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trunk/esys2/escript/py_src/linearPDEs.py revision 104 by jgs, Fri Dec 17 07:43:12 2004 UTC trunk/escript/py_src/linearPDEs.py revision 304 by gross, Fri Dec 2 06:04:06 2005 UTC
# Line 1  Line 1 
1  # $Id$  # $Id$
2    
3  ## @file linearPDEs.py  #
4    #      COPYRIGHT ACcESS 2004 -  All Rights Reserved
5    #
6    #   This software is the property of ACcESS.  No part of this code
7    #   may be copied in any form or by any means without the expressed written
8    #   consent of ACcESS.  Copying, use or modification of this software
9    #   by any unauthorised person is illegal unless that
10    #   person has a software license agreement with ACcESS.
11    #
12  """  """
13  @brief Functions and classes for linear PDEs  The module provides an interface to define and solve linear partial
14    differential equations (PDEs) within L{escript}. L{linearPDEs} does not provide any
15    solver capabilities in itself but hands the PDE over to
16    the PDE solver library defined through the L{Domain<escript.Domain>} of the PDE.
17    The general interface is provided through the L{LinearPDE} class. The
18    L{AdvectivePDE} which is derived from the L{LinearPDE} class
19    provides an interface to PDE dominated by its advective terms. The L{Poisson},
20    L{Helmholtz}, L{LameEquation}
21    classs which are also derived form the L{LinearPDE} class should be used
22    to define of solve these sepecial PDEs.
23    
24    @var __author__: name of author
25    @var __licence__: licence agreement
26    @var __url__: url entry point on documentation
27    @var __version__: version
28    @var __date__: date of the version
29  """  """
30    
31  import escript  import escript
32  import util  import util
33  import numarray  import numarray
34    
35  def identifyDomain(domain=None,data={}):  __author__="Lutz Gross, l.gross@uq.edu.au"
36       """  __licence__="contact: esys@access.uq.edu.au"
37       @brief Return the Domain which is equal to the input domain (if not None)  __url__="http://www.iservo.edu.au/esys/escript"
38       and is the domain of all Data objects in the dictionary data.  __version__="$Revision$"
39       An exception is raised if this is not possible  __date__="$Date$"
40    
      @param domain  
      @param data  
      """  
      # get the domain used by any Data object in the list data:  
      data_domain=None  
      for d in data.itervalues():  
           if isinstance(d,escript.Data):  
              if not d.isEmpty(): data_domain=d.getDomain()  
      # check if domain and data_domain are identical?  
      if domain == None:  
          if data_domain == None:  
               raise ValueError,"Undefined PDE domain. Specify a domain or use a Data class object as coefficient"  
      else:  
          if data_domain == None:  
               data_domain=domain  
          else:  
            if not data_domain == domain:  
                  raise ValueError,"Domain of coefficients doesnot match specified domain"  
      # now we check if all Data class object coefficients are defined on data_domain:  
      for i,d in data.iteritems():  
          if isinstance(d,escript.Data):  
             if not d.isEmpty():  
                if not data_domain==d.getDomain():  
                  raise ValueError,"Illegal domain for coefficient %s."%i  
      # done:  
      return data_domain  
   
 def identifyNumEquationsAndSolutions(dim,coef={}):  
      # get number of equations and number of unknowns:  
      numEquations=0  
      numSolutions=0  
      for i in coef.iterkeys():  
         if not coef[i].isEmpty():  
            res=_PDECoefficientTypes[i].estimateNumEquationsAndNumSolutions(coef[i].getShape(),dim)  
            if res==None:  
                raise ValueError,"Illegal shape %s of coefficient %s"%(coef[i].getShape().__str__(),i)  
            else:  
                numEquations=max(numEquations,res[0])  
                numSolutions=max(numSolutions,res[1])  
      return numEquations,numSolutions  
   
   
 def _CompTuple2(t1,t2):  
    """  
    @brief  
   
    @param t1  
    @param t2  
    """  
    dif=t1[0]+t1[1]-(t2[0]+t2[1])  
    if dif<0: return 1  
    elif dif>0: return -1  
    else: return 0  
41    
42  class PDECoefficientType:  class IllegalCoefficient(ValueError):
43       """
44       raised if an illegal coefficient of the general ar particular PDE is requested.
45       """
46    
47    class IllegalCoefficientValue(ValueError):
48       """
49       raised if an incorrect value for a coefficient is used.
50       """
51    
52    class UndefinedPDEError(ValueError):
53       """
54       raised if a PDE is not fully defined yet.
55       """
56    
57    class PDECoefficient(object):
58      """      """
59      @brief      A class for describing a PDE coefficient
60    
61        @cvar INTERIOR: indicator that coefficient is defined on the interior of the PDE domain
62        @cvar BOUNDARY: indicator that coefficient is defined on the boundary of the PDE domain
63        @cvar CONTACT: indicator that coefficient is defined on the contact region within the PDE domain
64        @cvar SOLUTION: indicator that coefficient is defined trough a solution of the PDE
65        @cvar REDUCED: indicator that coefficient is defined trough a reduced solution of the PDE
66        @cvar BY_EQUATION: indicator that the dimension of the coefficient shape is defined by the number PDE equations
67        @cvar BY_SOLUTION: indicator that the dimension of the coefficient shape is defined by the number PDE solutions
68        @cvar BY_DIM: indicator that the dimension of the coefficient shape is defined by the spatial dimension
69        @cvar OPERATOR: indicator that the the coefficient alters the operator of the PDE
70        @cvar RIGHTHANDSIDE: indicator that the the coefficient alters the right hand side of the PDE
71        @cvar BOTH: indicator that the the coefficient alters the operator as well as the right hand side of the PDE
72    
73      """      """
     # identifier for location of Data objects defining coefficients  
74      INTERIOR=0      INTERIOR=0
75      BOUNDARY=1      BOUNDARY=1
76      CONTACT=2      CONTACT=2
77      CONTINUOUS=3      SOLUTION=3
78      # identifier in the pattern of coefficients:      REDUCED=4
79      # the pattern is a tuple of EQUATION,SOLUTION,DIM where DIM represents the spatial dimension, EQUATION the number of equations and SOLUTION the      BY_EQUATION=5
80      # number of unknowns.      BY_SOLUTION=6
81      EQUATION=3      BY_DIM=7
82      SOLUTION=4      OPERATOR=10
83      DIM=5      RIGHTHANDSIDE=11
84      # indicator for what is altered if the coefficient is altered:      BOTH=12
85      OPERATOR=5  
     RIGHTHANDSIDE=6  
     BOTH=7  
86      def __init__(self,where,pattern,altering):      def __init__(self,where,pattern,altering):
87         """         """
88         @brief Initialise a PDE Coefficient type         Initialise a PDE Coefficient type
89    
90           @param where: describes where the coefficient lives
91           @type where: one of L{INTERIOR}, L{BOUNDARY}, L{CONTACT}, L{SOLUTION}, L{REDUCED}
92           @param pattern: describes the shape of the coefficient and how the shape is build for a given
93                  spatial dimension and numbers of equation and solution in then PDE. For instance,
94                  (L{BY_EQUATION},L{BY_SOLUTION},L{BY_DIM}) descrbes a rank 3 coefficient which
95                  is instanciated as shape (3,2,2) in case of a three equations and two solution components
96                  on a 2-dimensional domain. In the case of single equation and a single solution component
97                  the shape compoments marked by L{BY_EQUATION} or L{BY_SOLUTION} are dropped. In this case
98                  the example would be read as (2,).
99           @type pattern: C{tuple} of L{BY_EQUATION}, L{BY_SOLUTION}, L{BY_DIM}
100           @param altering: indicates what part of the PDE is altered if the coefficiennt is altered
101           @type altering: one of L{OPERATOR}, L{RIGHTHANDSIDE}, L{BOTH}
102    
103         """         """
104           super(PDECoefficient, self).__init__()
105         self.what=where         self.what=where
106         self.pattern=pattern         self.pattern=pattern
107         self.altering=altering         self.altering=altering
108           self.resetValue()
109    
110      def getFunctionSpace(self,domain):      def resetValue(self):
111         """         """
112         @brief defines the FunctionSpace of the coefficient on the domain         resets coefficient value to default
   
        @param domain  
113         """         """
114         if self.what==self.INTERIOR: return escript.Function(domain)         self.value=escript.Data()
115         elif self.what==self.BOUNDARY: return escript.FunctionOnBoundary(domain)  
116         elif self.what==self.CONTACT: return escript.FunctionOnContactZero(domain)      def getFunctionSpace(self,domain,reducedEquationOrder=False,reducedSolutionOrder=False):
117         elif self.what==self.CONTINUOUS: return escript.ContinuousFunction(domain)         """
118           defines the L{FunctionSpace<escript.FunctionSpace>} of the coefficient
119    
120           @param domain: domain on which the PDE uses the coefficient
121           @type domain: L{Domain<escript.Domain>}
122           @param reducedEquationOrder: True to indicate that reduced order is used to represent the equation
123           @type domain: C{bool}
124           @param reducedSolutionOrder: True to indicate that reduced order is used to represent the solution
125           @type domain: C{bool}
126           @return:  L{FunctionSpace<escript.FunctionSpace>} of the coefficient
127           @rtype:  L{FunctionSpace<escript.FunctionSpace>}
128           """
129           if self.what==self.INTERIOR:
130                return escript.Function(domain)
131           elif self.what==self.BOUNDARY:
132                return escript.FunctionOnBoundary(domain)
133           elif self.what==self.CONTACT:
134                return escript.FunctionOnContactZero(domain)
135           elif self.what==self.SOLUTION:
136                if reducedEquationOrder and reducedSolutionOrder:
137                    return escript.ReducedSolution(domain)
138                else:
139                    return escript.Solution(domain)
140           elif self.what==self.REDUCED:
141                return escript.ReducedSolution(domain)
142    
143        def getValue(self):
144           """
145           returns the value of the coefficient
146    
147           @return:  value of the coefficient
148           @rtype:  L{Data<escript.Data>}
149           """
150           return self.value
151    
152        def setValue(self,domain,numEquations=1,numSolutions=1,reducedEquationOrder=False,reducedSolutionOrder=False,newValue=None):
153           """
154           set the value of the coefficient to a new value
155    
156           @param domain: domain on which the PDE uses the coefficient
157           @type domain: L{Domain<escript.Domain>}
158           @param numEquations: number of equations of the PDE
159           @type numEquations: C{int}
160           @param numSolutions: number of components of the PDE solution
161           @type numSolutions: C{int}
162           @param reducedEquationOrder: True to indicate that reduced order is used to represent the equation
163           @type domain: C{bool}
164           @param reducedSolutionOrder: True to indicate that reduced order is used to represent the solution
165           @type domain: C{bool}
166           @param newValue: number of components of the PDE solution
167           @type newValue: any object that can be converted into a L{Data<escript.Data>} object with the appropriate shape and L{FunctionSpace<escript.FunctionSpace>}
168           @raise IllegalCoefficientValue: if the shape of the assigned value does not match the shape of the coefficient
169           """
170           if newValue==None:
171               newValue=escript.Data()
172           elif isinstance(newValue,escript.Data):
173               if not newValue.isEmpty():
174                  try:
175                     newValue=escript.Data(newValue,self.getFunctionSpace(domain,reducedEquationOrder,reducedSolutionOrder))
176                  except:
177                     raise IllegalCoefficientValue,"Unable to interpolate coefficient to function space %s"%self.getFunctionSpace(domain)
178           else:
179               newValue=escript.Data(newValue,self.getFunctionSpace(domain,reducedEquationOrder,reducedSolutionOrder))
180           if not newValue.isEmpty():
181               if not self.getShape(domain,numEquations,numSolutions)==newValue.getShape():
182                   raise IllegalCoefficientValue,"Expected shape of coefficient is %s but actual shape is %s."%(self.getShape(domain,numEquations,numSolutions),newValue.getShape())
183           self.value=newValue
184    
185      def isAlteringOperator(self):      def isAlteringOperator(self):
186          """          """
187      @brief return true if the operator of the PDE is changed when the coefficient is changed          checks if the coefficient alters the operator of the PDE
188    
189            @return:  True if the operator of the PDE is changed when the coefficient is changed
190            @rtype:  C{bool}
191      """      """
192          if self.altering==self.OPERATOR or self.altering==self.BOTH:          if self.altering==self.OPERATOR or self.altering==self.BOTH:
193              return not None              return not None
# Line 119  class PDECoefficientType: Line 196  class PDECoefficientType:
196    
197      def isAlteringRightHandSide(self):      def isAlteringRightHandSide(self):
198          """          """
199      @brief return true if the right hand side of the PDE is changed when the coefficient is changed          checks if the coefficeint alters the right hand side of the PDE
200    
201        @rtype:  C{bool}
202            @return:  True if the right hand side of the PDE is changed when the coefficient is changed
203      """      """
204          if self.altering==self.RIGHTHANDSIDE or self.altering==self.BOTH:          if self.altering==self.RIGHTHANDSIDE or self.altering==self.BOTH:
205              return not None              return not None
206          else:          else:
207              return None              return None
208    
209      def estimateNumEquationsAndNumSolutions(self,shape=(),dim=3):      def estimateNumEquationsAndNumSolutions(self,domain,shape=()):
210         """         """
211         @brief tries to estimate the number of equations in a given tensor shape for a given spatial dimension dim         tries to estimate the number of equations and number of solutions if the coefficient has the given shape
212    
213         @param shape         @param domain: domain on which the PDE uses the coefficient
214         @param dim         @type domain: L{Domain<escript.Domain>}
215           @param shape: suggested shape of the coefficient
216           @type shape: C{tuple} of C{int} values
217           @return: the number of equations and number of solutions of the PDE is the coefficient has shape s.
218                     If no appropriate numbers could be identified, C{None} is returned
219           @rtype: C{tuple} of two C{int} values or C{None}
220         """         """
221           dim=domain.getDim()
222         if len(shape)>0:         if len(shape)>0:
223             num=max(shape)+1             num=max(shape)+1
224         else:         else:
225             num=1             num=1
226         search=[]         search=[]
227         for u in range(num):         if self.definesNumEquation() and self.definesNumSolutions():
228            for e in range(num):            for u in range(num):
229               search.append((e,u))               for e in range(num):
230         search.sort(_CompTuple2)                  search.append((e,u))
231         for item in search:            search.sort(self.__CompTuple2)
232               s=self.buildShape(item[0],item[1],dim)            for item in search:
233                 s=self.getShape(domain,item[0],item[1])
234               if len(s)==0 and len(shape)==0:               if len(s)==0 and len(shape)==0:
235                   return (1,1)                   return (1,1)
236               else:               else:
237                   if s==shape: return item                   if s==shape: return item
238           elif self.definesNumEquation():
239              for e in range(num,0,-1):
240                 s=self.getShape(domain,e,0)
241                 if len(s)==0 and len(shape)==0:
242                     return (1,None)
243                 else:
244                     if s==shape: return (e,None)
245    
246           elif self.definesNumSolutions():
247              for u in range(num,0,-1):
248                 s=self.getShape(domain,0,u)
249                 if len(s)==0 and len(shape)==0:
250                     return (None,1)
251                 else:
252                     if s==shape: return (None,u)
253         return None         return None
254        def definesNumSolutions(self):
255           """
256           checks if the coefficient allows to estimate the number of solution components
257    
258      def buildShape(self,e=1,u=1,dim=3):         @return: True if the coefficient allows an estimate of the number of solution components
259          """         @rtype: C{bool}
260      @brief builds the required shape for a given number of equations e, number of unknowns u and spatial dimension dim         """
261           for i in self.pattern:
262                 if i==self.BY_SOLUTION: return True
263           return False
264    
265      @param e      def definesNumEquation(self):
266      @param u         """
267      @param dim         checks if the coefficient allows to estimate the number of equations
268      """  
269          s=()         @return: True if the coefficient allows an estimate of the number of equations
270          for i in self.pattern:         @rtype: C{bool}
271               if i==self.EQUATION:         """
272                  if e>1: s=s+(e,)         for i in self.pattern:
273               elif i==self.SOLUTION:               if i==self.BY_EQUATION: return True
274                  if u>1: s=s+(u,)         return False
275    
276        def __CompTuple2(self,t1,t2):
277          """
278          Compare two tuples of possible number of equations and number of solutions
279    
280          @param t1: The first tuple
281          @param t2: The second tuple
282    
283          """
284    
285          dif=t1[0]+t1[1]-(t2[0]+t2[1])
286          if dif<0: return 1
287          elif dif>0: return -1
288          else: return 0
289    
290        def getShape(self,domain,numEquations=1,numSolutions=1):
291           """
292           builds the required shape of the coefficient
293    
294           @param domain: domain on which the PDE uses the coefficient
295           @type domain: L{Domain<escript.Domain>}
296           @param numEquations: number of equations of the PDE
297           @type numEquations: C{int}
298           @param numSolutions: number of components of the PDE solution
299           @type numSolutions: C{int}
300           @return: shape of the coefficient
301           @rtype: C{tuple} of C{int} values
302           """
303           dim=domain.getDim()
304           s=()
305           for i in self.pattern:
306                 if i==self.BY_EQUATION:
307                    if numEquations>1: s=s+(numEquations,)
308                 elif i==self.BY_SOLUTION:
309                    if numSolutions>1: s=s+(numSolutions,)
310               else:               else:
311                  s=s+(dim,)                  s=s+(dim,)
312          return s         return s
   
 _PDECoefficientTypes={  
 "A"         : PDECoefficientType(PDECoefficientType.INTERIOR,(PDECoefficientType.EQUATION,PDECoefficientType.DIM,PDECoefficientType.SOLUTION,PDECoefficientType.DIM),PDECoefficientType.OPERATOR),  
 "B"         : PDECoefficientType(PDECoefficientType.INTERIOR,(PDECoefficientType.EQUATION,PDECoefficientType.DIM,PDECoefficientType.SOLUTION),PDECoefficientType.OPERATOR),  
 "C"         : PDECoefficientType(PDECoefficientType.INTERIOR,(PDECoefficientType.EQUATION,PDECoefficientType.SOLUTION,PDECoefficientType.DIM),PDECoefficientType.OPERATOR),  
 "D"         : PDECoefficientType(PDECoefficientType.INTERIOR,(PDECoefficientType.EQUATION,PDECoefficientType.SOLUTION),PDECoefficientType.OPERATOR),  
 "X"         : PDECoefficientType(PDECoefficientType.INTERIOR,(PDECoefficientType.EQUATION,PDECoefficientType.DIM),PDECoefficientType.RIGHTHANDSIDE),  
 "Y"         : PDECoefficientType(PDECoefficientType.INTERIOR,(PDECoefficientType.EQUATION,),PDECoefficientType.RIGHTHANDSIDE),  
 "d"         : PDECoefficientType(PDECoefficientType.BOUNDARY,(PDECoefficientType.EQUATION,PDECoefficientType.SOLUTION),PDECoefficientType.OPERATOR),  
 "y"         : PDECoefficientType(PDECoefficientType.BOUNDARY,(PDECoefficientType.EQUATION,),PDECoefficientType.RIGHTHANDSIDE),  
 "d_contact" : PDECoefficientType(PDECoefficientType.CONTACT,(PDECoefficientType.EQUATION,PDECoefficientType.SOLUTION),PDECoefficientType.OPERATOR),  
 "y_contact" : PDECoefficientType(PDECoefficientType.CONTACT,(PDECoefficientType.EQUATION,),PDECoefficientType.RIGHTHANDSIDE),  
 "r"         : PDECoefficientType(PDECoefficientType.CONTINUOUS,(PDECoefficientType.EQUATION,),PDECoefficientType.RIGHTHANDSIDE),  
 "q"         : PDECoefficientType(PDECoefficientType.CONTINUOUS,(PDECoefficientType.SOLUTION,),PDECoefficientType.BOTH),  
 }  
313    
314  class LinearPDE:  class LinearPDE(object):
315     """     """
316     @brief Class to define a linear PDE     This class is used to define a general linear, steady, second order PDE
317         for an unknown function M{u} on a given domain defined through a L{Domain<escript.Domain>} object.
    class to define a linear PDE of the form  
318    
319       -(A_{ijkl}u_{k,l})_{,j} -(B_{ijk}u_k)_{,j} + C_{ikl}u_{k,l} +D_{ik}u_k = - (X_{ij})_{,j} + Y_i     For a single PDE with a solution with a single component the linear PDE is defined in the following form:
320    
321       with boundary conditons:     M{-grad(A[j,l]*grad(u)[l]+B[j]u)[j]+C[l]*grad(u)[l]+D*u =-grad(X)[j,j]+Y}
322    
323          n_j*(A_{ijkl}u_{k,l}+B_{ijk}u_k)_{,j} + d_{ik}u_k = - n_j*X_{ij} + y_i     where M{grad(F)} denotes the spatial derivative of M{F}. Einstein's summation convention,
324       ie. summation over indexes appearing twice in a term of a sum is performed, is used.
325       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
326       L{Function<escript.Function>} on the PDE or objects that can be converted into such L{Data<escript.Data>} objects.
327       M{A} is a rank two, M{B}, M{C} and M{X} are rank one and M{D} and M{Y} are scalar.
328    
329      and contact conditions     The following natural boundary conditions are considered:
330    
331          n_j*(A_{ijkl}u_{k,l}+B_{ijk}u_k)_{,j} + d_contact_{ik}[u_k] = - n_j*X_{ij} + y_contact_i     M{n[j]*(A[i,j]*grad(u)[l]+B[j]*u)+d*u=n[j]*X[j]+y}
332    
333      and constraints:     where M{n} is the outer normal field calculated by L{getNormal<escript.FunctionSpace.getNormal>} of L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
334       Notice that the coefficients M{A}, M{B} and M{X} are defined in the PDE. The coefficients M{d} and M{y} are
335       each a scalar in the L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
336    
          u_i=r_i where q_i>0  
337    
338     """     Constraints for the solution prescribing the value of the solution at certain locations in the domain. They have the form
    DEFAULT_METHOD=util.DEFAULT_METHOD  
    DIRECT=util.DIRECT  
    CHOLEVSKY=util.CHOLEVSKY  
    PCG=util.PCG  
    CR=util.CR  
    CGS=util.CGS  
    BICGSTAB=util.BICGSTAB  
    SSOR=util.SSOR  
    GMRES=util.GMRES  
    PRES20=util.PRES20  
339    
340     def __init__(self,domain,numEquations=0,numSolutions=0):     M{u=r}  where M{q>0}
      """  
      @brief initializes a new linear PDE.  
341    
342       @param args     M{r} and M{q} are each scalar where M{q} is the characteristic function defining where the constraint is applied.
343       """     The constraints override any other condition set by the PDE or the boundary condition.
344    
345       The PDE is symmetrical if
346    
347       M{A[i,j]=A[j,i]}  and M{B[j]=C[j]}
348    
349       For a system of PDEs and a solution with several components the PDE has the form
350    
351       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] }
352    
353       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.
354       The natural boundary conditions take the form:
355    
356       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]}
357    
358    
359       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
360    
361    
362       M{u[i]=r[i]}  where  M{q[i]>0}
363    
364       M{r} and M{q} are each rank one. Notice that at some locations not necessarily all components must have a constraint.
365    
366       The system of PDEs is symmetrical if
367    
368            - M{A[i,j,k,l]=A[k,l,i,j]}
369            - M{B[i,j,k]=C[k,i,j]}
370            - M{D[i,k]=D[i,k]}
371            - M{d[i,k]=d[k,i]}
372    
373       L{LinearPDE} also supports solution discontinuities over a contact region in the domain. To specify the conditions across the
374       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
375       defined as
376    
377       M{J[i,j]=A[i,j,k,l]*grad(u[k])[l]+B[i,j,k]*u[k]-X[i,j]}
378    
379       For the case of single solution component and single PDE M{J} is defined
380    
381       M{J_{j}=A[i,j]*grad(u)[j]+B[i]*u-X[i]}
382    
383       In the context of discontinuities M{n} denotes the normal on the discontinuity pointing from side 0 towards side 1
384       calculated from L{getNormal<escript.FunctionSpace.getNormal>} of L{FunctionOnContactZero<escript.FunctionOnContactZero>}. For a system of PDEs
385       the contact condition takes the form
386    
387       M{n[j]*J0[i,j]=n[j]*J1[i,j]=y_contact[i]- d_contact[i,k]*jump(u)[k]}
388    
389       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
390       of the solution at side 1 and at side 0, denotes the jump of M{u} across discontinuity along the normal calcualted by
391       L{jump<util.jump>}.
392       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>}.
393       In case of a single PDE and a single component solution the contact condition takes the form
394    
395       M{n[j]*J0_{j}=n[j]*J1_{j}=y_contact-d_contact*jump(u)}
396    
397       In this case the the coefficient M{d_contact} and M{y_contact} are eaach scalar
398       both in the L{FunctionOnContactZero<escript.FunctionOnContactZero>} or L{FunctionOnContactOne<escript.FunctionOnContactOne>}.
399    
400       @cvar DEFAULT: The default method used to solve the system of linear equations
401       @cvar DIRECT: The direct solver based on LDU factorization
402       @cvar CHOLEVSKY: The direct solver based on LDLt factorization (can only be applied for symmetric PDEs)
403       @cvar PCG: The preconditioned conjugate gradient method (can only be applied for symmetric PDEs)
404       @cvar CR: The conjugate residual method
405       @cvar CGS: The conjugate gardient square method
406       @cvar BICGSTAB: The stabilized BiConjugate Gradient method.
407       @cvar SSOR: The symmetric overrealaxtion method
408       @cvar ILU0: The incomplete LU factorization preconditioner  with no fill in
409       @cvar ILUT: The incomplete LU factorization preconditioner with will in
410       @cvar JACOBI: The Jacobi preconditioner
411       @cvar GMRES: The Gram-Schmidt minimum residual method
412       @cvar PRES20: Special GMRES with restart after 20 steps and truncation after 5 residuals
413       @cvar LUMPING: Matrix lumping.
414       @cvar NO_REORDERING: No matrix reordering allowed
415       @cvar MINIMUM_FILL_IN: Reorder matrix to reduce fill-in during factorization
416       @cvar NESTED_DISSECTION: Reorder matrix to improve load balancing during factorization
417       @cvar PASO: PASO solver package
418       @cvar SCSL: SGI SCSL solver library
419       @cvar MKL: Intel's MKL solver library
420       @cvar UMFPACK: the UMFPACK library
421       @cvar ITERATIVE: The default iterative solver
422    
423       """
424       DEFAULT= 0
425       DIRECT= 1
426       CHOLEVSKY= 2
427       PCG= 3
428       CR= 4
429       CGS= 5
430       BICGSTAB= 6
431       SSOR= 7
432       ILU0= 8
433       ILUT= 9
434       JACOBI= 10
435       GMRES= 11
436       PRES20= 12
437       LUMPING= 13
438       NO_REORDERING= 17
439       MINIMUM_FILL_IN= 18
440       NESTED_DISSECTION= 19
441       SCSL= 14
442       MKL= 15
443       UMFPACK= 16
444       ITERATIVE= 20
445       PASO= 21
446    
447       __TOL=1.e-13
448       __PACKAGE_KEY="package"
449       __METHOD_KEY="method"
450       __SYMMETRY_KEY="symmetric"
451       __TOLERANCE_KEY="tolerance"
452    
453    
454       def __init__(self,domain,numEquations=None,numSolutions=None,debug=False):
455         """
456         initializes a new linear PDE
457    
458         @param domain: domain of the PDE
459         @type domain: L{Domain<escript.Domain>}
460         @param numEquations: number of equations. If numEquations==None the number of equations
461                              is exracted from the PDE coefficients.
462         @param numSolutions: number of solution components. If  numSolutions==None the number of solution components
463                              is exracted from the PDE coefficients.
464         @param debug: if True debug informations are printed.
465    
466         """
467         super(LinearPDE, self).__init__()
468         #
469         #   the coefficients of the general PDE:
470         #
471         self.__COEFFICIENTS_OF_GENEARL_PDE={
472           "A"         : PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_DIM,PDECoefficient.BY_SOLUTION,PDECoefficient.BY_DIM),PDECoefficient.OPERATOR),
473           "B"         : PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_DIM,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),
474           "C"         : PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION,PDECoefficient.BY_DIM),PDECoefficient.OPERATOR),
475           "D"         : PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),
476           "X"         : PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_DIM),PDECoefficient.RIGHTHANDSIDE),
477           "Y"         : PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
478           "d"         : PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),
479           "y"         : PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
480           "d_contact" : PDECoefficient(PDECoefficient.CONTACT,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_SOLUTION),PDECoefficient.OPERATOR),
481           "y_contact" : PDECoefficient(PDECoefficient.CONTACT,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
482           "r"         : PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_SOLUTION,),PDECoefficient.RIGHTHANDSIDE),
483           "q"         : PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_SOLUTION,),PDECoefficient.BOTH)}
484    
485         # COEFFICIENTS can be overwritten by subclasses:
486         self.COEFFICIENTS=self.__COEFFICIENTS_OF_GENEARL_PDE
487         self.__altered_coefficients=False
488       # initialize attributes       # initialize attributes
489       self.__debug=None       self.__debug=debug
490       self.__domain=domain       self.__domain=domain
491       self.__numEquations=numEquations       self.__numEquations=numEquations
492       self.__numSolutions=numSolutions       self.__numSolutions=numSolutions
493       self.cleanCoefficients()       self.__resetSystem()
   
      self.__operator=escript.Operator()  
      self.__operator_isValid=False  
      self.__righthandside=escript.Data()  
      self.__righthandside_isValid=False  
      self.__solution=escript.Data()  
      self.__solution_isValid=False  
494    
495       # set some default values:       # set some default values:
496       self.__homogeneous_constraint=True       self.__reduce_equation_order=False
497       self.__row_function_space=escript.Solution(self.__domain)       self.__reduce_solution_order=False
      self.__column_function_space=escript.Solution(self.__domain)  
498       self.__tolerance=1.e-8       self.__tolerance=1.e-8
499       self.__solver_method=util.DEFAULT_METHOD       self.__solver_method=self.DEFAULT
500       self.__matrix_type=self.__domain.getSystemMatrixTypeId(util.DEFAULT_METHOD,False)       self.__solver_package=self.DEFAULT
501         self.__matrix_type=self.__domain.getSystemMatrixTypeId(self.DEFAULT,self.DEFAULT,False)
502       self.__sym=False       self.__sym=False
      self.__lumping=False  
503    
504     def getCoefficient(self,name):       self.resetCoefficients()
505         self.trace("PDE Coeffients are %s"%str(self.COEFFICIENTS.keys()))
506       # =============================================================================
507       #    general stuff:
508       # =============================================================================
509       def __str__(self):
510         """
511         returns string representation of the PDE
512    
513         @return: a simple representation of the PDE
514         @rtype: C{str}
515         """
516         return "<LinearPDE %d>"%id(self)
517       # =============================================================================
518       #    debug :
519       # =============================================================================
520       def setDebugOn(self):
521       """       """
522       @brief return the value of the coefficient name       switches on debugging
523         """
524         self.__debug=not None
525    
526       @param name     def setDebugOff(self):
527       """       """
528       return self.__coefficient[name]       switches off debugging
529         """
530         self.__debug=None
531    
532     def setValue(self,**coefficients):     def trace(self,text):
533        """       """
534        @brief sets new values to coefficients       print the text message if debugging is swiched on.
535         @param text: message
536         @type text: C{string}
537         """
538         if self.__debug: print "%s: %s"%(str(self),text)
539    
540        @param coefficients     # =============================================================================
541        """     # some service functions:
542        self._setValue(**coefficients)     # =============================================================================
543             def getDomain(self):
544         """
545         returns the domain of the PDE
546    
547     def _setValue(self,**coefficients):       @return: the domain of the PDE
548        """       @rtype: L{Domain<escript.Domain>}
549        @brief sets new values to coefficients       """
550         return self.__domain
551    
552        @param coefficients     def getDim(self):
553        """       """
554               returns the spatial dimension of the PDE
       # get the dictionary of the coefficinets been altered:  
       alteredCoefficients={}  
       for i,d in coefficients.iteritems():  
          if self.hasCoefficient(i):  
             if d == None:  
                 alteredCoefficients[i]=escript.Data()  
             elif isinstance(d,escript.Data):  
                 if d.isEmpty():  
                   alteredCoefficients[i]=escript.Data()  
                 else:  
                   alteredCoefficients[i]=escript.Data(d,self.getFunctionSpaceOfCoefficient(i))  
             else:  
                 alteredCoefficients[i]=escript.Data(d,self.getFunctionSpaceOfCoefficient(i))  
          else:  
             raise ValueError,"Attempt to set undefined coefficient %s"%i  
       # if numEquations and numSolutions is undefined we try identify their values based on the coefficients:  
       if self.__numEquations<1 or self.__numSolutions<1:  
             numEquations,numSolutions=identifyNumEquationsAndSolutions(self.getDomain().getDim(),alteredCoefficients)  
             if self.__numEquations<1 and numEquations>0: self.__numEquations=numEquations  
             if self.__numSolutions<1 and numSolutions>0: self.__numSolutions=numSolutions  
             if self.debug() and self.__numEquations>0: print "PDE Debug: identified number of equations is ",self.__numEquations  
             if self.debug() and self.__numSolutions>0: print "PDE Debug: identified number of solutions is ",self.__numSolutions  
555    
556        # now we check the shape of the coefficient if numEquations and numSolutions are set:       @return: the spatial dimension of the PDE domain
557        if  self.__numEquations>0 and  self.__numSolutions>0:       @rtype: C{int}
558           for i in self.__coefficient.iterkeys():       """
559               if alteredCoefficients.has_key(i) and not alteredCoefficients[i].isEmpty():       return self.getDomain().getDim()
                  if not self.getShapeOfCoefficient(i)==alteredCoefficients[i].getShape():  
                     raise ValueError,"Expected shape for coefficient %s is %s but actual shape is %s."%(i,self.getShapeOfCoefficient(i),alteredCoefficients[i].getShape())  
              else:  
                  if not self.__coefficient[i].isEmpty():  
                     if not self.getShapeOfCoefficient(i)==self.__coefficient[i].getShape():  
                        raise ValueError,"Expected shape for coefficient %s is %s but actual shape is %s."%(i,self.getShapeOfCoefficient(i),self.__coefficient[i].getShape())  
       # overwrite new values:  
       for i,d in alteredCoefficients.iteritems():  
          if self.debug(): print "PDE Debug: Coefficient %s has been altered."%i  
          self.__coefficient[i]=d  
          self.alteredCoefficient(i)  
   
       # reset the HomogeneousConstraintFlag:  
       self.__setHomogeneousConstraintFlag()  
       if not "q" in alteredCoefficients and not self.__homogeneous_constraint: self.__rebuildSystem()  
   
    def cleanCoefficients(self):  
      """  
      @brief resets all coefficients to default values.  
      """  
      self.__coefficient={}  
      for i in _PDECoefficientTypes.iterkeys():  
          self.__coefficient[i]=escript.Data()  
560    
561     def getShapeOfCoefficient(self,name):     def getNumEquations(self):
562       """       """
563       @brief return the shape of the coefficient name       returns the number of equations
564    
565       @param name       @return: the number of equations
566         @rtype: C{int}
567         @raise UndefinedPDEError: if the number of equations is not be specified yet.
568       """       """
569       if self.hasCoefficient(name):       if self.__numEquations==None:
570          return _PDECoefficientTypes[name].buildShape(self.getNumEquations(),self.getNumSolutions(),self.getDomain().getDim())           raise UndefinedPDEError,"Number of equations is undefined. Please specify argument numEquations."
571       else:       else:
572          raise ValueError,"Solution coefficient %s requested"%name           return self.__numEquations
573    
574     def getFunctionSpaceOfCoefficient(self,name):     def getNumSolutions(self):
575       """       """
576       @brief return the atoms of the coefficient name       returns the number of unknowns
577    
578       @param name       @return: the number of unknowns
579         @rtype: C{int}
580         @raise UndefinedPDEError: if the number of unknowns is not be specified yet.
581       """       """
582       if self.hasCoefficient(name):       if self.__numSolutions==None:
583          return _PDECoefficientTypes[name].getFunctionSpace(self.getDomain())          raise UndefinedPDEError,"Number of solution is undefined. Please specify argument numSolutions."
584       else:       else:
585          raise ValueError,"Solution coefficient %s requested"%name          return self.__numSolutions
586    
587     def alteredCoefficient(self,name):     def reduceEquationOrder(self):
588       """       """
589       @brief annonced that coefficient name has been changed       return status for order reduction for equation
590    
591       @param name       @return: return True is reduced interpolation order is used for the represenation of the equation
592         @rtype: L{bool}
593       """       """
594       if self.hasCoefficient(name):       return self.__reduce_equation_order
         if _PDECoefficientTypes[name].isAlteringOperator(): self.__rebuildOperator()  
         if _PDECoefficientTypes[name].isAlteringRightHandSide(): self.__rebuildRightHandSide()  
      else:  
         raise ValueError,"Solution coefficient %s requested"%name  
   
    def __setHomogeneousConstraintFlag(self):  
       """  
       @brief checks if the constraints are homogeneous and sets self.__homogeneous_constraint accordingly.  
       """  
       self.__homogeneous_constraint=True  
       q=self.getCoefficient("q")  
       r=self.getCoefficient("r")  
       if not q.isEmpty() and not r.isEmpty():  
          print (q*r).Lsup(), 1.e-13*r.Lsup()  
          if (q*r).Lsup()>=1.e-13*r.Lsup(): self.__homogeneous_constraint=False  
       if self.debug():  
            if self.__homogeneous_constraint:  
                print "PDE Debug: Constraints are homogeneous."  
            else:  
                print "PDE Debug: Constraints are inhomogeneous."  
   
595    
596     def hasCoefficient(self,name):     def reduceSolutionOrder(self):
597        """       """
598        @brief return true if name is the name of a coefficient       return status for order reduction for the solution
599    
600        @param name       @return: return True is reduced interpolation order is used for the represenation of the solution
601        """       @rtype: L{bool}
602        return self.__coefficient.has_key(name)       """
603         return self.__reduce_solution_order
604    
605     def getFunctionSpaceForEquation(self):     def getFunctionSpaceForEquation(self):
606       """       """
607       @brief return true if the test functions should use reduced order       returns the L{FunctionSpace<escript.FunctionSpace>} used to discretize the equation
608    
609         @return: representation space of equation
610         @rtype: L{FunctionSpace<escript.FunctionSpace>}
611       """       """
612       return self.__row_function_space       if self.reduceEquationOrder():
613             return escript.ReducedSolution(self.getDomain())
614         else:
615             return escript.Solution(self.getDomain())
616    
617     def getFunctionSpaceForSolution(self):     def getFunctionSpaceForSolution(self):
618       """       """
619       @brief return true if the interpolation of the solution should use reduced order       returns the L{FunctionSpace<escript.FunctionSpace>} used to represent the solution
620    
621         @return: representation space of solution
622         @rtype: L{FunctionSpace<escript.FunctionSpace>}
623       """       """
624       return self.__column_function_space       if self.reduceSolutionOrder():
625             return escript.ReducedSolution(self.getDomain())
626         else:
627             return escript.Solution(self.getDomain())
628    
    # ===== debug ==============================================================  
    def setDebugOn(self):  
        """  
        @brief  
        """  
        self.__debug=not None  
629    
630     def setDebugOff(self):     def getOperator(self):
631         """       """
632         @brief       provides access to the operator of the PDE
        """  
        self.__debug=None  
633    
634     def debug(self):       @return: the operator of the PDE
635         """       @rtype: L{Operator<escript.Operator>}
636         @brief returns true if the PDE is in the debug mode       """
637         """       m=self.getSystem()[0]
638         return self.__debug       if self.isUsingLumping():
639             return self.copyConstraint(1./m)
640         else:
641             return m
642    
643     #===== Lumping ===========================     def getRightHandSide(self):
644     def setLumpingOn(self):       """
645        """       provides access to the right hand side of the PDE
646        @brief indicates to use matrix lumping       @return: the right hand side of the PDE
647        """       @rtype: L{Data<escript.Data>}
648        if not self.isUsingLumping():       """
649           raise SystemError,"Lumping is not working yet! Talk to the experts"       r=self.getSystem()[1]
650           if self.debug() : print "PDE Debug: lumping is set on"       if self.isUsingLumping():
651           self.__rebuildOperator()           return self.copyConstraint(r)
652           self.__lumping=True       else:
653             return r
654    
655     def setLumpingOff(self):     def applyOperator(self,u=None):
656        """       """
657        @brief switches off matrix lumping       applies the operator of the PDE to a given u or the solution of PDE if u is not present.
658        """  
659        if self.isUsingLumping():       @param u: argument of the operator. It must be representable in C{elf.getFunctionSpaceForSolution()}. If u is not present or equals L{None}
660           if self.debug() : print "PDE Debug: lumping is set off"                 the current solution is used.
661           self.__rebuildOperator()       @type u: L{Data<escript.Data>} or None
662           self.__lumping=False       @return: image of u
663         @rtype: L{Data<escript.Data>}
664         """
665         if u==None:
666              return self.getOperator()*self.getSolution()
667         else:
668            self.getOperator()*escript.Data(u,self.getFunctionSpaceForSolution())
669    
670       def getResidual(self,u=None):
671         """
672         return the residual of u or the current solution if u is not present.
673    
674     def setLumping(self,flag=False):       @param u: argument in the residual calculation. It must be representable in C{elf.getFunctionSpaceForSolution()}. If u is not present or equals L{None}
675                   the current solution is used.
676         @type u: L{Data<escript.Data>} or None
677         @return: residual of u
678         @rtype: L{Data<escript.Data>}
679         """
680         return self.applyOperator(u)-self.getRightHandSide()
681    
682       def checkSymmetry(self,verbose=True):
683        """        """
684        @brief set the matrix lumping flag to flag        test the PDE for symmetry.
685    
686          @param verbose: if equal to True or not present a report on coefficients which are breaking the symmetry is printed.
687          @type verbose: C{bool}
688          @return:  True if the PDE is symmetric.
689          @rtype: L{Data<escript.Data>}
690          @note: This is a very expensive operation. It should be used for degugging only! The symmetry flag is not altered.
691        """        """
692        if flag:        verbose=verbose or self.__debug
693           self.setLumpingOn()        out=True
694          if self.getNumSolutions()!=self.getNumEquations():
695             if verbose: print "non-symmetric PDE because of different number of equations and solutions"
696             out=False
697        else:        else:
698           self.setLumpingOff()           A=self.getCoefficientOfGeneralPDE("A")
699             if not A.isEmpty():
700                tol=util.Lsup(A)*self.__TOL
701                if self.getNumSolutions()>1:
702                   for i in range(self.getNumEquations()):
703                      for j in range(self.getDim()):
704                         for k in range(self.getNumSolutions()):
705                            for l in range(self.getDim()):
706                                if util.Lsup(A[i,j,k,l]-A[k,l,i,j])>tol:
707                                   if verbose: print "non-symmetric PDE because A[%d,%d,%d,%d]!=A[%d,%d,%d,%d]"%(i,j,k,l,k,l,i,j)
708                                   out=False
709                else:
710                   for j in range(self.getDim()):
711                      for l in range(self.getDim()):
712                         if util.Lsup(A[j,l]-A[l,j])>tol:
713                            if verbose: print "non-symmetric PDE because A[%d,%d]!=A[%d,%d]"%(j,l,l,j)
714                            out=False
715             B=self.getCoefficientOfGeneralPDE("B")
716             C=self.getCoefficientOfGeneralPDE("C")
717             if B.isEmpty() and not C.isEmpty():
718                if verbose: print "non-symmetric PDE because B is not present but C is"
719                out=False
720             elif not B.isEmpty() and C.isEmpty():
721                if verbose: print "non-symmetric PDE because C is not present but B is"
722                out=False
723             elif not B.isEmpty() and not C.isEmpty():
724                tol=(util.Lsup(B)+util.Lsup(C))*self.__TOL/2.
725                if self.getNumSolutions()>1:
726                   for i in range(self.getNumEquations()):
727                       for j in range(self.getDim()):
728                          for k in range(self.getNumSolutions()):
729                             if util.Lsup(B[i,j,k]-C[k,i,j])>tol:
730                                  if verbose: print "non-symmetric PDE because B[%d,%d,%d]!=C[%d,%d,%d]"%(i,j,k,k,i,j)
731                                  out=False
732                else:
733                   for j in range(self.getDim()):
734                      if util.Lsup(B[j]-C[j])>tol:
735                         if verbose: print "non-symmetric PDE because B[%d]!=C[%d]"%(j,j)
736                         out=False
737             if self.getNumSolutions()>1:
738               D=self.getCoefficientOfGeneralPDE("D")
739               if not D.isEmpty():
740                 tol=util.Lsup(D)*self.__TOL
741                 for i in range(self.getNumEquations()):
742                    for k in range(self.getNumSolutions()):
743                      if util.Lsup(D[i,k]-D[k,i])>tol:
744                          if verbose: print "non-symmetric PDE because D[%d,%d]!=D[%d,%d]"%(i,k,k,i)
745                          out=False
746               d=self.getCoefficientOfGeneralPDE("d")
747               if not d.isEmpty():
748                 tol=util.Lsup(d)*self.__TOL
749                 for i in range(self.getNumEquations()):
750                    for k in range(self.getNumSolutions()):
751                      if util.Lsup(d[i,k]-d[k,i])>tol:
752                          if verbose: print "non-symmetric PDE because d[%d,%d]!=d[%d,%d]"%(i,k,k,i)
753                          out=False
754               d_contact=self.getCoefficientOfGeneralPDE("d_contact")
755               if not d_contact.isEmpty():
756                 tol=util.Lsup(d_contact)*self.__TOL
757                 for i in range(self.getNumEquations()):
758                    for k in range(self.getNumSolutions()):
759                      if util.Lsup(d_contact[i,k]-d_contact[k,i])>tol:
760                          if verbose: print "non-symmetric PDE because d_contact[%d,%d]!=d_contact[%d,%d]"%(i,k,k,i)
761                          out=False
762          return out
763    
764     def isUsingLumping(self):     def getSolution(self,**options):
765        """         """
766        @brief         returns the solution of the PDE. If the solution is not valid the PDE is solved.
767        """  
768        return self.__lumping         @return: the solution
769           @rtype: L{Data<escript.Data>}
770           @param options: solver options
771           @keyword verbose: True to get some information during PDE solution
772           @type verbose: C{bool}
773           @keyword reordering: reordering scheme to be used during elimination. Allowed values are
774                                L{NO_REORDERING}, L{MINIMUM_FILL_IN}, L{NESTED_DISSECTION}
775           @keyword preconditioner: preconditioner method to be used. Allowed values are
776                                    L{SSOR}, L{ILU0}, L{ILUT}, L{JACOBI}
777           @keyword iter_max: maximum number of iteration steps allowed.
778           @keyword drop_tolerance: threshold for drupping in L{ILUT}
779           @keyword drop_storage: maximum of allowed memory in L{ILUT}
780           @keyword truncation: maximum number of residuals in L{GMRES}
781           @keyword restart: restart cycle length in L{GMRES}
782           """
783           if not self.__solution_isValid:
784              mat,f=self.getSystem()
785              if self.isUsingLumping():
786                 self.__solution=self.copyConstraint(f*mat)
787              else:
788                 options[self.__TOLERANCE_KEY]=self.getTolerance()
789                 options[self.__METHOD_KEY]=self.getSolverMethod()
790                 options[self.__PACKAGE_KEY]=self.getSolverPackage()
791                 options[self.__SYMMETRY_KEY]=self.isSymmetric()
792                 self.trace("PDE is resolved.")
793                 self.trace("solver options: %s"%str(options))
794                 self.__solution=mat.solve(f,options)
795              self.__solution_isValid=True
796           return self.__solution
797    
798       def getFlux(self,u=None):
799         """
800         returns the flux M{J} for a given M{u}
801    
802         M{J[i,j]=A[i,j,k,l]*grad(u[k])[l]+B[i,j,k]u[k]-X[i,j]}
803    
804         or
805    
806         M{J[j]=A[i,j]*grad(u)[l]+B[j]u-X[j]}
807    
808     #============ method business =========================================================       @param u: argument in the flux. If u is not present or equals L{None} the current solution is used.
809     def setSolverMethod(self,solver=util.DEFAULT_METHOD):       @type u: L{Data<escript.Data>} or None
810         @return: flux
811         @rtype: L{Data<escript.Data>}
812         """
813         if u==None: u=self.getSolution()
814         return util.tensormult(self.getCoefficientOfGeneralPDE("A"),util.grad(u))+util.matrixmult(self.getCoefficientOfGeneralPDE("B"),u)-util.self.getCoefficientOfGeneralPDE("X")
815       # =============================================================================
816       #   solver settings:
817       # =============================================================================
818       def setSolverMethod(self,solver=None):
819         """         """
820         @brief sets a new solver         sets a new solver
821    
822           @param solver: sets a new solver method.
823           @type solver: one of L{DEFAULT}, L{ITERATIVE} L{DIRECT}, L{CHOLEVSKY}, L{PCG}, L{CR}, L{CGS}, L{BICGSTAB}, L{SSOR}, L{GMRES}, L{PRES20}, L{LUMPING}.
824         """         """
825           if solver==None: solve=self.DEFAULT
826         if not solver==self.getSolverMethod():         if not solver==self.getSolverMethod():
827             self.__solver_method=solver             self.__solver_method=solver
            if self.debug() : print "PDE Debug: New solver is %s"%solver  
828             self.__checkMatrixType()             self.__checkMatrixType()
829               self.trace("New solver is %s"%self.getSolverMethodName())
830    
831       def getSolverMethodName(self):
832           """
833           returns the name of the solver currently used
834    
835           @return: the name of the solver currently used.
836           @rtype: C{string}
837           """
838    
839           m=self.getSolverMethod()
840           p=self.getSolverPackage()
841           if m==self.DEFAULT: method="DEFAULT"
842           elif m==self.DIRECT: method= "DIRECT"
843           elif m==self.ITERATIVE: method= "ITERATIVE"
844           elif m==self.CHOLEVSKY: method= "CHOLEVSKY"
845           elif m==self.PCG: method= "PCG"
846           elif m==self.CR: method= "CR"
847           elif m==self.CGS: method= "CGS"
848           elif m==self.BICGSTAB: method= "BICGSTAB"
849           elif m==self.SSOR: method= "SSOR"
850           elif m==self.GMRES: method= "GMRES"
851           elif m==self.PRES20: method= "PRES20"
852           elif m==self.LUMPING: method= "LUMPING"
853           else : method="unknown"
854           if p==self.DEFAULT: package="DEFAULT"
855           elif p==self.PASO: package= "PASO"
856           elif p==self.MKL: package= "MKL"
857           elif p==self.SCSL: package= "SCSL"
858           elif p==self.UMFPACK: package= "UMFPACK"
859           else : method="unknown"
860           return "%s solver of %s package"%(method,package)
861    
862    
863     def getSolverMethod(self):     def getSolverMethod(self):
864         """         """
865         @brief returns the solver method         returns the solver method
866    
867           @return: the solver method currently be used.
868           @rtype: C{int}
869         """         """
870         return self.__solver_method         return self.__solver_method
871    
872     #============ tolerance business =========================================================     def setSolverPackage(self,package=None):
873           """
874           sets a new solver package
875    
876           @param solver: sets a new solver method.
877           @type solver: one of L{DEFAULT}, L{PASO} L{SCSL}, L{MKL}, L{UMLPACK}
878           """
879           if package==None: package=self.DEFAULT
880           if not package==self.getSolverPackage():
881               self.__solver_method=solver
882               self.__checkMatrixType()
883               self.trace("New solver is %s"%self.getSolverMethodName())
884    
885       def getSolverPackage(self):
886           """
887           returns the package of the solver
888    
889           @return: the solver package currently being used.
890           @rtype: C{int}
891           """
892           return self.__solver_package
893    
894       def isUsingLumping(self):
895          """
896          checks if matrix lumping is used a solver method
897    
898          @return: True is lumping is currently used a solver method.
899          @rtype: C{bool}
900          """
901          return self.getSolverMethod()==self.LUMPING
902    
903     def setTolerance(self,tol=1.e-8):     def setTolerance(self,tol=1.e-8):
904         """         """
905         @brief resets the tolerance to tol.         resets the tolerance for the solver method to tol where for an appropriate norm M{|.|}
906    
907           M{|L{getResidual}()|<tol*|L{getRightHandSide}()|}
908    
909           defines the stopping criterion.
910    
911           @param tol: new tolerance for the solver. If the tol is lower then the current tolerence
912                       the system will be resolved.
913           @type tol: positive C{float}
914           @raise ValueException: if tolerance is not positive.
915         """         """
916         if not tol>0:         if not tol>0:
917             raise ValueException,"Tolerance as to be positive"             raise ValueException,"Tolerance as to be positive"
918         if tol<self.getTolerance(): self.__rebuildSolution()         if tol<self.getTolerance(): self.__invalidateSolution()
919         if self.debug() : print "PDE Debug: New tolerance %e",tol         self.trace("New tolerance %e"%tol)
920         self.__tolerance=tol         self.__tolerance=tol
921         return         return
922    
923     def getTolerance(self):     def getTolerance(self):
924         """         """
925         @brief returns the tolerance set for the solution         returns the tolerance set for the solution
926    
927           @return: tolerance currently used.
928           @rtype: C{float}
929         """         """
930         return self.__tolerance         return self.__tolerance
931    
932     #===== symmetry  flag ==========================     # =============================================================================
933       #    symmetry  flag:
934       # =============================================================================
935     def isSymmetric(self):     def isSymmetric(self):
936        """        """
937        @brief returns true is the operator is considered to be symmetric        checks if symmetry is indicated.
938    
939          @return: True is a symmetric PDE is indicated, otherwise False is returned
940          @rtype: C{bool}
941        """        """
942        return self.__sym        return self.__sym
943    
944     def setSymmetryOn(self):     def setSymmetryOn(self):
945        """        """
946        @brief sets the symmetry flag to true        sets the symmetry flag.
947        """        """
948        if not self.isSymmetric():        if not self.isSymmetric():
949           if self.debug() : print "PDE Debug: Operator is set to be symmetric"           self.trace("PDE is set to be symmetric")
950           self.__sym=True           self.__sym=True
951           self.__checkMatrixType()           self.__checkMatrixType()
952    
953     def setSymmetryOff(self):     def setSymmetryOff(self):
954        """        """
955        @brief sets the symmetry flag to false        removes the symmetry flag.
956        """        """
957        if self.isSymmetric():        if self.isSymmetric():
958           if self.debug() : print "PDE Debug: Operator is set to be unsymmetric"           self.trace("PDE is set to be unsymmetric")
959           self.__sym=False           self.__sym=False
960           self.__checkMatrixType()           self.__checkMatrixType()
961    
962     def setSymmetryTo(self,flag=False):     def setSymmetryTo(self,flag=False):
963       """        """
964       @brief sets the symmetry flag to flag        sets the symmetry flag to flag
965    
966       @param flag        @param flag: If flag, the symmetry flag is set otherwise the symmetry flag is released.
967       """        @type flag: C{bool}
968       if flag:        """
969          self.setSymmetryOn()        if flag:
970       else:           self.setSymmetryOn()
971          self.setSymmetryOff()        else:
972             self.setSymmetryOff()
973    
974     #===== order reduction ==========================     # =============================================================================
975       # function space handling for the equation as well as the solution
976       # =============================================================================
977     def setReducedOrderOn(self):     def setReducedOrderOn(self):
978       """       """
979       @brief switches to on reduced order       switches on reduced order for solution and equation representation
980    
981         @raise RuntimeError: if order reduction is altered after a coefficient has been set.
982       """       """
983       self.setReducedOrderForSolutionOn()       self.setReducedOrderForSolutionOn()
984       self.setReducedOrderForEquationOn()       self.setReducedOrderForEquationOn()
985    
986     def setReducedOrderOff(self):     def setReducedOrderOff(self):
987       """       """
988       @brief switches to full order       switches off reduced order for solution and equation representation
989    
990         @raise RuntimeError: if order reduction is altered after a coefficient has been set.
991       """       """
992       self.setReducedOrderForSolutionOff()       self.setReducedOrderForSolutionOff()
993       self.setReducedOrderForEquationOff()       self.setReducedOrderForEquationOff()
994    
995     def setReducedOrderTo(self,flag=False):     def setReducedOrderTo(self,flag=False):
996       """       """
997       @brief sets order according to flag       sets order reduction for both solution and equation representation according to flag.
998         @param flag: if flag is True, the order reduction is switched on for both  solution and equation representation, otherwise or
999       @param flag                    if flag is not present order reduction is switched off
1000         @type flag: C{bool}
1001         @raise RuntimeError: if order reduction is altered after a coefficient has been set.
1002       """       """
1003       self.setReducedOrderForSolutionTo(flag)       self.setReducedOrderForSolutionTo(flag)
1004       self.setReducedOrderForEquationTo(flag)       self.setReducedOrderForEquationTo(flag)
                                                                                                                                                             
1005    
1006     #===== order reduction solution ==========================  
1007     def setReducedOrderForSolutionOn(self):     def setReducedOrderForSolutionOn(self):
1008       """       """
1009       @brief switches to reduced order to interpolate solution       switches on reduced order for solution representation
1010    
1011         @raise RuntimeError: if order reduction is altered after a coefficient has been set.
1012       """       """
1013       new_fs=escript.ReducedSolution(self.getDomain())       if not self.__reduce_solution_order:
1014       if self.getFunctionSpaceForSolution()!=new_fs:           if self.__altered_coefficients:
1015           if self.debug() : print "PDE Debug: Reduced order is used to interpolate solution."                raise RuntimeError,"order cannot be altered after coefficients have been defined."
1016           self.__column_function_space=new_fs           self.trace("Reduced order is used to solution representation.")
1017           self.__rebuildSystem(deep=True)           self.__reduce_solution_order=True
1018             self.__resetSystem()
1019    
1020     def setReducedOrderForSolutionOff(self):     def setReducedOrderForSolutionOff(self):
1021       """       """
1022       @brief switches to full order to interpolate solution       switches off reduced order for solution representation
1023    
1024         @raise RuntimeError: if order reduction is altered after a coefficient has been set.
1025       """       """
1026       new_fs=escript.Solution(self.getDomain())       if self.__reduce_solution_order:
1027       if self.getFunctionSpaceForSolution()!=new_fs:           if self.__altered_coefficients:
1028           if self.debug() : print "PDE Debug: Full order is used to interpolate solution."                raise RuntimeError,"order cannot be altered after coefficients have been defined."
1029           self.__column_function_space=new_fs           self.trace("Full order is used to interpolate solution.")
1030           self.__rebuildSystem(deep=True)           self.__reduce_solution_order=False
1031             self.__resetSystem()
1032    
1033     def setReducedOrderForSolutionTo(self,flag=False):     def setReducedOrderForSolutionTo(self,flag=False):
1034       """       """
1035       @brief sets order for test functions according to flag       sets order for test functions according to flag
1036    
1037       @param flag       @param flag: if flag is True, the order reduction is switched on for solution representation, otherwise or
1038                      if flag is not present order reduction is switched off
1039         @type flag: C{bool}
1040         @raise RuntimeError: if order reduction is altered after a coefficient has been set.
1041       """       """
1042       if flag:       if flag:
1043          self.setReducedOrderForSolutionOn()          self.setReducedOrderForSolutionOn()
1044       else:       else:
1045          self.setReducedOrderForSolutionOff()          self.setReducedOrderForSolutionOff()
1046                                                                                                                                                              
    #===== order reduction equation ==========================  
1047     def setReducedOrderForEquationOn(self):     def setReducedOrderForEquationOn(self):
1048       """       """
1049       @brief switches to reduced order for test functions       switches on reduced order for equation representation
1050    
1051         @raise RuntimeError: if order reduction is altered after a coefficient has been set.
1052       """       """
1053       new_fs=escript.ReducedSolution(self.getDomain())       if not self.__reduce_equation_order:
1054       if self.getFunctionSpaceForEquation()!=new_fs:           if self.__altered_coefficients:
1055           if self.debug() : print "PDE Debug: Reduced order is used for test functions."                raise RuntimeError,"order cannot be altered after coefficients have been defined."
1056           self.__row_function_space=new_fs           self.trace("Reduced order is used for test functions.")
1057           self.__rebuildSystem(deep=True)           self.__reduce_equation_order=True
1058             self.__resetSystem()
1059    
1060     def setReducedOrderForEquationOff(self):     def setReducedOrderForEquationOff(self):
1061       """       """
1062       @brief switches to full order for test functions       switches off reduced order for equation representation
1063    
1064         @raise RuntimeError: if order reduction is altered after a coefficient has been set.
1065       """       """
1066       new_fs=escript.Solution(self.getDomain())       if self.__reduce_equation_order:
1067       if self.getFunctionSpaceForEquation()!=new_fs:           if self.__altered_coefficients:
1068           if self.debug() : print "PDE Debug: Full order is used for test functions."                raise RuntimeError,"order cannot be altered after coefficients have been defined."
1069           self.__row_function_space=new_fs           self.trace("Full order is used for test functions.")
1070           self.__rebuildSystem(deep=True)           self.__reduce_equation_order=False
1071             self.__resetSystem()
1072    
1073     def setReducedOrderForEquationTo(self,flag=False):     def setReducedOrderForEquationTo(self,flag=False):
1074       """       """
1075       @brief sets order for test functions according to flag       sets order for test functions according to flag
1076    
1077       @param flag       @param flag: if flag is True, the order reduction is switched on for equation representation, otherwise or
1078                      if flag is not present order reduction is switched off
1079         @type flag: C{bool}
1080         @raise RuntimeError: if order reduction is altered after a coefficient has been set.
1081       """       """
1082       if flag:       if flag:
1083          self.setReducedOrderForEquationOn()          self.setReducedOrderForEquationOn()
1084       else:       else:
1085          self.setReducedOrderForEquationOff()          self.setReducedOrderForEquationOff()
                                                                                                                                                             
1086    
1087     # ==== initialization =====================================================================     # =============================================================================
1088     def __makeNewOperator(self):     # private method:
1089       # =============================================================================
1090       def __checkMatrixType(self):
1091         """
1092         reassess the matrix type and, if a new matrix is needed, resets the system.
1093         """
1094         new_matrix_type=self.getDomain().getSystemMatrixTypeId(self.getSolverMethod(),self.getSolverPackage(),self.isSymmetric())
1095         if not new_matrix_type==self.__matrix_type:
1096             self.trace("Matrix type is now %d."%new_matrix_type)
1097             self.__matrix_type=new_matrix_type
1098             self.__resetSystem()
1099       #
1100       #   rebuild switches :
1101       #
1102       def __invalidateSolution(self):
1103           """
1104           indicates the PDE has to be resolved if the solution is requested
1105           """
1106           if self.__solution_isValid: self.trace("PDE has to be resolved.")
1107           self.__solution_isValid=False
1108    
1109       def __invalidateOperator(self):
1110           """
1111           indicates the operator has to be rebuilt next time it is used
1112           """
1113           if self.__operator_is_Valid: self.trace("Operator has to be rebuilt.")
1114           self.__invalidateSolution()
1115           self.__operator_is_Valid=False
1116    
1117       def __invalidateRightHandSide(self):
1118         """         """
1119         @brief         indicates the right hand side has to be rebuild next time it is used
1120         """         """
1121           if self.__righthandside_isValid: self.trace("Right hand side has to be rebuilt.")
1122           self.__invalidateSolution()
1123           self.__righthandside_isValid=False
1124    
1125       def __invalidateSystem(self):
1126           """
1127           annonced that everthing has to be rebuild:
1128           """
1129           if self.__righthandside_isValid: self.trace("System has to be rebuilt.")
1130           self.__invalidateSolution()
1131           self.__invalidateOperator()
1132           self.__invalidateRightHandSide()
1133    
1134       def __resetSystem(self):
1135           """
1136           annonced that everthing has to be rebuild:
1137           """
1138           self.trace("New System is built from scratch.")
1139           self.__operator=escript.Operator()
1140           self.__operator_is_Valid=False
1141           self.__righthandside=escript.Data()
1142           self.__righthandside_isValid=False
1143           self.__solution=escript.Data()
1144           self.__solution_isValid=False
1145       #
1146       #    system initialization:
1147       #
1148       def __getNewOperator(self):
1149           """
1150           returns an instance of a new operator
1151           """
1152           self.trace("New operator is allocated.")
1153         return self.getDomain().newOperator( \         return self.getDomain().newOperator( \
1154                             self.getNumEquations(), \                             self.getNumEquations(), \
1155                             self.getFunctionSpaceForEquation(), \                             self.getFunctionSpaceForEquation(), \
# Line 617  class LinearPDE: Line 1157  class LinearPDE:
1157                             self.getFunctionSpaceForSolution(), \                             self.getFunctionSpaceForSolution(), \
1158                             self.__matrix_type)                             self.__matrix_type)
1159    
1160     def __makeNewRightHandSide(self):     def __getNewRightHandSide(self):
1161         """         """
1162         @brief         returns an instance of a new right hand side
1163         """         """
1164         return escript.Data(0.,(self.getNumEquations(),),self.getFunctionSpaceForEquation(),True)         self.trace("New right hand side is allocated.")
1165           if self.getNumEquations()>1:
1166               return escript.Data(0.,(self.getNumEquations(),),self.getFunctionSpaceForEquation(),True)
1167           else:
1168               return escript.Data(0.,(),self.getFunctionSpaceForEquation(),True)
1169    
1170     def __makeNewSolution(self):     def __getNewSolution(self):
1171         """         """
1172         @brief         returns an instance of a new solution
1173         """         """
1174         return escript.Data(0.,(self.getNumSolutions(),),self.getFunctionSpaceForSolution(),True)         self.trace("New solution is allocated.")
1175           if self.getNumSolutions()>1:
1176               return escript.Data(0.,(self.getNumSolutions(),),self.getFunctionSpaceForSolution(),True)
1177           else:
1178               return escript.Data(0.,(),self.getFunctionSpaceForSolution(),True)
1179    
1180     def __getFreshOperator(self):     def __makeFreshSolution(self):
1181         """         """
1182         @brief         makes sure that the solution is instantiated and returns it initialized by zeros
1183         """         """
1184         if self.__operator.isEmpty():         if self.__solution.isEmpty():
1185             self.__operator=self.__makeNewOperator()             self.__solution=self.__getNewSolution()
            if self.debug() : print "PDE Debug: New operator allocated"  
1186         else:         else:
1187             self.__operator.setValue(0.)             self.__solution*=0
1188             if self.debug() : print "PDE Debug: Operator reset to zero"             self.trace("Solution is reset to zero.")
1189         return self.__operator         return self.__solution
1190    
1191     def __getFreshRightHandSide(self):     def __makeFreshRightHandSide(self):
1192         """         """
1193         @brief         makes sure that the right hand side is instantiated and returns it initialized by zeros
1194         """         """
1195         if self.__righthandside.isEmpty():         if self.__righthandside.isEmpty():
1196             self.__righthandside=self.__makeNewRightHandSide()             self.__righthandside=self.__getNewRightHandSide()
            if self.debug() : print "PDE Debug: New right hand side allocated"  
1197         else:         else:
1198             print "fix self.__righthandside*=0"             self.__righthandside*=0
1199             self.__righthandside*=0.             self.trace("Right hand side is reset to zero.")
1200             if self.debug() : print "PDE Debug: Right hand side reset to zero"         return self.__righthandside
        return  self.__righthandside  
1201    
1202     # ==== rebuild switches =====================================================================     def __makeFreshOperator(self):
    def __rebuildSolution(self,deep=False):  
1203         """         """
1204         @brief indicates the PDE has to be reolved if the solution is requested         makes sure that the operator is instantiated and returns it initialized by zeros
1205         """         """
1206         if self.__solution_isValid and self.debug() : print "PDE Debug: PDE has to be resolved."         if self.__operator.isEmpty():
1207         self.__solution_isValid=False             self.__operator=self.__getNewOperator()
1208         if deep: self.__solution=escript.Data(deep)         else:
1209               self.__operator.resetValues()
1210               self.trace("Operator reset to zero")
1211           return self.__operator
1212    
1213     def __rebuildOperator(self,deep=False):     def __applyConstraint(self):
1214         """         """
1215         @brief indicates the operator has to be rebuilt next time it is used         applies the constraints defined by q and r to the system
1216         """         """
1217         if self.__operator_isValid and self.debug() : print "PDE Debug: Operator has to be rebuilt."         if not self.isUsingLumping():
1218         self.__rebuildSolution(deep)            q=self.getCoefficientOfGeneralPDE("q")
1219         self.__operator_isValid=False            r=self.getCoefficientOfGeneralPDE("r")
1220         if deep: self.__operator=escript.Operator()            if not q.isEmpty() and not self.__operator.isEmpty():
1221                 # q is the row and column mask to indicate where constraints are set:
1222                 row_q=escript.Data(q,self.getFunctionSpaceForEquation())
1223                 col_q=escript.Data(q,self.getFunctionSpaceForSolution())
1224                 u=self.__getNewSolution()
1225                 if r.isEmpty():
1226                    r_s=self.__getNewSolution()
1227                 else:
1228                    r_s=escript.Data(r,self.getFunctionSpaceForSolution())
1229                 u.copyWithMask(r_s,col_q)
1230                 if not self.__righthandside.isEmpty():
1231                    self.__righthandside-=self.__operator*u
1232                    self.__righthandside=self.copyConstraint(self.__righthandside)
1233                 self.__operator.nullifyRowsAndCols(row_q,col_q,1.)
1234       # =============================================================================
1235       # function giving access to coefficients of the general PDE:
1236       # =============================================================================
1237       def getCoefficientOfGeneralPDE(self,name):
1238         """
1239         return the value of the coefficient name of the general PDE.
1240    
1241         @note: This method is called by the assembling routine it can be overwritten
1242               to map coefficients of a particular PDE to the general PDE.
1243         @param name: name of the coefficient requested.
1244         @type name: C{string}
1245         @return: the value of the coefficient  name
1246         @rtype: L{Data<escript.Data>}
1247         @raise IllegalCoefficient: if name is not one of coefficients
1248                      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}.
1249         """
1250         if self.hasCoefficientOfGeneralPDE(name):
1251            return self.getCoefficient(name)
1252         else:
1253            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1254    
1255     def __rebuildRightHandSide(self,deep=False):     def hasCoefficientOfGeneralPDE(self,name):
1256         """       """
1257         @brief indicates the right hand side has to be rebuild next time it is used       checks if name is a the name of a coefficient of the general PDE.
1258         """  
1259         if self.__righthandside_isValid and self.debug() : print "PDE Debug: Right hand side has to be rebuilt."       @param name: name of the coefficient enquired.
1260         self.__rebuildSolution(deep)       @type name: C{string}
1261         self.__righthandside_isValid=False       @return: True if name is the name of a coefficient of the general PDE. Otherwise False.
1262         if not self.__homogeneous_constraint: self.__rebuildOperator()       @rtype: C{bool}
        if deep: self.__righthandside=escript.Data()  
1263    
    def __rebuildSystem(self,deep=False):  
        """  
        @brief annonced that all coefficient name has been changed  
        """  
        self.__rebuildSolution(deep)  
        self.__rebuildOperator(deep)  
        self.__rebuildRightHandSide(deep)  
     
    def __checkMatrixType(self):  
1264       """       """
1265       @brief reassess the matrix type and, if needed, initiates an operator rebuild       return self.__COEFFICIENTS_OF_GENEARL_PDE.has_key(name)
1266    
1267       def createCoefficientOfGeneralPDE(self,name):
1268       """       """
1269       new_matrix_type=self.getDomain().getSystemMatrixTypeId(self.getSolverMethod(),self.isSymmetric())       returns a new instance of a coefficient for coefficient name of the general PDE
1270       if not new_matrix_type==self.__matrix_type:  
1271           if self.debug() : print "PDE Debug: Matrix type is now %d."%new_matrix_type       @param name: name of the coefficient requested.
1272           self.__matrix_type=new_matrix_type       @type name: C{string}
1273           self.__rebuildOperator(deep=True)       @return: a coefficient name initialized to 0.
1274         @rtype: L{Data<escript.Data>}
1275         @raise IllegalCoefficient: if name is not one of coefficients
1276                      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}.
1277         """
1278         if self.hasCoefficientOfGeneralPDE(name):
1279            return escript.Data(0,self.getShapeOfCoefficientOfGeneralPDE(name),self.getFunctionSpaceForCoefficientOfGeneralPDE(name))
1280         else:
1281            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1282    
1283       def getFunctionSpaceForCoefficientOfGeneralPDE(self,name):
1284         """
1285         return the L{FunctionSpace<escript.FunctionSpace>} to be used for coefficient name of the general PDE
1286    
1287         @param name: name of the coefficient enquired.
1288         @type name: C{string}
1289         @return: the function space to be used for coefficient name
1290         @rtype: L{FunctionSpace<escript.FunctionSpace>}
1291         @raise IllegalCoefficient: if name is not one of coefficients
1292                      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}.
1293         """
1294         if self.hasCoefficientOfGeneralPDE(name):
1295            return self.__COEFFICIENTS_OF_GENEARL_PDE[name].getFunctionSpace(self.getDomain())
1296         else:
1297            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1298    
1299       def getShapeOfCoefficientOfGeneralPDE(self,name):
1300         """
1301         return the shape of the coefficient name of the general PDE
1302    
1303         @param name: name of the coefficient enquired.
1304         @type name: C{string}
1305         @return: the shape of the coefficient name
1306         @rtype: C{tuple} of C{int}
1307         @raise IllegalCoefficient: if name is not one of coefficients
1308                      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}.
1309         """
1310         if self.hasCoefficientOfGeneralPDE(name):
1311            return self.__COEFFICIENTS_OF_GENEARL_PDE[name].getShape(self.getDomain(),self.getNumEquations(),self.getNumSolutions())
1312         else:
1313            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1314    
1315       # =============================================================================
1316       # functions giving access to coefficients of a particular PDE implementation:
1317       # =============================================================================
1318       def getCoefficient(self,name):
1319         """
1320         returns the value of the coefficient name
1321    
1322         @param name: name of the coefficient requested.
1323         @type name: C{string}
1324         @return: the value of the coefficient name
1325         @rtype: L{Data<escript.Data>}
1326         @raise IllegalCoefficient: if name is not a coefficient of the PDE.
1327         """
1328         if self.hasCoefficient(name):
1329             return self.COEFFICIENTS[name].getValue()
1330         else:
1331            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1332    
1333       def hasCoefficient(self,name):
1334         """
1335         return True if name is the name of a coefficient
1336    
1337         @param name: name of the coefficient enquired.
1338         @type name: C{string}
1339         @return: True if name is the name of a coefficient of the general PDE. Otherwise False.
1340         @rtype: C{bool}
1341         """
1342         return self.COEFFICIENTS.has_key(name)
1343    
1344       def createCoefficient(self, name):
1345         """
1346         create a L{Data<escript.Data>} object corresponding to coefficient name
1347    
1348         @return: a coefficient name initialized to 0.
1349         @rtype: L{Data<escript.Data>}
1350         @raise IllegalCoefficient: if name is not a coefficient of the PDE.
1351         """
1352         if self.hasCoefficient(name):
1353            return escript.Data(0.,self.getShapeOfCoefficient(name),self.getFunctionSpaceForCoefficient(name))
1354         else:
1355            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1356    
1357       def getFunctionSpaceForCoefficient(self,name):
1358         """
1359         return the L{FunctionSpace<escript.FunctionSpace>} to be used for coefficient name
1360    
1361         @param name: name of the coefficient enquired.
1362         @type name: C{string}
1363         @return: the function space to be used for coefficient name
1364         @rtype: L{FunctionSpace<escript.FunctionSpace>}
1365         @raise IllegalCoefficient: if name is not a coefficient of the PDE.
1366         """
1367         if self.hasCoefficient(name):
1368            return self.COEFFICIENTS[name].getFunctionSpace(self.getDomain())
1369         else:
1370            raise ValueError,"unknown coefficient %s requested"%name
1371       def getShapeOfCoefficient(self,name):
1372         """
1373         return the shape of the coefficient name
1374    
1375         @param name: name of the coefficient enquired.
1376         @type name: C{string}
1377         @return: the shape of the coefficient name
1378         @rtype: C{tuple} of C{int}
1379         @raise IllegalCoefficient: if name is not a coefficient of the PDE.
1380         """
1381         if self.hasCoefficient(name):
1382            return self.COEFFICIENTS[name].getShape(self.getDomain(),self.getNumEquations(),self.getNumSolutions())
1383         else:
1384            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1385    
1386       def resetCoefficients(self):
1387         """
1388         resets all coefficients to there default values.
1389         """
1390         for i in self.COEFFICIENTS.iterkeys():
1391             self.COEFFICIENTS[i].resetValue()
1392    
1393     #============ assembling =======================================================     def alteredCoefficient(self,name):
1394     def __copyConstraint(self,u):       """
1395         announce that coefficient name has been changed
1396    
1397         @param name: name of the coefficient enquired.
1398         @type name: C{string}
1399         @raise IllegalCoefficient: if name is not a coefficient of the PDE.
1400         @note: if name is q or r, the method will not trigger a rebuilt of the system as constraints are applied to the solved system.
1401         """
1402         if self.hasCoefficient(name):
1403            self.trace("Coefficient %s has been altered."%name)
1404            if not ((name=="q" or name=="r") and self.isUsingLumping()):
1405               if self.COEFFICIENTS[name].isAlteringOperator(): self.__invalidateOperator()
1406               if self.COEFFICIENTS[name].isAlteringRightHandSide(): self.__invalidateRightHandSide()
1407         else:
1408            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1409    
1410       def copyConstraint(self,u):
1411        """        """
1412        @brief copies the constrint condition into u        copies the constraint into u and returns u.
1413    
1414          @param u: a function of rank 0 is a single PDE is solved and of shape (numSolution,) for a system of PDEs
1415          @type u: L{Data<escript.Data>}
1416          @return: the input u modified by the constraints.
1417          @rtype: L{Data<escript.Data>}
1418          @warning: u is altered if it has the appropriate L{FunctionSpace<escript.FunctionSpace>}
1419        """        """
1420        q=self.getCoefficient("q")        q=self.getCoefficientOfGeneralPDE("q")
1421        r=self.getCoefficient("r")        r=self.getCoefficientOfGeneralPDE("r")
1422        if not q.isEmpty():        if not q.isEmpty():
1423            if r.isEmpty():           if u.isEmpty(): u=escript.Data(0.,q.getShape(),q.getFunctionSpace())
1424               r2=escript.Data(0,u.getShape(),u.getFunctionSpace())           if r.isEmpty():
1425            else:               r=escript.Data(0,u.getShape(),u.getFunctionSpace())
1426               r2=escript.Data(r,u.getFunctionSpace())           else:
1427            u.copyWithMask(r2,escript.Data(q,u.getFunctionSpace()))               r=escript.Data(r,u.getFunctionSpace())
1428             u.copyWithMask(r,escript.Data(q,u.getFunctionSpace()))
1429     def __applyConstraint(self,rhs_update=True):        return u
        """  
        @brief applies the constraints  defined by q and r to the system  
        """  
        q=self.getCoefficient("q")  
        r=self.getCoefficient("r")  
        if not q.isEmpty() and not self.__operator.isEmpty():  
           # q is the row and column mask to indicate where constraints are set:  
           row_q=escript.Data(q,self.getFunctionSpaceForEquation())  
           col_q=escript.Data(q,self.getFunctionSpaceForSolution())  
           u=self.__makeNewSolution()  
           if r.isEmpty():  
              r_s=self.__makeNewSolution()  
           else:  
              r_s=escript.Data(r,self.getFunctionSpaceForSolution())  
           u.copyWithMask(r_s,col_q)  
           if not self.__righthandside.isEmpty() and rhs_update: self.__righthandside-=self.__operator*u  
           self.__operator.nullifyRowsAndCols(row_q,col_q,1.)  
   
    def getOperator(self):  
        """  
        @brief returns the operator of the PDE  
        """  
        if not self.__operator_isValid:  
            # some Constraints are applying for a lumpled stifness matrix:  
            if self.isUsingLumping():  
               if self.getFunctionSpaceForEquation()==self.getFunctionSpaceForSolution():  
                        raise TypeError,"Lumped matrix requires same order for equations and unknowns"  
               if not self.getCoefficient("A").isEmpty():  
                        raise Warning,"Lumped matrix does not allow coefficient A"  
               if not self.getCoefficient("B").isEmpty():  
                        raise Warning,"Lumped matrix does not allow coefficient B"  
               if not self.getCoefficient("C").isEmpty():  
                        raise Warning,"Lumped matrix does not allow coefficient C"  
               if not self.getCoefficient("D").isEmpty():  
                        raise Warning,"Lumped matrix does not allow coefficient D"  
               if self.debug() : print "PDE Debug: New lumped operator is built."  
               mat=self.__makeNewOperator(self)  
            else:  
               if self.debug() : print "PDE Debug: New operator is built."  
               mat=self.__getFreshOperator()  
   
            self.getDomain().addPDEToSystem(mat,escript.Data(), \  
                         self.getCoefficient("A"), \  
                         self.getCoefficient("B"), \  
                         self.getCoefficient("C"), \  
                         self.getCoefficient("D"), \  
                         escript.Data(), \  
                         escript.Data(), \  
                         self.getCoefficient("d"), \  
                         escript.Data(),\  
                         self.getCoefficient("d_contact"), \  
                         escript.Data())  
            if self.isUsingLumping():  
               self.__operator=mat*escript.Data(1,(self.getNumSolutions(),),self.getFunctionSpaceOfSolution(),True)  
            else:  
               self.__applyConstraint(rhs_update=False)  
            self.__operator_isValid=True  
        return self.__operator  
1430    
1431     def getRightHandSide(self,ignoreConstraint=False):     def setValue(self,**coefficients):
1432         """        """
1433         @brief returns the right hand side of the PDE        sets new values to coefficients
1434    
1435         @param ignoreConstraint        @param coefficients: new values assigned to coefficients
1436         """        @keyword A: value for coefficient A.
1437         if not self.__righthandside_isValid:        @type A: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1438             if self.debug() : print "PDE Debug: New right hand side is built."        @keyword B: value for coefficient B
1439             self.getDomain().addPDEToRHS(self.__getFreshRightHandSide(), \        @type B: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1440                           self.getCoefficient("X"), \        @keyword C: value for coefficient C
1441                           self.getCoefficient("Y"),\        @type C: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1442                           self.getCoefficient("y"),\        @keyword D: value for coefficient D
1443                           self.getCoefficient("y_contact"))        @type D: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1444             self.__righthandside_isValid=True        @keyword X: value for coefficient X
1445             if ignoreConstraint: self.__copyConstraint(self.__righthandside)        @type X: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1446         return self.__righthandside        @keyword Y: value for coefficient Y
1447          @type Y: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1448          @keyword d: value for coefficient d
1449          @type d: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
1450          @keyword y: value for coefficient y
1451          @type y: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
1452          @keyword d_contact: value for coefficient d_contact
1453          @type d_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>}.
1454                           or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.
1455          @keyword y_contact: value for coefficient y_contact
1456          @type y_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>}.
1457                           or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.
1458          @keyword r: values prescribed to the solution at the locations of constraints
1459          @type r: any type that can be casted to L{Data<escript.Data>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1460                   depending of reduced order is used for the solution.
1461          @keyword q: mask for location of constraints
1462          @type q: any type that can be casted to L{Data<escript.Data>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1463                   depending of reduced order is used for the representation of the equation.
1464          @raise IllegalCoefficient: if an unknown coefficient keyword is used.
1465          """
1466          # check if the coefficients are  legal:
1467          for i in coefficients.iterkeys():
1468             if not self.hasCoefficient(i):
1469                raise IllegalCoefficient,"Attempt to set unknown coefficient %s"%i
1470          # if the number of unknowns or equations is still unknown we try to estimate them:
1471          if self.__numEquations==None or self.__numSolutions==None:
1472             for i,d in coefficients.iteritems():
1473                if hasattr(d,"shape"):
1474                    s=d.shape
1475                elif hasattr(d,"getShape"):
1476                    s=d.getShape()
1477                else:
1478                    s=numarray.array(d).shape
1479                if s!=None:
1480                    # get number of equations and number of unknowns:
1481                    res=self.COEFFICIENTS[i].estimateNumEquationsAndNumSolutions(self.getDomain(),s)
1482                    if res==None:
1483                        raise IllegalCoefficientValue,"Illegal shape %s of coefficient %s"%(s,i)
1484                    else:
1485                        if self.__numEquations==None: self.__numEquations=res[0]
1486                        if self.__numSolutions==None: self.__numSolutions=res[1]
1487          if self.__numEquations==None: raise UndefinedPDEError,"unidententified number of equations"
1488          if self.__numSolutions==None: raise UndefinedPDEError,"unidententified number of solutions"
1489          # now we check the shape of the coefficient if numEquations and numSolutions are set:
1490          for i,d in coefficients.iteritems():
1491            try:
1492               self.COEFFICIENTS[i].setValue(self.getDomain(),self.getNumEquations(),self.getNumSolutions(),self.reduceEquationOrder(),self.reduceSolutionOrder(),d)
1493            except IllegalCoefficientValue,m:
1494               raise IllegalCoefficientValue("Coefficient %s:%s"%(i,m))
1495            self.alteredCoefficient(i)
1496    
1497          self.__altered_coefficients=True
1498          # check if the systrem is inhomogeneous:
1499          if len(coefficients)>0 and not self.isUsingLumping():
1500             q=self.getCoefficientOfGeneralPDE("q")
1501             r=self.getCoefficientOfGeneralPDE("r")
1502             homogeneous_constraint=True
1503             if not q.isEmpty() and not r.isEmpty():
1504                 if util.Lsup(q*r)>=1.e-13*util.Lsup(r):
1505                   self.trace("Inhomogeneous constraint detected.")
1506                   self.__invalidateSystem()
1507    
1508     def getSystem(self):     def getSystem(self):
1509         """         """
1510         @brief         return the operator and right hand side of the PDE
1511    
1512           @return: the discrete version of the PDE
1513           @rtype: C{tuple} of L{Operator,<escript.Operator>} and L{Data<escript.Data>}.
1514         """         """
1515         if not self.__operator_isValid and not self.__righthandside_isValid:         if not self.__operator_is_Valid or not self.__righthandside_isValid:
           if self.debug() : print "PDE Debug: New PDE is built."  
1516            if self.isUsingLumping():            if self.isUsingLumping():
1517                self.getRightHandSide(ignoreConstraint=True)                if not self.__operator_is_Valid:
1518                self.getOperator()                   if not self.getFunctionSpaceForEquation()==self.getFunctionSpaceForSolution(): raise TypeError,"Lumped matrix requires same order for equations and unknowns"
1519                     if not self.getCoefficientOfGeneralPDE("A").isEmpty(): raise Warning,"Using coefficient A in lumped matrix can produce wrong results"
1520                     if not self.getCoefficientOfGeneralPDE("B").isEmpty(): raise Warning,"Using coefficient B in lumped matrix can produce wrong results"
1521                     if not self.getCoefficientOfGeneralPDE("C").isEmpty(): raise Warning,"Using coefficient C in lumped matrix can produce wrong results"
1522                     mat=self.__getNewOperator()
1523                     self.getDomain().addPDEToSystem(mat,escript.Data(), \
1524                               self.getCoefficientOfGeneralPDE("A"), \
1525                               self.getCoefficientOfGeneralPDE("B"), \
1526                               self.getCoefficientOfGeneralPDE("C"), \
1527                               self.getCoefficientOfGeneralPDE("D"), \
1528                               escript.Data(), \
1529                               escript.Data(), \
1530                               self.getCoefficientOfGeneralPDE("d"), \
1531                               escript.Data(),\
1532                               self.getCoefficientOfGeneralPDE("d_contact"), \
1533                               escript.Data())
1534                     self.__operator=1./(mat*escript.Data(1,(self.getNumSolutions(),),self.getFunctionSpaceForSolution(),True))
1535                     del mat
1536                     self.trace("New lumped operator has been built.")
1537                     self.__operator_is_Valid=True
1538                  if not self.__righthandside_isValid:
1539                     self.getDomain().addPDEToRHS(self.__makeFreshRightHandSide(), \
1540                                   self.getCoefficientOfGeneralPDE("X"), \
1541                                   self.getCoefficientOfGeneralPDE("Y"),\
1542                                   self.getCoefficientOfGeneralPDE("y"),\
1543                                   self.getCoefficientOfGeneralPDE("y_contact"))
1544                     self.trace("New right hand side as been built.")
1545                     self.__righthandside_isValid=True
1546            else:            else:
1547                self.getDomain().addPDEToSystem(self.__getFreshOperator(),self.__getFreshRightHandSide(), \               if not self.__operator_is_Valid and not self.__righthandside_isValid:
1548                              self.getCoefficient("A"), \                   self.getDomain().addPDEToSystem(self.__makeFreshOperator(),self.__makeFreshRightHandSide(), \
1549                              self.getCoefficient("B"), \                                 self.getCoefficientOfGeneralPDE("A"), \
1550                              self.getCoefficient("C"), \                                 self.getCoefficientOfGeneralPDE("B"), \
1551                              self.getCoefficient("D"), \                                 self.getCoefficientOfGeneralPDE("C"), \
1552                              self.getCoefficient("X"), \                                 self.getCoefficientOfGeneralPDE("D"), \
1553                              self.getCoefficient("Y"), \                                 self.getCoefficientOfGeneralPDE("X"), \
1554                              self.getCoefficient("d"), \                                 self.getCoefficientOfGeneralPDE("Y"), \
1555                              self.getCoefficient("y"), \                                 self.getCoefficientOfGeneralPDE("d"), \
1556                              self.getCoefficient("d_contact"), \                                 self.getCoefficientOfGeneralPDE("y"), \
1557                              self.getCoefficient("y_contact"))                                 self.getCoefficientOfGeneralPDE("d_contact"), \
1558            self.__operator_isValid=True                                 self.getCoefficientOfGeneralPDE("y_contact"))
1559            self.__righthandside_isValid=True                   self.__applyConstraint()
1560            self.__applyConstraint()                   self.__righthandside=self.copyConstraint(self.__righthandside)
1561            self.__copyConstraint(self.__righthandside)                   self.trace("New system has been built.")
1562         elif not self.__operator_isValid:                   self.__operator_is_Valid=True
1563            self.getOperator()                   self.__righthandside_isValid=True
1564         elif not self.__righthandside_isValid:               elif not self.__righthandside_isValid:
1565            self.getRightHandSide()                   self.getDomain().addPDEToRHS(self.__makeFreshRightHandSide(), \
1566                                   self.getCoefficientOfGeneralPDE("X"), \
1567                                   self.getCoefficientOfGeneralPDE("Y"),\
1568                                   self.getCoefficientOfGeneralPDE("y"),\
1569                                   self.getCoefficientOfGeneralPDE("y_contact"))
1570                     self.__righthandside=self.copyConstraint(self.__righthandside)
1571                     self.trace("New right hand side has been built.")
1572                     self.__righthandside_isValid=True
1573                 elif not self.__operator_is_Valid:
1574                     self.getDomain().addPDEToSystem(self.__makeFreshOperator(),escript.Data(), \
1575                                self.getCoefficientOfGeneralPDE("A"), \
1576                                self.getCoefficientOfGeneralPDE("B"), \
1577                                self.getCoefficientOfGeneralPDE("C"), \
1578                                self.getCoefficientOfGeneralPDE("D"), \
1579                                escript.Data(), \
1580                                escript.Data(), \
1581                                self.getCoefficientOfGeneralPDE("d"), \
1582                                escript.Data(),\
1583                                self.getCoefficientOfGeneralPDE("d_contact"), \
1584                                escript.Data())
1585                     self.__applyConstraint()
1586                     self.trace("New operator has been built.")
1587                     self.__operator_is_Valid=True
1588         return (self.__operator,self.__righthandside)         return (self.__operator,self.__righthandside)
1589    
    def solve(self,**options):  
       """  
       @brief solve the PDE  
1590    
1591        @param options  class Poisson(LinearPDE):
1592        """     """
1593        mat,f=self.getSystem()     Class to define a Poisson equation problem, which is genear L{LinearPDE} of the form
       if self.isUsingLumping():  
          out=f/mat  
          self.__copyConstraint(out)  
       else:  
          options[util.TOLERANCE_KEY]=self.getTolerance()  
          options[util.METHOD_KEY]=self.getSolverMethod()  
          options[util.SYMMETRY_KEY]=self.isSymmetric()  
          if self.debug() : print "PDE Debug: solver options: ",options  
          out=mat.solve(f,options)  
       return out  
1594    
1595     def getSolution(self,**options):     M{-grad(grad(u)[j])[j] = f}
        """  
        @brief returns the solution of the PDE  
1596    
1597         @param options     with natural boundary conditons
1598         """  
1599         if not self.__solution_isValid:     M{n[j]*grad(u)[j] = 0 }
1600             if self.debug() : print "PDE Debug: PDE is resolved."  
1601             self.__solution=self.solve(**options)     and constraints:
1602             self.__solution_isValid=True  
1603         return self.__solution     M{u=0} where M{q>0}
1604     #============ some serivice functions  =====================================================  
1605     def getDomain(self):     """
1606       """  
1607       @brief returns the domain of the PDE     def __init__(self,domain,f=escript.Data(),q=escript.Data(),debug=False):
1608       """       """
1609       return self.__domain       initializes a new Poisson equation
1610    
1611         @param domain: domain of the PDE
1612         @type domain: L{Domain<escript.Domain>}
1613         @param debug: if True debug informations are printed.
1614    
    def getDim(self):  
1615       """       """
1616       @brief returns the spatial dimension of the PDE       super(Poisson, self).__init__(domain,1,1,debug)
1617         self.COEFFICIENTS={"f": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1618                              "q": PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH)}
1619         self.setSymmetryOn()
1620    
1621       def setValue(self,**coefficients):
1622       """       """
1623       return self.getDomain().getDim()       sets new values to coefficients
1624    
1625     def getNumEquations(self):       @param coefficients: new values assigned to coefficients
1626         @keyword f: value for right hand side M{f}
1627         @type f: any type that can be casted to L{Scalar<escript.Scalar>} object on L{Function<escript.Function>}.
1628         @keyword q: mask for location of constraints
1629         @type q: any type that can be casted to rank zeo L{Data<escript.Data>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1630                   depending of reduced order is used for the representation of the equation.
1631         @raise IllegalCoefficient: if an unknown coefficient keyword is used.
1632         """
1633         super(Poisson, self).setValue(**coefficients)
1634    
1635       def getCoefficientOfGeneralPDE(self,name):
1636         """
1637         return the value of the coefficient name of the general PDE
1638         @param name: name of the coefficient requested.
1639         @type name: C{string}
1640         @return: the value of the coefficient  name
1641         @rtype: L{Data<escript.Data>}
1642         @raise IllegalCoefficient: if name is not one of coefficients
1643                      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}.
1644         @note: This method is called by the assembling routine to map the Possion equation onto the general PDE.
1645         """
1646         if name == "A" :
1647             return escript.Data(numarray.identity(self.getDim()),escript.Function(self.getDomain()))
1648         elif name == "B" :
1649             return escript.Data()
1650         elif name == "C" :
1651             return escript.Data()
1652         elif name == "D" :
1653             return escript.Data()
1654         elif name == "X" :
1655             return escript.Data()
1656         elif name == "Y" :
1657             return self.getCoefficient("f")
1658         elif name == "d" :
1659             return escript.Data()
1660         elif name == "y" :
1661             return escript.Data()
1662         elif name == "d_contact" :
1663             return escript.Data()
1664         elif name == "y_contact" :
1665             return escript.Data()
1666         elif name == "r" :
1667             return escript.Data()
1668         elif name == "q" :
1669             return self.getCoefficient("q")
1670         else:
1671            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1672    
1673    class Helmholtz(LinearPDE):
1674       """
1675       Class to define a Helmhotz equation problem, which is genear L{LinearPDE} of the form
1676    
1677       M{S{omega}*u - grad(k*grad(u)[j])[j] = f}
1678    
1679       with natural boundary conditons
1680    
1681       M{k*n[j]*grad(u)[j] = g- S{alpha}u }
1682    
1683       and constraints:
1684    
1685       M{u=r} where M{q>0}
1686    
1687       """
1688    
1689       def __init__(self,domain,debug=False):
1690       """       """
1691       @brief returns the number of equations       initializes a new Poisson equation
1692    
1693         @param domain: domain of the PDE
1694         @type domain: L{Domain<escript.Domain>}
1695         @param debug: if True debug informations are printed.
1696    
1697         """
1698         super(Helmholtz, self).__init__(domain,1,1,debug)
1699         self.COEFFICIENTS={"omega": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.OPERATOR),
1700                            "k": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.OPERATOR),
1701                            "f": PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1702                            "alpha": PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.OPERATOR),
1703                            "g": PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1704                            "r": PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH),
1705                            "q": PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH)}
1706         self.setSymmetryOn()
1707    
1708       def setValue(self,**coefficients):
1709       """       """
1710       if self.__numEquations>0:       sets new values to coefficients
1711           return self.__numEquations  
1712         @param coefficients: new values assigned to coefficients
1713         @keyword omega: value for coefficient M{S{omega}}
1714         @type omega: any type that can be casted to L{Scalar<escript.Scalar>} object on L{Function<escript.Function>}.
1715         @keyword k: value for coefficeint M{k}
1716         @type k: any type that can be casted to L{Scalar<escript.Scalar>} object on L{Function<escript.Function>}.
1717         @keyword f: value for right hand side M{f}
1718         @type f: any type that can be casted to L{Scalar<escript.Scalar>} object on L{Function<escript.Function>}.
1719         @keyword alpha: value for right hand side M{S{alpha}}
1720         @type alpha: any type that can be casted to L{Scalar<escript.Scalar>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
1721         @keyword g: value for right hand side M{g}
1722         @type g: any type that can be casted to L{Scalar<escript.Scalar>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
1723         @keyword r: prescribed values M{r} for the solution in constraints.
1724         @type r: any type that can be casted to L{Scalar<escript.Scalar>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1725                   depending of reduced order is used for the representation of the equation.
1726         @keyword q: mask for location of constraints
1727         @type q: any type that can be casted to L{Scalar<escript.Scalar>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1728                   depending of reduced order is used for the representation of the equation.
1729         @raise IllegalCoefficient: if an unknown coefficient keyword is used.
1730         """
1731         super(Helmholtz, self).setValue(**coefficients)
1732    
1733       def getCoefficientOfGeneralPDE(self,name):
1734         """
1735         return the value of the coefficient name of the general PDE
1736    
1737         @param name: name of the coefficient requested.
1738         @type name: C{string}
1739         @return: the value of the coefficient  name
1740         @rtype: L{Data<escript.Data>}
1741         @raise IllegalCoefficient: if name is not one of coefficients
1742                      "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}.
1743         @note: This method is called by the assembling routine to map the Possion equation onto the general PDE.
1744         """
1745         if name == "A" :
1746             return escript.Data(numarray.identity(self.getDim()),escript.Function(self.getDomain()))*self.getCoefficient("k")
1747         elif name == "B" :
1748             return escript.Data()
1749         elif name == "C" :
1750             return escript.Data()
1751         elif name == "D" :
1752             return self.getCoefficient("omega")
1753         elif name == "X" :
1754             return escript.Data()
1755         elif name == "Y" :
1756             return self.getCoefficient("f")
1757         elif name == "d" :
1758             return self.getCoefficient("alpha")
1759         elif name == "y" :
1760             return self.getCoefficient("g")
1761         elif name == "d_contact" :
1762             return escript.Data()
1763         elif name == "y_contact" :
1764             return escript.Data()
1765         elif name == "r" :
1766             return self.getCoefficient("r")
1767         elif name == "q" :
1768             return self.getCoefficient("q")
1769       else:       else:
1770           raise ValueError,"Number of equations is undefined. Please specify argument numEquations."          raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1771    
1772     def getNumSolutions(self):  class LameEquation(LinearPDE):
1773       """     """
1774       @brief returns the number of unknowns     Class to define a Lame equation problem:
1775    
1776       M{-grad(S{mu}*(grad(u[i])[j]+grad(u[j])[i]))[j] - grad(S{lambda}*grad(u[j])[i])[j] = F_i -grad(S{sigma}[i,j])[j] }
1777    
1778       with natural boundary conditons:
1779    
1780       M{n[j]*(S{mu}*(grad(u[i])[j]+grad(u[j])[i]) - S{lambda}*grad(u[j])[i]) = f_i -n[j]*S{sigma}[i,j] }
1781    
1782       and constraints:
1783    
1784       M{u[i]=r[i]} where M{q[i]>0}
1785    
1786       """
1787    
1788       def __init__(self,domain,debug=False):
1789          super(LameEquation, self).__init__(domain,\
1790                                             domain.getDim(),domain.getDim(),debug)
1791          self.COEFFICIENTS={ "lame_lambda"  : PDECoefficient(PDECoefficient.INTERIOR,(),PDECoefficient.OPERATOR),
1792                              "lame_mu"      : PDECoefficient(PDECoefficient.INTERIOR,(),PDECoefficient.OPERATOR),
1793                              "F"            : PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1794                              "sigma"        : PDECoefficient(PDECoefficient.INTERIOR,(PDECoefficient.BY_EQUATION,PDECoefficient.BY_DIM),PDECoefficient.RIGHTHANDSIDE),
1795                              "f"            : PDECoefficient(PDECoefficient.BOUNDARY,(PDECoefficient.BY_EQUATION,),PDECoefficient.RIGHTHANDSIDE),
1796                              "r"            : PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH),
1797                              "q"            : PDECoefficient(PDECoefficient.SOLUTION,(PDECoefficient.BY_EQUATION,),PDECoefficient.BOTH)}
1798          self.setSymmetryOn()
1799    
1800       def setValue(self,**coefficients):
1801       """       """
1802       if self.__numSolutions>0:       sets new values to coefficients
1803          return self.__numSolutions  
1804         @param coefficients: new values assigned to coefficients
1805         @keyword lame_mu: value for coefficient M{S{mu}}
1806         @type lame_mu: any type that can be casted to L{Scalar<escript.Scalar>} object on L{Function<escript.Function>}.
1807         @keyword lame_lambda: value for coefficient M{S{lambda}}
1808         @type lame_lambda: any type that can be casted to L{Scalar<escript.Scalar>} object on L{Function<escript.Function>}.
1809         @keyword F: value for internal force M{F}
1810         @type F: any type that can be casted to L{Vector<escript.Vector>} object on L{Function<escript.Function>}
1811         @keyword sigma: value for initial stress M{S{sigma}}
1812         @type sigma: any type that can be casted to L{Tensor<escript.Tensor>} object on L{Function<escript.Function>}
1813         @keyword f: value for extrenal force M{f}
1814         @type f: any type that can be casted to L{Vector<escript.Vector>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}
1815         @keyword r: prescribed values M{r} for the solution in constraints.
1816         @type r: any type that can be casted to L{Vector<escript.Vector>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1817                   depending of reduced order is used for the representation of the equation.
1818         @keyword q: mask for location of constraints
1819         @type q: any type that can be casted to L{Vector<escript.Vector>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1820                   depending of reduced order is used for the representation of the equation.
1821         @raise IllegalCoefficient: if an unknown coefficient keyword is used.
1822         """
1823         super(LameEquation, self).setValue(**coefficients)
1824    
1825       def getCoefficientOfGeneralPDE(self,name):
1826         """
1827         return the value of the coefficient name of the general PDE
1828    
1829         @param name: name of the coefficient requested.
1830         @type name: C{string}
1831         @return: the value of the coefficient  name
1832         @rtype: L{Data<escript.Data>}
1833         @raise IllegalCoefficient: if name is not one of coefficients
1834                      "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}.
1835         @note: This method is called by the assembling routine to map the Possion equation onto the general PDE.
1836         """
1837         if name == "A" :
1838             out =self.createCoefficientOfGeneralPDE("A")
1839             for i in range(self.getDim()):
1840               for j in range(self.getDim()):
1841                 out[i,i,j,j] += self.getCoefficient("lame_lambda")
1842                 out[i,j,j,i] += self.getCoefficient("lame_mu")
1843                 out[i,j,i,j] += self.getCoefficient("lame_mu")
1844             return out
1845         elif name == "B" :
1846             return escript.Data()
1847         elif name == "C" :
1848             return escript.Data()
1849         elif name == "D" :
1850             return escript.Data()
1851         elif name == "X" :
1852             return self.getCoefficient("sigma")
1853         elif name == "Y" :
1854             return self.getCoefficient("F")
1855         elif name == "d" :
1856             return escript.Data()
1857         elif name == "y" :
1858             return self.getCoefficient("f")
1859         elif name == "d_contact" :
1860             return escript.Data()
1861         elif name == "y_contact" :
1862             return escript.Data()
1863         elif name == "r" :
1864             return self.getCoefficient("r")
1865         elif name == "q" :
1866             return self.getCoefficient("q")
1867       else:       else:
1868          raise ValueError,"Number of solution is undefined. Please specify argument numSolutions."          raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
1869    
1870    class AdvectivePDE(LinearPDE):
1871       """
1872       In cases of PDEs dominated by the advection terms M{B} and M{C} against the adevctive terms M{A}
1873       up-winding has been used.  The L{AdvectivePDE} class applies SUPG upwinding to the advective terms.
1874    
1875     def checkSymmetry(self):     In the following we set
       """  
       @brief returns if the Operator is symmetric. This is a very expensive operation!!! The symmetry flag is not altered.  
       """  
       raise SystemError,"checkSymmetry is not implemented yet"  
1876    
1877        return None     M{Z[j]=C[j]-B[j]}
1878    
1879     def getFlux(self,u):     or
        """  
        @brief returns the flux J_ij for a given u  
1880    
1881              J_ij=A_{ijkl}u_{k,l}+B_{ijk}u_k-X_{ij}     M{Z[i,k,l]=C[i,k,l]-B[i,l,k]}
1882    
1883         @param u argument of the operator     To measure the dominance of the advective terms over the diffusive term M{A} the
1884       X{Pelclet number} M{P} is used. It is defined as
1885    
1886         """     M{P=h|Z|/(2|A|)}
        raise SystemError,"getFlux is not implemented yet"  
        return None  
1887    
1888     def applyOperator(self,u):     where M{|.|} denotes the L{length<util.length>} of the arument and M{h} is the local cell size
1889         """     from L{getSize<escript.Domain.getSize>}. Where M{|A|==0} M{P} is M{S{infinity}}.
        @brief applies the operator of the PDE to a given solution u in weak from  
1890    
1891         @param u argument of the operator     From the X{Pelclet number} the stabilization parameters M{S{Xi}} and M{S{Xi}} are calculated:
1892    
1893         """     M{S{Xi}=S{xi}(P) h/|Z|}
        return self.getOperator()*escript.Data(u,self.getFunctionSpaceForSolution())  
                                                                                                                                                             
    def getResidual(self,u):  
        """  
        @brief return the residual of u in the weak from  
1894    
1895         @param u     where M{S{xi}} is a suitable function of the Peclet number.
1896         """  
1897         return self.applyOperator(u)-self.getRightHandSide()     In the case of a single PDE the coefficient are up-dated in the following way:
1898             - M{A[i,j] S{<-} A[i,j] + S{Xi} * Z[j] * Z[l]}
1899             - M{B[j] S{<-} B[j] + S{Xi} * C[j] * D}
1900             - M{C[j] S{<-} C[j] + S{Xi} * B[j] * D}
1901             - M{X[j] S{<-} X[j] + S{Xi} * Z[j] * Y}
1902    
1903       Similar for the case of a systems of PDEs:
1904             - 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]}
1905             - M{B[i,j,k] S{<-} B[i,j,k] +  S{delta}[p,m] * S{Xi} * D[p,k] * C[m,i,j]}
1906             - M{C[i,k,l] S{<-} C[i,k,l] +  S{delta}[p,m] * S{Xi} * D[p,k] * B[m,l,i]}
1907             - M{X[i,j] S{<-} X[i,j] + S{delta}[p,m] * S{Xi}  * Y[p] * Z[m,i,j]}
1908    
1909       where M{S{delta}} is L{kronecker}.
1910       Using upwinding in this form, introduces an additonal error which is proprtional to the cell size M{h}
1911       but with the intension to stabilize the solution.
1912    
 class Poisson(LinearPDE):  
1913     """     """
1914     @brief Class to define a Poisson equstion problem:     def __init__(self,domain,numEquations=None,numSolutions=None,xi=None,debug=False):
1915                                                                                                                                                                      """
1916     class to define a linear PDE of the form        creates a linear, steady, second order PDE on a L{Domain<escript.Domain>}
1917                                                                                                                                                                
1918          -u_{,jj} = f        @param domain: domain of the PDE
1919                                                                                                                                                                      @type domain: L{Domain<escript.Domain>}
1920       with boundary conditons:        @param numEquations: number of equations. If numEquations==None the number of equations
1921                                                                                                                                                                                           is exracted from the PDE coefficients.
1922          n_j*u_{,j} = 0        @param numSolutions: number of solution components. If  numSolutions==None the number of solution components
1923                                                                                                                                                                                           is exracted from the PDE coefficients.
1924      and constraints:        @param xi: defines a function which returns for any given Preclet number as L{Scalar<escript.Scalar>} object the
1925                                                                                                                                                                                 M{S{xi}}-value used to define the stabilization parameters. If equal to None, L{ELMAN_RAMAGE} is used.
1926           u=0 where q>0        @type xi: callable object which returns a L{Scalar<escript.Scalar>} object.
1927                                                                                                                                                                      @param debug: if True debug informations are printed.
1928     """        """
1929          super(AdvectivePDE, self).__init__(domain,\
1930     def __init__(self,domain=None,f=escript.Data(),q=escript.Data()):                                           numEquations,numSolutions,debug)
1931         LinearPDE.__init__(self,domain=identifyDomain(domain,{"f":f, "q":q}))        if xi==None:
1932         self._setValue(A=numarray.identity(self.getDomain().getDim()))           self.__xi=AdvectivePDE.ELMAN_RAMAGE
1933         self.setSymmetryOn()        else:
1934         self.setValue(f,q)           self.__xi=xi
1935          self.__Xi=escript.Data()
1936     def setValue(self,f=escript.Data(),q=escript.Data()):  
1937         self._setValue(Y=f,q=q)     def setValue(**coefficients):
1938          """
1939                                                                                                                                                                    sets new values to coefficients
1940    
1941          @param coefficients: new values assigned to coefficients
1942          @keyword A: value for coefficient A.
1943          @type A: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1944          @keyword B: value for coefficient B
1945          @type B: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1946          @keyword C: value for coefficient C
1947          @type C: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1948          @keyword D: value for coefficient D
1949          @type D: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1950          @keyword X: value for coefficient X
1951          @type X: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1952          @keyword Y: value for coefficient Y
1953          @type Y: any type that can be casted to L{Data<escript.Data>} object on L{Function<escript.Function>}.
1954          @keyword d: value for coefficient d
1955          @type d: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
1956          @keyword y: value for coefficient y
1957          @type y: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnBoundary<escript.FunctionOnBoundary>}.
1958          @keyword d_contact: value for coefficient d_contact
1959          @type d_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>}.
1960                           or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.
1961          @keyword y_contact: value for coefficient y_contact
1962          @type y_contact: any type that can be casted to L{Data<escript.Data>} object on L{FunctionOnContactOne<escript.FunctionOnContactOne>}.
1963                           or  L{FunctionOnContactZero<escript.FunctionOnContactZero>}.
1964          @keyword r: values prescribed to the solution at the locations of constraints
1965          @type r: any type that can be casted to L{Data<escript.Data>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1966                   depending of reduced order is used for the solution.
1967          @keyword q: mask for location of constraints
1968          @type q: any type that can be casted to L{Data<escript.Data>} object on L{Solution<escript.Solution>} or L{ReducedSolution<escript.ReducedSolution>}
1969                   depending of reduced order is used for the representation of the equation.
1970          @raise IllegalCoefficient: if an unknown coefficient keyword is used.
1971    
1972          """
1973          if "A" in coefficients.keys()   or "B" in coefficients.keys() or "C" in coefficients.keys(): self.__Xi=escript.Data()
1974          super(AdvectivePDE, self).setValue(**coefficients)
1975    
1976       def ELMAN_RAMAGE(self,P):
1977         """
1978         Predefined function to set a values for M{S{xi}} from a Preclet number M{P}.
1979         This function uses the method suggested by H.C. Elman and A. Ramage, I{SIAM J. Numer. Anal.}, B{40} (2002)
1980              - M{S{xi}(P)=0} for M{P<1}
1981              - M{S{xi}(P)=(1-1/P)/2} otherwise
1982    
1983         @param P: Preclet number
1984         @type P: L{Scalar<escript.Scalar>}
1985         @return: up-wind weightimg factor
1986         @rtype: L{Scalar<escript.Scalar>}
1987         """
1988         return util.wherePositive(P-1.)*0.5*(1.-1./(P+1.e-15))
1989    
1990       def SIMPLIFIED_BROOK_HUGHES(self,P):
1991         """
1992         Predefined function to set a values for M{S{xi}} from a Preclet number M{P}.
1993         The original methods is
1994    
1995         M{S{xi}(P)=coth(P)-1/P}
1996    
1997         As the evaluation of M{coth} is expensive we are using the approximation:
1998    
1999             - M{S{xi}(P)=P/3} where M{P<3}
2000             - M{S{xi}(P)=1/2} otherwise
2001    
2002         @param P: Preclet number
2003         @type P: L{Scalar<escript.Scalar>}
2004         @return: up-wind weightimg factor
2005         @rtype: L{Scalar<escript.Scalar>}
2006         """
2007         c=util.whereNegative(P-3.)
2008         return P/6.*c+1./2.*(1.-c)
2009    
2010       def HALF(self,P):
2011         """
2012         Predefined function to set value M{1/2} for M{S{xi}}
2013    
2014         @param P: Preclet number
2015         @type P: L{Scalar<escript.Scalar>}
2016         @return: up-wind weightimg factor
2017         @rtype: L{Scalar<escript.Scalar>}
2018         """
2019         return escript.Scalar(0.5,P.getFunctionSpace())
2020    
2021       def __calculateXi(self,peclet_factor,Z,h):
2022           Z_max=util.Lsup(Z)
2023           if Z_max>0.:
2024              return h*self.__xi(Z*peclet_factor)/(Z+Z_max*self.__TOL)
2025           else:
2026              return 0.
2027    
2028       def __getXi(self):
2029          if self.__Xi.isEmpty():
2030             B=self.getCoefficient("B")
2031             C=self.getCoefficient("C")
2032             A=self.getCoefficient("A")
2033             h=self.getDomain().getSize()
2034             self.__Xi=escript.Scalar(0.,self.getFunctionSpaceForCoefficient("A"))
2035             if not C.isEmpty() or not B.isEmpty():
2036                if not C.isEmpty() and not B.isEmpty():
2037                    Z2=escript.Scalar(0,self.getFunctionSpaceForCoefficient("A"))
2038                    if self.getNumEquations()>1:
2039                       if self.getNumSolutions()>1:
2040                          for i in range(self.getNumEquations()):
2041                             for k in range(self.getNumSolutions()):
2042                                for l in range(self.getDim()): Z2+=(C[i,k,l]-B[i,l,k])**2
2043                       else:
2044                          for i in range(self.getNumEquations()):
2045                             for l in range(self.getDim()): Z2+=(C[i,l]-B[i,l])**2
2046                    else:
2047                       if self.getNumSolutions()>1:
2048                          for k in range(self.getNumSolutions()):
2049                             for l in range(self.getDim()): Z2+=(C[k,l]-B[l,k])**2
2050                       else:
2051                          for l in range(self.getDim()): Z2+=(C[l]-B[l])**2
2052                    length_of_Z=util.sqrt(Z2)
2053                elif C.isEmpty():
2054                  length_of_Z=util.length(B)
2055                else:
2056                  length_of_Z=util.length(C)
2057    
2058                Z_max=util.Lsup(length_of_Z)
2059                if Z_max>0.:
2060                   length_of_A=util.length(A)
2061                   A_max=util.Lsup(length_of_A)
2062                   if A_max>0:
2063                        inv_A=1./(length_of_A+A_max*self.__TOL)
2064                   else:
2065                        inv_A=1./self.__TOL
2066                   peclet_number=length_of_Z*h/2*inv_A
2067                   xi=self.__xi(peclet_number)
2068                   self.__Xi=h*xi/(length_of_Z+Z_max*self.__TOL)
2069                   self.trace("preclet number = %e"%util.Lsup(peclet_number))
2070          return self.__Xi
2071    
2072    
2073       def getCoefficientOfGeneralPDE(self,name):
2074         """
2075         return the value of the coefficient name of the general PDE
2076    
2077         @param name: name of the coefficient requested.
2078         @type name: C{string}
2079         @return: the value of the coefficient name
2080         @rtype: L{Data<escript.Data>}
2081         @raise IllegalCoefficient: if name is not one of coefficients
2082                      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}.
2083         @note: This method is called by the assembling routine to map the Possion equation onto the general PDE.
2084         """
2085         if not self.getNumEquations() == self.getNumSolutions():
2086              raise ValueError,"AdvectivePDE expects the number of solution componets and the number of equations to be equal."
2087    
2088         if name == "A" :
2089             A=self.getCoefficient("A")
2090             B=self.getCoefficient("B")
2091             C=self.getCoefficient("C")
2092             if B.isEmpty() and C.isEmpty():
2093                Aout=A
2094             else:
2095                if A.isEmpty():
2096                   Aout=self.createNewCoefficient("A")
2097                else:
2098                   Aout=A[:]
2099                Xi=self.__getXi()
2100                if self.getNumEquations()>1:
2101                    for i in range(self.getNumEquations()):
2102                       for j in range(self.getDim()):
2103                          for k in range(self.getNumSolutions()):
2104                             for l in range(self.getDim()):
2105                                if not C.isEmpty() and not B.isEmpty():
2106                                   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])
2107                                elif C.isEmpty():
2108                                   for p in range(self.getNumEquations()): Aout[i,j,k,l]+=Xi*B[p,j,i]*B[p,l,k]
2109                                else:
2110                                   for p in range(self.getNumEquations()): Aout[i,j,k,l]+=Xi*C[p,i,j]*C[p,k,l]
2111                else:
2112                    for j in range(self.getDim()):
2113                       for l in range(self.getDim()):
2114                          if not C.isEmpty() and not B.isEmpty():
2115                              Aout[j,l]+=Xi*(C[j]-B[j])*(C[l]-B[l])
2116                          elif C.isEmpty():
2117                              Aout[j,l]+=Xi*B[j]*B[l]
2118                          else:
2119                              Aout[j,l]+=Xi*C[j]*C[l]
2120             return Aout
2121         elif name == "B" :
2122             B=self.getCoefficient("B")
2123             C=self.getCoefficient("C")
2124             D=self.getCoefficient("D")
2125             if C.isEmpty() or D.isEmpty():
2126                Bout=B
2127             else:
2128                Xi=self.__getXi()
2129                if B.isEmpty():
2130                    Bout=self.createNewCoefficient("B")
2131                else:
2132                    Bout=B[:]
2133                if self.getNumEquations()>1:
2134                   for k in range(self.getNumSolutions()):
2135                      for p in range(self.getNumEquations()):
2136                         tmp=Xi*D[p,k]
2137                         for i in range(self.getNumEquations()):
2138                            for j in range(self.getDim()):
2139                               Bout[i,j,k]+=tmp*C[p,i,j]
2140                else:
2141                   tmp=Xi*D
2142                   for j in range(self.getDim()): Bout[j]+=tmp*C[j]
2143             return Bout
2144         elif name == "C" :
2145             B=self.getCoefficient("B")
2146             C=self.getCoefficient("C")
2147             D=self.getCoefficient("D")
2148             if B.isEmpty() or D.isEmpty():
2149                Cout=C
2150             else:
2151                Xi=self.__getXi()
2152                if C.isEmpty():
2153                    Cout=self.createNewCoefficient("C")
2154                else:
2155                    Cout=C[:]
2156                if self.getNumEquations()>1:
2157                   for k in range(self.getNumSolutions()):
2158                       for p in range(self.getNumEquations()):
2159                          tmp=Xi*D[p,k]
2160                          for i in range(self.getNumEquations()):
2161                            for l in range(self.getDim()):
2162                                     Cout[i,k,l]+=tmp*B[p,l,i]
2163                else:
2164                   tmp=Xi*D
2165                   for j in range(self.getDim()): Cout[j]+=tmp*B[j]
2166             return Cout
2167         elif name == "D" :
2168             return self.getCoefficient("D")
2169         elif name == "X" :
2170             X=self.getCoefficient("X")
2171             Y=self.getCoefficient("Y")
2172             B=self.getCoefficient("B")
2173             C=self.getCoefficient("C")
2174             if Y.isEmpty() or (B.isEmpty() and C.isEmpty()):
2175                Xout=X
2176             else:
2177                if X.isEmpty():
2178                    Xout=self.createNewCoefficient("X")
2179                else:
2180                    Xout=X[:]
2181                Xi=self.__getXi()
2182                if self.getNumEquations()>1:
2183                     for p in range(self.getNumEquations()):
2184                        tmp=Xi*Y[p]
2185                        for i in range(self.getNumEquations()):
2186                           for j in range(self.getDim()):
2187                              if not C.isEmpty() and not B.isEmpty():
2188                                 Xout[i,j]+=tmp*(C[p,i,j]-B[p,j,i])
2189                              elif C.isEmpty():
2190                                 Xout[i,j]-=tmp*B[p,j,i]
2191                              else:
2192                                 Xout[i,j]+=tmp*C[p,i,j]
2193                else:
2194                     tmp=Xi*Y
2195                     for j in range(self.getDim()):
2196                        if not C.isEmpty() and not B.isEmpty():
2197                           Xout[j]+=tmp*(C[j]-B[j])
2198                        elif C.isEmpty():
2199                           Xout[j]-=tmp*B[j]
2200                        else:
2201                           Xout[j]+=tmp*C[j]
2202             return Xout
2203         elif name == "Y" :
2204             return self.getCoefficient("Y")
2205         elif name == "d" :
2206             return self.getCoefficient("d")
2207         elif name == "y" :
2208             return self.getCoefficient("y")
2209         elif name == "d_contact" :
2210             return self.getCoefficient("d_contact")
2211         elif name == "y_contact" :
2212             return self.getCoefficient("y_contact")
2213         elif name == "r" :
2214             return self.getCoefficient("r")
2215         elif name == "q" :
2216             return self.getCoefficient("q")
2217         else:
2218            raise IllegalCoefficient,"illegal coefficient %s requested for general PDE."%name
2219    
2220    
2221  # $Log$  # $Log$
2222  # Revision 1.3  2004/12/17 07:43:10  jgs  # Revision 1.14  2005/09/22 01:54:57  jgs
2223  # *** empty log message ***  # Merge of development branch dev-02 back to main trunk on 2005-09-22
2224    #
2225    # Revision 1.13  2005/09/15 03:44:19  jgs
2226    # Merge of development branch dev-02 back to main trunk on 2005-09-15
2227    #
2228    # Revision 1.12  2005/09/01 03:31:28  jgs
2229    # Merge of development branch dev-02 back to main trunk on 2005-09-01
2230    #
2231    # Revision 1.11  2005/08/23 01:24:28  jgs
2232    # Merge of development branch dev-02 back to main trunk on 2005-08-23
2233    #
2234    # Revision 1.10  2005/08/12 01:45:36  jgs
2235    # erge of development branch dev-02 back to main trunk on 2005-08-12
2236    #
2237    # Revision 1.9.2.17  2005/09/21 07:03:33  matt
2238    # PDECoefficient and LinearPDE are now new style classes (introduced in Python
2239    # 2.2). Classes Poisson, Helmholtz, LameEquation and AdvectivePDE have been
2240    # modified to instead use portable/cooperative "super" calls to extend base
2241    # class methods.
2242    #
2243    # Revision 1.9.2.16  2005/09/16 01:54:37  matt
2244    # Removed redundant if-loop.
2245    #
2246    # Revision 1.9.2.15  2005/09/14 08:09:18  matt
2247    # Added "REDUCED" solution PDECoefficient descriptors for LinearPDEs.
2248    #
2249    # Revision 1.9.2.14  2005/09/07 06:26:16  gross
2250    # the solver from finley are put into the standalone package paso now
2251    #
2252    # Revision 1.9.2.13  2005/08/31 08:45:03  gross
2253    # in the case of lumping no new system is allocated if the constraint is changed.
2254    #
2255    # Revision 1.9.2.12  2005/08/31 07:10:23  gross
2256    # test for Lumping added
2257    #
2258    # Revision 1.9.2.11  2005/08/30 01:53:45  gross
2259    # bug in format fixed.
2260    #
2261    # Revision 1.9.2.10  2005/08/26 07:14:17  gross
2262    # a few more bugs in linearPDE fixed. remaining problem are finley problems
2263    #
2264    # Revision 1.9.2.9  2005/08/26 06:30:45  gross
2265    # fix for reported bug  0000004. test_linearPDE passes a few more tests
2266    #
2267    # Revision 1.9.2.8  2005/08/26 04:30:13  gross
2268    # gneric unit testing for linearPDE
2269    #
2270    # Revision 1.9.2.7  2005/08/25 07:06:50  gross
2271    # linearPDE documentation is parsed now by epydoc. there is still a problem with links into escriptcpp.so
2272    #
2273    # Revision 1.9.2.6  2005/08/24 05:01:24  gross
2274    # problem with resetting the matrix in case of resetting its values to 0 fixed.
2275    #
2276    # Revision 1.9.2.5  2005/08/24 02:03:28  gross
2277    # epydoc mark up partially fixed
2278    #
2279    # Revision 1.9.2.4  2005/08/22 07:11:09  gross
2280    # some problems with LinearPDEs fixed.
2281    #
2282    # Revision 1.9.2.3  2005/08/18 04:48:48  gross
2283    # the methods SetLumping*() are removed. Lumping is set trough setSolverMethod(LinearPDE.LUMPING)
2284    #
2285    # Revision 1.9.2.2  2005/08/18 04:39:32  gross
2286    # the constants have been removed from util.py as they not needed anymore. PDE related constants are accessed through LinearPDE attributes now
2287    #
2288    # Revision 1.9.2.1  2005/07/29 07:10:27  gross
2289    # new functions in util and a new pde type in linearPDEs
2290    #
2291    # Revision 1.1.2.25  2005/07/28 04:21:09  gross
2292    # Lame equation: (linear elastic, isotropic) added
2293    #
2294    # Revision 1.1.2.24  2005/07/22 06:37:11  gross
2295    # some extensions to modellib and linearPDEs
2296    #
2297    # Revision 1.1.2.23  2005/05/13 00:55:20  cochrane
2298    # Fixed up some docstrings.  Moved module-level functions to top of file so
2299    # that epydoc and doxygen can pick them up properly.
2300    #
2301    # Revision 1.1.2.22  2005/05/12 11:41:30  gross
2302    # some basic Models have been added
2303    #
2304    # Revision 1.1.2.21  2005/05/12 07:16:12  cochrane
2305    # Moved ELMAN_RAMAGE, SIMPLIFIED_BROOK_HUGHES, and HALF functions to bottom of
2306    # file so that the AdvectivePDE class is picked up by doxygen.  Some
2307    # reformatting of docstrings.  Addition of code to make equations come out
2308    # as proper LaTeX.
2309    #
2310    # Revision 1.1.2.20  2005/04/15 07:09:08  gross
2311    # some problems with functionspace and linearPDEs fixed.
2312    #
2313    # Revision 1.1.2.19  2005/03/04 05:27:07  gross
2314    # bug in SystemPattern fixed.
2315    #
2316    # Revision 1.1.2.18  2005/02/08 06:16:45  gross
2317    # Bugs in AdvectivePDE fixed, AdvectiveTest is stable but more testing is needed
2318    #
2319    # Revision 1.1.2.17  2005/02/08 05:56:19  gross
2320    # Reference Number handling added
2321    #
2322    # Revision 1.1.2.16  2005/02/07 04:41:28  gross
2323    # some function exposed to python to make mesh merging running
2324    #
2325    # Revision 1.1.2.15  2005/02/03 00:14:44  gross
2326    # timeseries add and ESySParameter.py renames esysXML.py for consistence
2327    #
2328    # Revision 1.1.2.14  2005/02/01 06:44:10  gross
2329    # new implementation of AdvectivePDE which now also updates right hand side. systems of PDEs are still not working
2330    #
2331    # Revision 1.1.2.13  2005/01/25 00:47:07  gross
2332    # updates in the documentation
2333    #
2334    # Revision 1.1.2.12  2005/01/12 01:28:04  matt
2335    # Added createCoefficient method for linearPDEs.
2336    #
2337    # Revision 1.1.2.11  2005/01/11 01:55:34  gross
2338    # a problem in linearPDE class fixed
2339    #
2340    # Revision 1.1.2.10  2005/01/07 01:13:29  gross
2341    # some bugs in linearPDE fixed
2342    #
2343    # Revision 1.1.2.9  2005/01/06 06:24:58  gross
2344    # some bugs in slicing fixed
2345    #
2346    # Revision 1.1.2.8  2005/01/05 04:21:40  gross
2347    # FunctionSpace checking/matchig in slicing added
2348    #
2349    # Revision 1.1.2.7  2004/12/29 10:03:41  gross
2350    # bug in setValue fixed
2351    #
2352    # Revision 1.1.2.6  2004/12/29 05:29:59  gross
2353    # AdvectivePDE successfully tested for Peclet number 1000000. there is still a problem with setValue and Data()
2354    #
2355    # Revision 1.1.2.5  2004/12/29 00:18:41  gross
2356    # AdvectivePDE added
2357    #
2358    # Revision 1.1.2.4  2004/12/24 06:05:41  gross
2359    # some changes in linearPDEs to add AdevectivePDE
2360  #  #
2361  # Revision 1.1.2.3  2004/12/16 00:12:34  gross  # Revision 1.1.2.3  2004/12/16 00:12:34  gross
2362  # __init__ of LinearPDE does not accept any coefficients anymore  # __init__ of LinearPDE does not accept any coefficient anymore
2363  #  #
2364  # Revision 1.1.2.2  2004/12/14 03:55:01  jgs  # Revision 1.1.2.2  2004/12/14 03:55:01  jgs
2365  # *** empty log message ***  # *** empty log message ***
# Line 998  class Poisson(LinearPDE): Line 2403  class Poisson(LinearPDE):
2403  # Revision 1.1  2004/08/28 12:58:06  gross  # Revision 1.1  2004/08/28 12:58:06  gross
2404  # SimpleSolve is not running yet: problem with == of functionsspace  # SimpleSolve is not running yet: problem with == of functionsspace
2405  #  #
 #  

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