  
      elif name == "y" :  
          return self.getCoefficient("y")  
      elif name == "d_contact" :  
          return self.getCoefficient("d_contact")  
      elif name == "y_contact" :  
          return self.getCoefficient("y_contact")  
      elif name == "r" :  
          return self.getCoefficient("r")  
      elif name == "q" :  
          return self.getCoefficient("q")  
      else:  
         raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name  
2353    
2354  # $Log$       def __getTransportProblem(self):
2355  # Revision 1.14  2005/09/22 01:54:57  jgs         if self.__reassemble:
2356  # Merge of development branch dev-02 back to main trunk on 2005-09-22               self.__source=self.__getNewSolutionVector()
2357  #               self.__transport_problem.reset()
2358  # Revision 1.13  2005/09/15 03:44:19  jgs               self.getDomain().addPDEToTransportProblem(
2359  # Merge of development branch dev-02 back to main trunk on 2005-09-15                           self.__transport_problem,
2360  #                           self.__source,
2361  # Revision 1.12  2005/09/01 03:31:28  jgs                           self.__M,
2362  # Merge of development branch dev-02 back to main trunk on 2005-09-01                           self.__A,
2363  #                           self.__B,
2364  # Revision 1.11  2005/08/23 01:24:28  jgs                           self.__C,
2365  # Merge of development branch dev-02 back to main trunk on 2005-08-23                           self.__D,
2366  #                           self.__X,
2367  # Revision 1.10  2005/08/12 01:45:36  jgs                           self.__Y,
2368  # erge of development branch dev-02 back to main trunk on 2005-08-12                           self.__d,
2369  #                           self.__y,
2370  # Revision 1.9.2.17  2005/09/21 07:03:33  matt                           self.__d_contact,
2371  # PDECoefficient and LinearPDE are now new style classes (introduced in Python                           self.__y_contact)
2372  # 2.2). Classes Poisson, Helmholtz, LameEquation and AdvectivePDE have been               self.__transport_problem.insertConstraint(self.__source,self.__q,self.__r)
2373  # modified to instead use portable/cooperative "super" calls to extend base               self.__reassemble=False
2374  # class methods.         return self.__transport_problem
2375  #       def setValue(self,M=None, A=None, B=None, C=None, D=None, X=None, Y=None,
2376  # Revision 1.9.2.16  2005/09/16 01:54:37  matt                    d=None, y=None, d_contact=None, y_contact=None, q=None, r=None):
2377  # Removed redundant if-loop.               if not M==None:
2378  #                    self.__reassemble=True
2379  # Revision 1.9.2.15  2005/09/14 08:09:18  matt                    self.__M=M
2380  # Added "REDUCED" solution PDECoefficient descriptors for LinearPDEs.               if not A==None:
2381  #                    self.__reassemble=True
2382  # Revision 1.9.2.14  2005/09/07 06:26:16  gross                    self.__A=A
2383  # the solver from finley are put into the standalone package paso now               if not B==None:
2384  #                    self.__reassemble=True
2385  # Revision 1.9.2.13  2005/08/31 08:45:03  gross                    self.__B=B
2386  # in the case of lumping no new system is allocated if the constraint is changed.               if not C==None:
2387  #                    self.__reassemble=True
2388  # Revision 1.9.2.12  2005/08/31 07:10:23  gross                    self.__C=C
2389  # test for Lumping added               if not D==None:
2390  #                    self.__reassemble=True
2391  # Revision 1.9.2.11  2005/08/30 01:53:45  gross                    self.__D=D
2392  # bug in format fixed.               if not X==None:
2393  #                    self.__reassemble=True
2394  # Revision 1.9.2.10  2005/08/26 07:14:17  gross                    self.__X=X
2395  # a few more bugs in linearPDE fixed. remaining problem are finley problems               if not Y==None:
2396  #                    self.__reassemble=True
2397  # Revision 1.9.2.9  2005/08/26 06:30:45  gross                    self.__Y=Y
2398  # fix for reported bug  0000004. test_linearPDE passes a few more tests               if not d==None:
2399  #                    self.__reassemble=True
2400  # Revision 1.9.2.8  2005/08/26 04:30:13  gross                    self.__d=d
2401  # gneric unit testing for linearPDE               if not y==None:
2402  #                    self.__reassemble=True
2403  # Revision 1.9.2.7  2005/08/25 07:06:50  gross                    self.__y=y
2404  # linearPDE documentation is parsed now by epydoc. there is still a problem with links into escriptcpp.so               if not d_contact==None:
2405  #                    self.__reassemble=True
2406  # Revision 1.9.2.6  2005/08/24 05:01:24  gross                    self.__d_contact=d_contact
2407  # problem with resetting the matrix in case of resetting its values to 0 fixed.               if not y_contact==None:
2408  #                    self.__reassemble=True
2409  # Revision 1.9.2.5  2005/08/24 02:03:28  gross                    self.__y_contact=y_contact
2410  # epydoc mark up partially fixed               if not q==None:
2411  #                    self.__reassemble=True
2412  # Revision 1.9.2.4  2005/08/22 07:11:09  gross                    self.__q=q
2413  # some problems with LinearPDEs fixed.               if not r==None:
2414  #                    self.__reassemble=True
2415  # Revision 1.9.2.3  2005/08/18 04:48:48  gross                    self.__r=r
2416  # the methods SetLumping*() are removed. Lumping is set trough setSolverMethod(LinearPDE.LUMPING)  
2417  #       def setInitialSolution(self,u):
2418  # Revision 1.9.2.2  2005/08/18 04:39:32  gross               if self.__useSUPG:
2419  # the constants have been removed from util.py as they not needed anymore. PDE related constants are accessed through LinearPDE attributes now                   self.__u=util.interpolate(u,self.getFunctionSpace())
2420  #               else:
2421  # Revision 1.9.2.1  2005/07/29 07:10:27  gross                   self.__transport_problem.setInitialValue(util.interpolate(u,self.getFunctionSpace()))
2422  # new functions in util and a new pde type in linearPDEs  
2423  #       def solve(self,dt,**kwarg):
2424  # Revision 1.1.2.25  2005/07/28 04:21:09  gross             if self.__useSUPG:
2425  # Lame equation: (linear elastic, isotropic) added                  if self.__reassemble:
2426  #                      self.__pde.setValue(D=self.__M,d=self.__d,d_contact=self.__d_contact,q=self.__q) # ,r=self.__r)
2427  # Revision 1.1.2.24  2005/07/22 06:37:11  gross                      self.__reassemble=False
2428  # some extensions to modellib and linearPDEs                  dt2=self.getSafeTimeStepSize()
2429  #                  nn=max(math.ceil(dt/self.getSafeTimeStepSize()),1.)
2430  # Revision 1.1.2.23  2005/05/13 00:55:20  cochrane                  dt2=dt/nn
2431  # Fixed up some docstrings.  Moved module-level functions to top of file so                  nnn=0
2432  # that epydoc and doxygen can pick them up properly.                  u=self.__u
2433  #                  self.trace("number of substeps is %d."%nn)
2434  # Revision 1.1.2.22  2005/05/12 11:41:30  gross                  while nnn<nn :
2435  # some basic Models have been added                      self.__setSUPG(u,u,dt2/2)
2436  #                      u_half=self.__pde.getSolution(verbose=True)
2437  # Revision 1.1.2.21  2005/05/12 07:16:12  cochrane                      self.__setSUPG(u,u_half,dt2)
2438  # Moved ELMAN_RAMAGE, SIMPLIFIED_BROOK_HUGHES, and HALF functions to bottom of                      u=self.__pde.getSolution(verbose=True)
2439  # file so that the AdvectivePDE class is picked up by doxygen.  Some                      nnn+=1
2440  # reformatting of docstrings.  Addition of code to make equations come out                  self.__u=u
2441  # as proper LaTeX.                  return self.__u
2442  #             else:
2443  # Revision 1.1.2.20  2005/04/15 07:09:08  gross                 kwarg["tolerance"]=self.__tolerance
2444  # some problems with functionspace and linearPDEs fixed.                 tp=self.__getTransportProblem()
2445  #                 return tp.solve(self.__source,dt,kwarg)
2446  # Revision 1.1.2.19  2005/03/04 05:27:07  gross       def __setSUPG(self,u0,u,dt):
2447  # bug in SystemPattern fixed.              g=util.grad(u)
2448  #              X=0
2449  # Revision 1.1.2.18  2005/02/08 06:16:45  gross              Y=self.__M*u0
2450  # Bugs in AdvectivePDE fixed, AdvectiveTest is stable but more testing is needed              X=0
2451  #              self.__pde.setValue(r=u0)
2452  # Revision 1.1.2.17  2005/02/08 05:56:19  gross              if not self.__A.isEmpty():
2453  # Reference Number handling added                 X=X+dt*util.matrixmult(self.__A,g)
2454  #              if not self.__B.isEmpty():
2455  # Revision 1.1.2.16  2005/02/07 04:41:28  gross                 X=X+dt*self.__B*u
2456  # some function exposed to python to make mesh merging running              if not  self.__C.isEmpty():
2457  #                 Y=Y+dt*util.inner(self.__C,g)
2458  # Revision 1.1.2.15  2005/02/03 00:14:44  gross              if not self.__D.isEmpty():
2459  # timeseries add and ESySParameter.py renames esysXML.py for consistence                 Y=Y+dt*self.__D*u
2460  #              if not self.__X.isEmpty():
2461  # Revision 1.1.2.14  2005/02/01 06:44:10  gross                 X=X+dt*self.__X
2462  # new implementation of AdvectivePDE which now also updates right hand side. systems of PDEs are still not working              if not self.__Y.isEmpty():
2463  #                 Y=Y+dt*self.__Y
2464  # Revision 1.1.2.13  2005/01/25 00:47:07  gross              self.__pde.setValue(X=X,Y=Y)
2465  # updates in the documentation              if not self.__y.isEmpty():
2466  #                 self.__pde.setValue(y=dt*self.__y)
2467  # Revision 1.1.2.12  2005/01/12 01:28:04  matt              if not self.__y_contact.isEmpty():
2468  # Added createCoefficient method for linearPDEs.                 self.__pde.setValue(y=dt*self.__y_contact)
2469  #              self.__pde.setValue(r=u0)
 # Revision 1.1.2.11  2005/01/11 01:55:34  gross  
 # a problem in linearPDE class fixed  
 #  
 # Revision 1.1.2.10  2005/01/07 01:13:29  gross  
 # some bugs in linearPDE fixed  
 #  
 # Revision 1.1.2.9  2005/01/06 06:24:58  gross  
 # some bugs in slicing fixed  
 #  
 # Revision 1.1.2.8  2005/01/05 04:21:40  gross  
 # FunctionSpace checking/matchig in slicing added  
 #  
 # Revision 1.1.2.7  2004/12/29 10:03:41  gross  
 # bug in setValue fixed  
 #  
 # Revision 1.1.2.6  2004/12/29 05:29:59  gross  
 # AdvectivePDE successfully tested for Peclet number 1000000. there is still a problem with setValue and Data()  
 #  
 # Revision 1.1.2.5  2004/12/29 00:18:41  gross  
 # AdvectivePDE added  
 #  
 # Revision 1.1.2.4  2004/12/24 06:05:41  gross  
 # some changes in linearPDEs to add AdevectivePDE  
 #  
 # Revision 1.1.2.3  2004/12/16 00:12:34  gross  
 # __init__ of LinearPDE does not accept any coefficient anymore  
 #  
 # Revision 1.1.2.2  2004/12/14 03:55:01  jgs  
 # *** empty log message ***  
 #  
 # Revision 1.1.2.1  2004/12/12 22:53:47  gross  
 # linearPDE has been renamed LinearPDE  
 #  
 # Revision 1.1.1.1.2.7  2004/12/07 10:13:08  gross  
 # GMRES added  
 #  
 # Revision 1.1.1.1.2.6  2004/12/07 03:19:50  gross  
 # options for GMRES and PRES20 added  
 #  
 # Revision 1.1.1.1.2.5  2004/12/01 06:25:15  gross  
 # some small changes  
 #  
 # Revision 1.1.1.1.2.4  2004/11/24 01:50:21  gross  
 # Finley solves 4M unknowns now  
 #  
 # Revision 1.1.1.1.2.3  2004/11/15 06:05:26  gross  
 # poisson solver added  
 #  
 # Revision 1.1.1.1.2.2  2004/11/12 06:58:15  gross  
 # a lot of changes to get the linearPDE class running: most important change is that there is no matrix format exposed to the user anymore. the format is chosen by the Domain according to the solver and symmetry  
 #  
 # Revision 1.1.1.1.2.1  2004/10/28 22:59:22  gross  
 # finley's RecTest.py is running now: problem in SystemMatrixAdapater fixed  
 #  
 # Revision 1.1.1.1  2004/10/26 06:53:56  jgs  
 # initial import of project esys2  
 #  
 # Revision 1.3.2.3  2004/10/26 06:43:48  jgs  
 # committing Lutz's and Paul's changes to brach jgs  
 #  
 # Revision 1.3.4.1  2004/10/20 05:32:51  cochrane  
 # Added incomplete Doxygen comments to files, or merely put the docstrings that already exist into Doxygen form.  
 #  
 # Revision 1.3  2004/09/23 00:53:23  jgs  
 # minor fixes  
 #  
 # Revision 1.1  2004/08/28 12:58:06  gross  
 # SimpleSolve is not running yet: problem with == of functionsspace  
 #  

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