/[escript]/trunk/escript/py_src/util.py
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revision 341 by gross, Mon Dec 12 05:26:10 2005 UTC revision 550 by gross, Wed Feb 22 02:14:38 2006 UTC
# Line 24  Utility functions for escript Line 24  Utility functions for escript
24  __author__="Lutz Gross, l.gross@uq.edu.au"  __author__="Lutz Gross, l.gross@uq.edu.au"
25  __licence__="contact: esys@access.uq.edu.au"  __licence__="contact: esys@access.uq.edu.au"
26  __url__="http://www.iservo.edu.au/esys/escript"  __url__="http://www.iservo.edu.au/esys/escript"
27  __version__="$Revision: 329 $"  __version__="$Revision$"
28  __date__="$Date$"  __date__="$Date$"
29    
30    
31  import math  import math
32  import numarray  import numarray
33    import numarray.linear_algebra
34  import escript  import escript
35  import os  import os
36    
# Line 43  import os Line 44  import os
44  # def matchType(arg0=0.,arg1=0.):  # def matchType(arg0=0.,arg1=0.):
45  # def matchShape(arg0,arg1):  # def matchShape(arg0,arg1):
46    
 # def maximum(arg0,arg1):  
 # def minimum(arg0,arg1):  
   
 # def transpose(arg,axis=None):  
 # def trace(arg,axis0=0,axis1=1):  
47  # def reorderComponents(arg,index):  # def reorderComponents(arg,index):
48    
 # def integrate(arg,where=None):  
 # def interpolate(arg,where):  
 # def div(arg,where=None):  
 # def grad(arg,where=None):  
   
49  #  #
50  # slicing: get  # slicing: get
51  #          set  #          set
# Line 125  def kronecker(d=3): Line 116  def kronecker(d=3):
116     return the kronecker S{delta}-symbol     return the kronecker S{delta}-symbol
117    
118     @param d: dimension or an object that has the C{getDim} method defining the dimension     @param d: dimension or an object that has the C{getDim} method defining the dimension
119     @type d: C{int} or any object with a C{getDim} method     @type d: C{int}, L{escript.Domain} or L{escript.FunctionSpace}
120     @return: the object u of rank 2 with M{u[i,j]=1} for M{i=j} and M{u[i,j]=0} otherwise     @return: the object u of rank 2 with M{u[i,j]=1} for M{i=j} and M{u[i,j]=0} otherwise
121     @rtype d: L{numarray.NumArray} of rank 2.     @rtype d: L{numarray.NumArray} or L{escript.Data} of rank 2.
    @remark: the function is identical L{identity}  
122     """     """
123     return identityTensor(d)     return identityTensor(d)
124    
# Line 147  def identity(shape=()): Line 137  def identity(shape=()):
137        if len(shape)==1:        if len(shape)==1:
138            for i0 in range(shape[0]):            for i0 in range(shape[0]):
139               out[i0,i0]=1.               out[i0,i0]=1.
   
140        elif len(shape)==2:        elif len(shape)==2:
141            for i0 in range(shape[0]):            for i0 in range(shape[0]):
142               for i1 in range(shape[1]):               for i1 in range(shape[1]):
# Line 163  def identityTensor(d=3): Line 152  def identityTensor(d=3):
152     return the dxd identity matrix     return the dxd identity matrix
153    
154     @param d: dimension or an object that has the C{getDim} method defining the dimension     @param d: dimension or an object that has the C{getDim} method defining the dimension
155     @type d: C{int} or any object with a C{getDim} method     @type d: C{int}, L{escript.Domain} or L{escript.FunctionSpace}
156     @return: the object u of rank 2 with M{u[i,j]=1} for M{i=j} and M{u[i,j]=0} otherwise     @return: the object u of rank 2 with M{u[i,j]=1} for M{i=j} and M{u[i,j]=0} otherwise
157     @rtype: L{numarray.NumArray} of rank 2.     @rtype d: L{numarray.NumArray} or L{escript.Data} of rank 2
158     """     """
159     if hasattr(d,"getDim"):     if isinstance(d,escript.FunctionSpace):
160        d=d.getDim()         return escript.Data(identity((d.getDim(),)),d)
161     return identity(shape=(d,))     elif isinstance(d,escript.Domain):
162           return identity((d.getDim(),))
163       else:
164           return identity((d,))
165    
166  def identityTensor4(d=3):  def identityTensor4(d=3):
167     """     """
# Line 178  def identityTensor4(d=3): Line 170  def identityTensor4(d=3):
170     @param d: dimension or an object that has the C{getDim} method defining the dimension     @param d: dimension or an object that has the C{getDim} method defining the dimension
171     @type d: C{int} or any object with a C{getDim} method     @type d: C{int} or any object with a C{getDim} method
172     @return: the object u of rank 4 with M{u[i,j,k,l]=1} for M{i=k and j=l} and M{u[i,j,k,l]=0} otherwise     @return: the object u of rank 4 with M{u[i,j,k,l]=1} for M{i=k and j=l} and M{u[i,j,k,l]=0} otherwise
173     @rtype: L{numarray.NumArray} of rank 4.     @rtype d: L{numarray.NumArray} or L{escript.Data} of rank 4.
174     """     """
175     if hasattr(d,"getDim"):     if isinstance(d,escript.FunctionSpace):
176        d=d.getDim()         return escript.Data(identity((d.getDim(),d.getDim())),d)
177     return identity((d,d))     elif isinstance(d,escript.Domain):
178           return identity((d.getDim(),d.getDim()))
179       else:
180           return identity((d,d))
181    
182  def unitVector(i=0,d=3):  def unitVector(i=0,d=3):
183     """     """
# Line 191  def unitVector(i=0,d=3): Line 186  def unitVector(i=0,d=3):
186     @param i: index     @param i: index
187     @type i: C{int}     @type i: C{int}
188     @param d: dimension or an object that has the C{getDim} method defining the dimension     @param d: dimension or an object that has the C{getDim} method defining the dimension
189     @type d: C{int} or any object with a C{getDim} method     @type d: C{int}, L{escript.Domain} or L{escript.FunctionSpace}
190     @return: the object u of rank 1 with M{u[j]=1} for M{j=i} and M{u[i]=0} otherwise     @return: the object u of rank 1 with M{u[j]=1} for M{j=i} and M{u[i]=0} otherwise
191     @rtype: L{numarray.NumArray} of rank 1.     @rtype d: L{numarray.NumArray} or L{escript.Data} of rank 1
192     """     """
193     return kronecker(d)[i]     return kronecker(d)[i]
194    
# Line 363  def testForZero(arg): Line 358  def testForZero(arg):
358      @return : True if the argument is identical to zero.      @return : True if the argument is identical to zero.
359      @rtype : C{bool}      @rtype : C{bool}
360      """      """
361      try:      if isinstance(arg,numarray.NumArray):
362         return not Lsup(arg)>0.         return not Lsup(arg)>0.
363      except TypeError:      elif isinstance(arg,escript.Data):
364           return False
365        elif isinstance(arg,float):
366           return not Lsup(arg)>0.
367        elif isinstance(arg,int):
368           return not Lsup(arg)>0.
369        elif isinstance(arg,Symbol):
370           return False
371        else:
372         return False         return False
373    
374  def matchType(arg0=0.,arg1=0.):  def matchType(arg0=0.,arg1=0.):
# Line 825  class Symbol(object): Line 828  class Symbol(object):
828         """         """
829         return power(other,self)         return power(other,self)
830    
831       def __getitem__(self,index):
832           """
833           returns the slice defined by index
834    
835           @param index: defines a
836           @type index: C{slice} or C{int} or a C{tuple} of them
837           @return: a S{Symbol} representing the slice defined by index
838           @rtype: L{DependendSymbol}
839           """
840           return GetSlice_Symbol(self,index)
841    
842  class DependendSymbol(Symbol):  class DependendSymbol(Symbol):
843     """     """
844     DependendSymbol extents L{Symbol} by modifying the == operator to allow two instances to be equal.     DependendSymbol extents L{Symbol} by modifying the == operator to allow two instances to be equal.
# Line 875  class DependendSymbol(Symbol): Line 889  class DependendSymbol(Symbol):
889  #=========================================================  #=========================================================
890  #  Unary operations prserving the shape  #  Unary operations prserving the shape
891  #========================================================  #========================================================
892    class GetSlice_Symbol(DependendSymbol):
893       """
894       L{Symbol} representing getting a slice for a L{Symbol}
895       """
896       def __init__(self,arg,index):
897          """
898          initialization of wherePositive L{Symbol} with argument arg
899          @param arg: argument
900          @type arg: L{Symbol}.
901          @param index: defines index
902          @type index: C{slice} or C{int} or a C{tuple} of them
903          @raises IndexError: if length of index is larger than rank of arg or a index start or stop is out of range
904          @raises ValueError: if a step is given
905          """
906          if not isinstance(index,tuple): index=(index,)
907          if len(index)>arg.getRank():
908               raise IndexError,"GetSlice_Symbol: index out of range."
909          sh=()
910          index2=()
911          for i in range(len(index)):
912             ix=index[i]
913             if isinstance(ix,int):
914                if ix<0 or ix>=arg.getShape()[i]:
915                   raise ValueError,"GetSlice_Symbol: index out of range."
916                index2=index2+(ix,)
917             else:
918               if not ix.step==None:
919                 raise ValueError,"GetSlice_Symbol: steping is not supported."
920               if ix.start==None:
921                  s=0
922               else:
923                  s=ix.start
924               if ix.stop==None:
925                  e=arg.getShape()[i]
926               else:
927                  e=ix.stop
928                  if e>arg.getShape()[i]:
929                     raise IndexError,"GetSlice_Symbol: index out of range."
930               index2=index2+(slice(s,e),)
931               if e>s:
932                   sh=sh+(e-s,)
933               elif s>e:
934                   raise IndexError,"GetSlice_Symbol: slice start must be less or equal slice end"
935          for i in range(len(index),arg.getRank()):
936              index2=index2+(slice(0,arg.getShape()[i]),)
937              sh=sh+(arg.getShape()[i],)
938          super(GetSlice_Symbol, self).__init__(args=[arg,index2],shape=sh,dim=arg.getDim())
939    
940       def getMyCode(self,argstrs,format="escript"):
941          """
942          returns a program code that can be used to evaluate the symbol.
943    
944          @param argstrs: gives for each argument a string representing the argument for the evaluation.
945          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
946          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
947          @type format: C{str}
948          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
949          @rtype: C{str}
950          @raise: NotImplementedError: if the requested format is not available
951          """
952          if format=="escript" or format=="str"  or format=="text":
953             return "%s.__getitem__(%s)"%(argstrs[0],argstrs[1])
954          else:
955             raise NotImplementedError,"GetItem_Symbol does not provide program code for format %s."%format
956    
957       def substitute(self,argvals):
958          """
959          assigns new values to symbols in the definition of the symbol.
960          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
961    
962          @param argvals: new values assigned to symbols
963          @type argvals: C{dict} with keywords of type L{Symbol}.
964          @return: result of the substitution process. Operations are executed as much as possible.
965          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
966          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
967          """
968          if argvals.has_key(self):
969             arg=argvals[self]
970             if self.isAppropriateValue(arg):
971                return arg
972             else:
973                raise TypeError,"%s: new value is not appropriate."%str(self)
974          else:
975             args=self.getSubstitutedArguments(argvals)
976             arg=args[0]
977             index=args[1]
978             return arg.__getitem__(index)
979    
980  def log10(arg):  def log10(arg):
981     """     """
982     returns base-10 logarithm of argument arg     returns base-10 logarithm of argument arg
# Line 907  def wherePositive(arg): Line 1009  def wherePositive(arg):
1009     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1010     """     """
1011     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
1012        if arg.rank==0:        out=numarray.greater(arg,numarray.zeros(arg.shape,numarray.Float))*1.
1013           if arg>0:        if isinstance(out,float): out=numarray.array(out)
1014             return numarray.array(1.)        return out
          else:  
            return numarray.array(0.)  
       else:  
          return numarray.greater(arg,numarray.zeros(arg.shape,numarray.Float))  
1015     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
1016        return arg._wherePositive()        return arg._wherePositive()
1017     elif isinstance(arg,float):     elif isinstance(arg,float):
# Line 993  def whereNegative(arg): Line 1091  def whereNegative(arg):
1091     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1092     """     """
1093     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
1094        if arg.rank==0:        out=numarray.less(arg,numarray.zeros(arg.shape,numarray.Float))*1.
1095           if arg<0:        if isinstance(out,float): out=numarray.array(out)
1096             return numarray.array(1.)        return out
          else:  
            return numarray.array(0.)  
       else:  
          return numarray.less(arg,numarray.zeros(arg.shape,numarray.Float))  
1097     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
1098        return arg._whereNegative()        return arg._whereNegative()
1099     elif isinstance(arg,float):     elif isinstance(arg,float):
# Line 1079  def whereNonNegative(arg): Line 1173  def whereNonNegative(arg):
1173     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1174     """     """
1175     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
1176        if arg.rank==0:        out=numarray.greater_equal(arg,numarray.zeros(arg.shape,numarray.Float))*1.
1177           if arg<0:        if isinstance(out,float): out=numarray.array(out)
1178             return numarray.array(0.)        return out
          else:  
            return numarray.array(1.)  
       else:  
          return numarray.greater_equal(arg,numarray.zeros(arg.shape,numarray.Float))  
1179     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
1180        return arg._whereNonNegative()        return arg._whereNonNegative()
1181     elif isinstance(arg,float):     elif isinstance(arg,float):
# Line 1113  def whereNonPositive(arg): Line 1203  def whereNonPositive(arg):
1203     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1204     """     """
1205     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
1206        if arg.rank==0:        out=numarray.less_equal(arg,numarray.zeros(arg.shape,numarray.Float))*1.
1207           if arg>0:        if isinstance(out,float): out=numarray.array(out)
1208             return numarray.array(0.)        return out
          else:  
            return numarray.array(1.)  
       else:  
          return numarray.less_equal(arg,numarray.zeros(arg.shape,numarray.Float))*1.  
1209     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
1210        return arg._whereNonPositive()        return arg._whereNonPositive()
1211     elif isinstance(arg,float):     elif isinstance(arg,float):
# Line 1149  def whereZero(arg,tol=0.): Line 1235  def whereZero(arg,tol=0.):
1235     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1236     """     """
1237     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
1238        if arg.rank==0:        out=numarray.less_equal(abs(arg)-tol,numarray.zeros(arg.shape,numarray.Float))*1.
1239           if abs(arg)<=tol:        if isinstance(out,float): out=numarray.array(out)
1240             return numarray.array(1.)        return out
          else:  
            return numarray.array(0.)  
       else:  
          return numarray.less_equal(abs(arg)-tol,numarray.zeros(arg.shape,numarray.Float))*1.  
1241     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
1242        if tol>0.:        if tol>0.:
1243           return whereNegative(abs(arg)-tol)           return whereNegative(abs(arg)-tol)
# Line 1236  def whereNonZero(arg,tol=0.): Line 1318  def whereNonZero(arg,tol=0.):
1318     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1319     """     """
1320     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
1321        if arg.rank==0:        out=numarray.greater(abs(arg)-tol,numarray.zeros(arg.shape,numarray.Float))*1.
1322          if abs(arg)>tol:        if isinstance(out,float): out=numarray.array(out)
1323             return numarray.array(1.)        return out
         else:  
            return numarray.array(0.)  
       else:  
          return numarray.greater(abs(arg)-tol,numarray.zeros(arg.shape,numarray.Float))*1.  
1324     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
1325        if tol>0.:        if tol>0.:
1326           return 1.-whereZero(arg,tol)           return 1.-whereZero(arg,tol)
# Line 2877  def length(arg): Line 2955  def length(arg):
2955     """     """
2956     return sqrt(inner(arg,arg))     return sqrt(inner(arg,arg))
2957    
2958    def trace(arg,axis_offset=0):
2959       """
2960       returns the trace of arg which the sum of arg[k,k] over k.
2961    
2962       @param arg: argument
2963       @type arg: L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2964       @param axis_offset: axis_offset to components to sum over. C{axis_offset} must be non-negative and less than the rank of arg +1. The dimensions on component
2965                      axis_offset and axis_offset+1 must be equal.
2966       @type axis_offset: C{int}
2967       @return: trace of arg. The rank of the returned object is minus 2 of the rank of arg.
2968       @rtype: L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
2969       """
2970       if isinstance(arg,numarray.NumArray):
2971          sh=arg.shape
2972          if len(sh)<2:
2973            raise ValueError,"trace: rank of argument must be greater than 1"
2974          if axis_offset<0 or axis_offset>len(sh)-2:
2975            raise ValueError,"trace: axis_offset must be between 0 and %s"%len(sh)-2
2976          s1=1
2977          for i in range(axis_offset): s1*=sh[i]
2978          s2=1
2979          for i in range(axis_offset+2,len(sh)): s2*=sh[i]
2980          if not sh[axis_offset] == sh[axis_offset+1]:
2981            raise ValueError,"trace: dimensions of component %s and %s must match."%(axis_offset.axis_offset+1)
2982          arg_reshaped=numarray.reshape(arg,(s1,sh[axis_offset],sh[axis_offset],s2))
2983          out=numarray.zeros([s1,s2],numarray.Float)
2984          for i1 in range(s1):
2985            for i2 in range(s2):
2986                for j in range(sh[axis_offset]): out[i1,i2]+=arg_reshaped[i1,j,j,i2]
2987          out.resize(sh[:axis_offset]+sh[axis_offset+2:])
2988          return out
2989       elif isinstance(arg,escript.Data):
2990          return escript_trace(arg,axis_offset)
2991       elif isinstance(arg,float):
2992          raise TypeError,"trace: illegal argument type float."
2993       elif isinstance(arg,int):
2994          raise TypeError,"trace: illegal argument type int."
2995       elif isinstance(arg,Symbol):
2996          return Trace_Symbol(arg,axis_offset)
2997       else:
2998          raise TypeError,"trace: Unknown argument type."
2999    
3000    def escript_trace(arg,axis_offset): # this should be escript._trace
3001          "arg si a Data objects!!!"
3002          if arg.getRank()<2:
3003            raise ValueError,"escript_trace: rank of argument must be greater than 1"
3004          if axis_offset<0 or axis_offset>arg.getRank()-2:
3005            raise ValueError,"escript_trace: axis_offset must be between 0 and %s"%arg.getRank()-2
3006          s=list(arg.getShape())        
3007          if not s[axis_offset] == s[axis_offset+1]:
3008            raise ValueError,"escript_trace: dimensions of component %s and %s must match."%(axis_offset.axis_offset+1)
3009          out=escript.Data(0.,tuple(s[0:axis_offset]+s[axis_offset+2:]),arg.getFunctionSpace())
3010          if arg.getRank()==2:
3011             for i0 in range(s[0]):
3012                out+=arg[i0,i0]
3013          elif arg.getRank()==3:
3014             if axis_offset==0:
3015                for i0 in range(s[0]):
3016                      for i2 in range(s[2]):
3017                             out[i2]+=arg[i0,i0,i2]
3018             elif axis_offset==1:
3019                for i0 in range(s[0]):
3020                   for i1 in range(s[1]):
3021                             out[i0]+=arg[i0,i1,i1]
3022          elif arg.getRank()==4:
3023             if axis_offset==0:
3024                for i0 in range(s[0]):
3025                      for i2 in range(s[2]):
3026                         for i3 in range(s[3]):
3027                             out[i2,i3]+=arg[i0,i0,i2,i3]
3028             elif axis_offset==1:
3029                for i0 in range(s[0]):
3030                   for i1 in range(s[1]):
3031                         for i3 in range(s[3]):
3032                             out[i0,i3]+=arg[i0,i1,i1,i3]
3033             elif axis_offset==2:
3034                for i0 in range(s[0]):
3035                   for i1 in range(s[1]):
3036                      for i2 in range(s[2]):
3037                             out[i0,i1]+=arg[i0,i1,i2,i2]
3038          return out
3039    class Trace_Symbol(DependendSymbol):
3040       """
3041       L{Symbol} representing the result of the trace function
3042       """
3043       def __init__(self,arg,axis_offset=0):
3044          """
3045          initialization of trace L{Symbol} with argument arg
3046          @param arg: argument of function
3047          @type arg: L{Symbol}.
3048          @param axis_offset: axis_offset to components to sum over. C{axis_offset} must be non-negative and less than the rank of arg +1. The dimensions on component
3049                      axis_offset and axis_offset+1 must be equal.
3050          @type axis_offset: C{int}
3051          """
3052          if arg.getRank()<2:
3053            raise ValueError,"Trace_Symbol: rank of argument must be greater than 1"
3054          if axis_offset<0 or axis_offset>arg.getRank()-2:
3055            raise ValueError,"Trace_Symbol: axis_offset must be between 0 and %s"%arg.getRank()-2
3056          s=list(arg.getShape())        
3057          if not s[axis_offset] == s[axis_offset+1]:
3058            raise ValueError,"Trace_Symbol: dimensions of component %s and %s must match."%(axis_offset.axis_offset+1)
3059          super(Trace_Symbol,self).__init__(args=[arg,axis_offset],shape=tuple(s[0:axis_offset]+s[axis_offset+2:]),dim=arg.getDim())
3060    
3061       def getMyCode(self,argstrs,format="escript"):
3062          """
3063          returns a program code that can be used to evaluate the symbol.
3064    
3065          @param argstrs: gives for each argument a string representing the argument for the evaluation.
3066          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
3067          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
3068          @type format: C{str}
3069          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3070          @rtype: C{str}
3071          @raise: NotImplementedError: if the requested format is not available
3072          """
3073          if format=="escript" or format=="str"  or format=="text":
3074             return "trace(%s,axis_offset=%s)"%(argstrs[0],argstrs[1])
3075          else:
3076             raise NotImplementedError,"Trace_Symbol does not provide program code for format %s."%format
3077    
3078       def substitute(self,argvals):
3079          """
3080          assigns new values to symbols in the definition of the symbol.
3081          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
3082    
3083          @param argvals: new values assigned to symbols
3084          @type argvals: C{dict} with keywords of type L{Symbol}.
3085          @return: result of the substitution process. Operations are executed as much as possible.
3086          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
3087          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
3088          """
3089          if argvals.has_key(self):
3090             arg=argvals[self]
3091             if self.isAppropriateValue(arg):
3092                return arg
3093             else:
3094                raise TypeError,"%s: new value is not appropriate."%str(self)
3095          else:
3096             arg=self.getSubstitutedArguments(argvals)
3097             return trace(arg[0],axis_offset=arg[1])
3098    
3099       def diff(self,arg):
3100          """
3101          differential of this object
3102    
3103          @param arg: the derivative is calculated with respect to arg
3104          @type arg: L{escript.Symbol}
3105          @return: derivative with respect to C{arg}
3106          @rtype: typically L{Symbol} but other types such as C{float}, L{escript.Data}, L{numarray.NumArray}  are possible.
3107          """
3108          if arg==self:
3109             return identity(self.getShape())
3110          else:
3111             return trace(self.getDifferentiatedArguments(arg)[0],axis_offset=self.getArgument()[1])
3112    
3113    def transpose(arg,axis_offset=None):
3114       """
3115       returns the transpose of arg by swaping the first axis_offset and the last rank-axis_offset components.
3116    
3117       @param arg: argument
3118       @type arg: L{escript.Data}, L{Symbol}, L{numarray.NumArray}, C{float}, C{int}
3119       @param axis_offset: the first axis_offset components are swapped with rest. If C{axis_offset} must be non-negative and less or equal the rank of arg.
3120                           if axis_offset is not present C{int(r/2)} where r is the rank of arg is used.
3121       @type axis_offset: C{int}
3122       @return: transpose of arg
3123       @rtype: L{escript.Data}, L{Symbol}, L{numarray.NumArray},C{float}, C{int} depending on the type of arg.
3124       """
3125       if isinstance(arg,numarray.NumArray):
3126          if axis_offset==None: axis_offset=int(arg.rank/2)
3127          return numarray.transpose(arg,axes=range(axis_offset,arg.rank)+range(0,axis_offset))
3128       elif isinstance(arg,escript.Data):
3129          if axis_offset==None: axis_offset=int(arg.getRank()/2)
3130          return escript_transpose(arg,axis_offset)
3131       elif isinstance(arg,float):
3132          if not ( axis_offset==0 or axis_offset==None):
3133            raise ValueError,"transpose: axis_offset must be 0 for float argument"
3134          return arg
3135       elif isinstance(arg,int):
3136          if not ( axis_offset==0 or axis_offset==None):
3137            raise ValueError,"transpose: axis_offset must be 0 for int argument"
3138          return float(arg)
3139       elif isinstance(arg,Symbol):
3140          if axis_offset==None: axis_offset=int(arg.getRank()/2)
3141          return Transpose_Symbol(arg,axis_offset)
3142       else:
3143          raise TypeError,"transpose: Unknown argument type."
3144    
3145    def escript_transpose(arg,axis_offset): # this should be escript._transpose
3146          "arg si a Data objects!!!"
3147          r=arg.getRank()
3148          if axis_offset<0 or axis_offset>r:
3149            raise ValueError,"escript_transpose: axis_offset must be between 0 and %s"%r
3150          s=arg.getShape()
3151          s_out=s[axis_offset:]+s[:axis_offset]
3152          out=escript.Data(0.,s_out,arg.getFunctionSpace())
3153          if r==4:
3154             if axis_offset==1:
3155                for i0 in range(s_out[0]):
3156                   for i1 in range(s_out[1]):
3157                      for i2 in range(s_out[2]):
3158                         for i3 in range(s_out[3]):
3159                             out[i0,i1,i2,i3]=arg[i3,i0,i1,i2]
3160             elif axis_offset==2:
3161                for i0 in range(s_out[0]):
3162                   for i1 in range(s_out[1]):
3163                      for i2 in range(s_out[2]):
3164                         for i3 in range(s_out[3]):
3165                             out[i0,i1,i2,i3]=arg[i2,i3,i0,i1]
3166             elif axis_offset==3:
3167                for i0 in range(s_out[0]):
3168                   for i1 in range(s_out[1]):
3169                      for i2 in range(s_out[2]):
3170                         for i3 in range(s_out[3]):
3171                             out[i0,i1,i2,i3]=arg[i1,i2,i3,i0]
3172             else:
3173                for i0 in range(s_out[0]):
3174                   for i1 in range(s_out[1]):
3175                      for i2 in range(s_out[2]):
3176                         for i3 in range(s_out[3]):
3177                             out[i0,i1,i2,i3]=arg[i0,i1,i2,i3]
3178          elif r==3:
3179             if axis_offset==1:
3180                for i0 in range(s_out[0]):
3181                   for i1 in range(s_out[1]):
3182                      for i2 in range(s_out[2]):
3183                             out[i0,i1,i2]=arg[i2,i0,i1]
3184             elif axis_offset==2:
3185                for i0 in range(s_out[0]):
3186                   for i1 in range(s_out[1]):
3187                      for i2 in range(s_out[2]):
3188                             out[i0,i1,i2]=arg[i1,i2,i0]
3189             else:
3190                for i0 in range(s_out[0]):
3191                   for i1 in range(s_out[1]):
3192                      for i2 in range(s_out[2]):
3193                             out[i0,i1,i2]=arg[i0,i1,i2]
3194          elif r==2:
3195             if axis_offset==1:
3196                for i0 in range(s_out[0]):
3197                   for i1 in range(s_out[1]):
3198                             out[i0,i1]=arg[i1,i0]
3199             else:
3200                for i0 in range(s_out[0]):
3201                   for i1 in range(s_out[1]):
3202                             out[i0,i1]=arg[i0,i1]
3203          elif r==1:
3204              for i0 in range(s_out[0]):
3205                   out[i0]=arg[i0]
3206          elif r==0:
3207                 out=arg+0.
3208          return out
3209    class Transpose_Symbol(DependendSymbol):
3210       """
3211       L{Symbol} representing the result of the transpose function
3212       """
3213       def __init__(self,arg,axis_offset=None):
3214          """
3215          initialization of transpose L{Symbol} with argument arg
3216    
3217          @param arg: argument of function
3218          @type arg: L{Symbol}.
3219           @param axis_offset: the first axis_offset components are swapped with rest. If C{axis_offset} must be non-negative and less or equal the rank of arg.
3220                           if axis_offset is not present C{int(r/2)} where r is the rank of arg is used.
3221          @type axis_offset: C{int}
3222          """
3223          if axis_offset==None: axis_offset=int(arg.getRank()/2)
3224          if axis_offset<0 or axis_offset>arg.getRank():
3225            raise ValueError,"escript_transpose: axis_offset must be between 0 and %s"%r
3226          s=arg.getShape()
3227          super(Transpose_Symbol,self).__init__(args=[arg,axis_offset],shape=s[axis_offset:]+s[:axis_offset],dim=arg.getDim())
3228    
3229       def getMyCode(self,argstrs,format="escript"):
3230          """
3231          returns a program code that can be used to evaluate the symbol.
3232    
3233          @param argstrs: gives for each argument a string representing the argument for the evaluation.
3234          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
3235          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
3236          @type format: C{str}
3237          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3238          @rtype: C{str}
3239          @raise: NotImplementedError: if the requested format is not available
3240          """
3241          if format=="escript" or format=="str"  or format=="text":
3242             return "transpose(%s,axis_offset=%s)"%(argstrs[0],argstrs[1])
3243          else:
3244             raise NotImplementedError,"Transpose_Symbol does not provide program code for format %s."%format
3245    
3246       def substitute(self,argvals):
3247          """
3248          assigns new values to symbols in the definition of the symbol.
3249          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
3250    
3251          @param argvals: new values assigned to symbols
3252          @type argvals: C{dict} with keywords of type L{Symbol}.
3253          @return: result of the substitution process. Operations are executed as much as possible.
3254          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
3255          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
3256          """
3257          if argvals.has_key(self):
3258             arg=argvals[self]
3259             if self.isAppropriateValue(arg):
3260                return arg
3261             else:
3262                raise TypeError,"%s: new value is not appropriate."%str(self)
3263          else:
3264             arg=self.getSubstitutedArguments(argvals)
3265             return transpose(arg[0],axis_offset=arg[1])
3266    
3267       def diff(self,arg):
3268          """
3269          differential of this object
3270    
3271          @param arg: the derivative is calculated with respect to arg
3272          @type arg: L{escript.Symbol}
3273          @return: derivative with respect to C{arg}
3274          @rtype: typically L{Symbol} but other types such as C{float}, L{escript.Data}, L{numarray.NumArray}  are possible.
3275          """
3276          if arg==self:
3277             return identity(self.getShape())
3278          else:
3279             return transpose(self.getDifferentiatedArguments(arg)[0],axis_offset=self.getArgument()[1])
3280    def symmetric(arg):
3281        """
3282        returns the symmetric part of the square matrix arg. This is (arg+transpose(arg))/2
3283    
3284        @param arg: square matrix. Must have rank 2 or 4 and be square.
3285        @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
3286        @return: symmetric part of arg
3287        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
3288        """
3289        if isinstance(arg,numarray.NumArray):
3290          if arg.rank==2:
3291            if not (arg.shape[0]==arg.shape[1]):
3292               raise ValueError,"symmetric: argument must be square."
3293          elif arg.rank==4:
3294            if not (arg.shape[0]==arg.shape[2] and arg.shape[1]==arg.shape[3]):
3295               raise ValueError,"symmetric: argument must be square."
3296          else:
3297            raise ValueError,"symmetric: rank 2 or 4 is required."
3298          return (arg+transpose(arg))/2
3299        elif isinstance(arg,escript.Data):
3300          return escript_symmetric(arg)
3301        elif isinstance(arg,float):
3302          return arg
3303        elif isinstance(arg,int):
3304          return float(arg)
3305        elif isinstance(arg,Symbol):
3306          if arg.getRank()==2:
3307            if not (arg.getShape()[0]==arg.getShape()[1]):
3308               raise ValueError,"symmetric: argument must be square."
3309          elif arg.getRank()==4:
3310            if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):
3311               raise ValueError,"symmetric: argument must be square."
3312          else:
3313            raise ValueError,"symmetric: rank 2 or 4 is required."
3314          return (arg+transpose(arg))/2
3315        else:
3316          raise TypeError,"symmetric: Unknown argument type."
3317    
3318    def escript_symmetric(arg): # this should be implemented in c++
3319          if arg.getRank()==2:
3320            if not (arg.getShape()[0]==arg.getShape()[1]):
3321               raise ValueError,"escript_symmetric: argument must be square."
3322            out=escript.Data(0.,arg.getShape(),arg.getFunctionSpace())
3323            for i0 in range(arg.getShape()[0]):
3324               for i1 in range(arg.getShape()[1]):
3325                  out[i0,i1]=(arg[i0,i1]+arg[i1,i0])/2.
3326          elif arg.getRank()==4:
3327            if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):
3328               raise ValueError,"escript_symmetric: argument must be square."
3329            out=escript.Data(0.,arg.getShape(),arg.getFunctionSpace())
3330            for i0 in range(arg.getShape()[0]):
3331               for i1 in range(arg.getShape()[1]):
3332                  for i2 in range(arg.getShape()[2]):
3333                     for i3 in range(arg.getShape()[3]):
3334                         out[i0,i1,i2,i3]=(arg[i0,i1,i2,i3]+arg[i2,i3,i0,i1])/2.
3335          else:
3336            raise ValueError,"escript_symmetric: rank 2 or 4 is required."
3337          return out
3338    
3339    def nonsymmetric(arg):
3340        """
3341        returns the nonsymmetric part of the square matrix arg. This is (arg-transpose(arg))/2
3342    
3343        @param arg: square matrix. Must have rank 2 or 4 and be square.
3344        @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
3345        @return: nonsymmetric part of arg
3346        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
3347        """
3348        if isinstance(arg,numarray.NumArray):
3349          if arg.rank==2:
3350            if not (arg.shape[0]==arg.shape[1]):
3351               raise ValueError,"nonsymmetric: argument must be square."
3352          elif arg.rank==4:
3353            if not (arg.shape[0]==arg.shape[2] and arg.shape[1]==arg.shape[3]):
3354               raise ValueError,"nonsymmetric: argument must be square."
3355          else:
3356            raise ValueError,"nonsymmetric: rank 2 or 4 is required."
3357          return (arg-transpose(arg))/2
3358        elif isinstance(arg,escript.Data):
3359          return escript_nonsymmetric(arg)
3360        elif isinstance(arg,float):
3361          return arg
3362        elif isinstance(arg,int):
3363          return float(arg)
3364        elif isinstance(arg,Symbol):
3365          if arg.getRank()==2:
3366            if not (arg.getShape()[0]==arg.getShape()[1]):
3367               raise ValueError,"nonsymmetric: argument must be square."
3368          elif arg.getRank()==4:
3369            if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):
3370               raise ValueError,"nonsymmetric: argument must be square."
3371          else:
3372            raise ValueError,"nonsymmetric: rank 2 or 4 is required."
3373          return (arg-transpose(arg))/2
3374        else:
3375          raise TypeError,"nonsymmetric: Unknown argument type."
3376    
3377    def escript_nonsymmetric(arg): # this should be implemented in c++
3378          if arg.getRank()==2:
3379            if not (arg.getShape()[0]==arg.getShape()[1]):
3380               raise ValueError,"escript_nonsymmetric: argument must be square."
3381            out=escript.Data(0.,arg.getShape(),arg.getFunctionSpace())
3382            for i0 in range(arg.getShape()[0]):
3383               for i1 in range(arg.getShape()[1]):
3384                  out[i0,i1]=(arg[i0,i1]-arg[i1,i0])/2.
3385          elif arg.getRank()==4:
3386            if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):
3387               raise ValueError,"escript_nonsymmetric: argument must be square."
3388            out=escript.Data(0.,arg.getShape(),arg.getFunctionSpace())
3389            for i0 in range(arg.getShape()[0]):
3390               for i1 in range(arg.getShape()[1]):
3391                  for i2 in range(arg.getShape()[2]):
3392                     for i3 in range(arg.getShape()[3]):
3393                         out[i0,i1,i2,i3]=(arg[i0,i1,i2,i3]-arg[i2,i3,i0,i1])/2.
3394          else:
3395            raise ValueError,"escript_nonsymmetric: rank 2 or 4 is required."
3396          return out
3397    
3398    
3399    def inverse(arg):
3400        """
3401        returns the inverse of the square matrix arg.
3402    
3403        @param arg: square matrix. Must have rank 2 and the first and second dimension must be equal.
3404        @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
3405        @return: inverse arg_inv of the argument. It will be matrixmul(inverse(arg),arg) almost equal to kronecker(arg.getShape()[0])
3406        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
3407        @remark: for L{escript.Data} objects the dimension is restricted to 3.
3408        """
3409        if isinstance(arg,numarray.NumArray):
3410          return numarray.linear_algebra.inverse(arg)
3411        elif isinstance(arg,escript.Data):
3412          return escript_inverse(arg)
3413        elif isinstance(arg,float):
3414          return 1./arg
3415        elif isinstance(arg,int):
3416          return 1./float(arg)
3417        elif isinstance(arg,Symbol):
3418          return Inverse_Symbol(arg)
3419        else:
3420          raise TypeError,"inverse: Unknown argument type."
3421    
3422    def escript_inverse(arg): # this should be escript._inverse and use LAPACK
3423          "arg is a Data objects!!!"
3424          if not arg.getRank()==2:
3425            raise ValueError,"escript_inverse: argument must have rank 2"
3426          s=arg.getShape()      
3427          if not s[0] == s[1]:
3428            raise ValueError,"escript_inverse: argument must be a square matrix."
3429          out=escript.Data(0.,s,arg.getFunctionSpace())
3430          if s[0]==1:
3431              if inf(abs(arg[0,0]))==0: # in c this should be done point wise as abs(arg[0,0](i))<=0.
3432                  raise ZeroDivisionError,"escript_inverse: argument not invertible"
3433              out[0,0]=1./arg[0,0]
3434          elif s[0]==2:
3435              A11=arg[0,0]
3436              A12=arg[0,1]
3437              A21=arg[1,0]
3438              A22=arg[1,1]
3439              D = A11*A22-A12*A21
3440              if inf(abs(D))==0: # in c this should be done point wise as abs(D(i))<=0.
3441                  raise ZeroDivisionError,"escript_inverse: argument not invertible"
3442              D=1./D
3443              out[0,0]= A22*D
3444              out[1,0]=-A21*D
3445              out[0,1]=-A12*D
3446              out[1,1]= A11*D
3447          elif s[0]==3:
3448              A11=arg[0,0]
3449              A21=arg[1,0]
3450              A31=arg[2,0]
3451              A12=arg[0,1]
3452              A22=arg[1,1]
3453              A32=arg[2,1]
3454              A13=arg[0,2]
3455              A23=arg[1,2]
3456              A33=arg[2,2]
3457              D  =  A11*(A22*A33-A23*A32)+ A12*(A31*A23-A21*A33)+A13*(A21*A32-A31*A22)
3458              if inf(abs(D))==0: # in c this should be done point wise as abs(D(i))<=0.
3459                  raise ZeroDivisionError,"escript_inverse: argument not invertible"
3460              D=1./D
3461              out[0,0]=(A22*A33-A23*A32)*D
3462              out[1,0]=(A31*A23-A21*A33)*D
3463              out[2,0]=(A21*A32-A31*A22)*D
3464              out[0,1]=(A13*A32-A12*A33)*D
3465              out[1,1]=(A11*A33-A31*A13)*D
3466              out[2,1]=(A12*A31-A11*A32)*D
3467              out[0,2]=(A12*A23-A13*A22)*D
3468              out[1,2]=(A13*A21-A11*A23)*D
3469              out[2,2]=(A11*A22-A12*A21)*D
3470          else:
3471             raise TypeError,"escript_inverse: only matrix dimensions 1,2,3 are supported right now."
3472          return out
3473    
3474    class Inverse_Symbol(DependendSymbol):
3475       """
3476       L{Symbol} representing the result of the inverse function
3477       """
3478       def __init__(self,arg):
3479          """
3480          initialization of inverse L{Symbol} with argument arg
3481          @param arg: argument of function
3482          @type arg: L{Symbol}.
3483          """
3484          if not arg.getRank()==2:
3485            raise ValueError,"Inverse_Symbol:: argument must have rank 2"
3486          s=arg.getShape()
3487          if not s[0] == s[1]:
3488            raise ValueError,"Inverse_Symbol:: argument must be a square matrix."
3489          super(Inverse_Symbol,self).__init__(args=[arg],shape=s,dim=arg.getDim())
3490    
3491       def getMyCode(self,argstrs,format="escript"):
3492          """
3493          returns a program code that can be used to evaluate the symbol.
3494    
3495          @param argstrs: gives for each argument a string representing the argument for the evaluation.
3496          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
3497          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
3498          @type format: C{str}
3499          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3500          @rtype: C{str}
3501          @raise: NotImplementedError: if the requested format is not available
3502          """
3503          if format=="escript" or format=="str"  or format=="text":
3504             return "inverse(%s)"%argstrs[0]
3505          else:
3506             raise NotImplementedError,"Inverse_Symbol does not provide program code for format %s."%format
3507    
3508       def substitute(self,argvals):
3509          """
3510          assigns new values to symbols in the definition of the symbol.
3511          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
3512    
3513          @param argvals: new values assigned to symbols
3514          @type argvals: C{dict} with keywords of type L{Symbol}.
3515          @return: result of the substitution process. Operations are executed as much as possible.
3516          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
3517          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
3518          """
3519          if argvals.has_key(self):
3520             arg=argvals[self]
3521             if self.isAppropriateValue(arg):
3522                return arg
3523             else:
3524                raise TypeError,"%s: new value is not appropriate."%str(self)
3525          else:
3526             arg=self.getSubstitutedArguments(argvals)
3527             return inverse(arg[0])
3528    
3529       def diff(self,arg):
3530          """
3531          differential of this object
3532    
3533          @param arg: the derivative is calculated with respect to arg
3534          @type arg: L{escript.Symbol}
3535          @return: derivative with respect to C{arg}
3536          @rtype: typically L{Symbol} but other types such as C{float}, L{escript.Data}, L{numarray.NumArray}  are possible.
3537          """
3538          if arg==self:
3539             return identity(self.getShape())
3540          else:
3541             return -matrixmult(matrixmult(self,self.getDifferentiatedArguments(arg)[0]),self)
3542    
3543    def eigenvalues(arg):
3544        """
3545        returns the eigenvalues of the square matrix arg.
3546    
3547        @param arg: square matrix. Must have rank 2 and the first and second dimension must be equal.
3548                    arg must be symmetric, ie. transpose(arg)==arg (this is not checked).
3549        @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
3550        @return: the eigenvalues in increasing order.
3551        @rtype: L{numarray.NumArray},L{escript.Data}, L{Symbol} depending on the input.
3552        @remark: for L{escript.Data} and L{Symbol} objects the dimension is restricted to 3.
3553        """
3554        if isinstance(arg,numarray.NumArray):
3555          if not arg.rank==2:
3556            raise ValueError,"eigenvalues: argument must have rank 2"
3557          s=arg.shape      
3558          if not s[0] == s[1]:
3559            raise ValueError,"eigenvalues: argument must be a square matrix."
3560          out=numarray.linear_algebra.eigenvalues((arg+numarray.transpose(arg))/2.)
3561          out.sort()
3562          return out
3563        elif isinstance(arg,escript.Data):
3564          return escript_eigenvalues(arg)
3565        elif isinstance(arg,Symbol):
3566          if not arg.getRank()==2:
3567            raise ValueError,"eigenvalues: argument must have rank 2"
3568          s=arg.getShape()      
3569          if not s[0] == s[1]:
3570            raise ValueError,"eigenvalues: argument must be a square matrix."
3571          if s[0]==1:
3572              return arg[0]
3573          elif s[0]==2:
3574              A11=arg[0,0]
3575              A12=arg[0,1]
3576              A22=arg[1,1]
3577              trA=(A11+A22)/2.
3578              A11-=trA
3579              A22-=trA
3580              s=sqrt(A12**2-A11*A22)
3581              return trA+s*numarray.array([-1.,1.])
3582          elif s[0]==3:
3583              A11=arg[0,0]
3584              A12=arg[0,1]
3585              A22=arg[1,1]
3586              A13=arg[0,2]
3587              A23=arg[1,2]
3588              A33=arg[2,2]
3589              trA=(A11+A22+A33)/3.
3590              A11-=trA
3591              A22-=trA
3592              A33-=trA
3593              A13_2=A13**2
3594              A23_2=A23**2
3595              A12_2=A12**2
3596              p=A13_2+A23_2+A12_2+(A11**2+A22**2+A33**2)/2.
3597              q=A13_2*A22+A23_2*A11+A12_2*A33-A11*A22*A33-2*A12*A23*A13
3598              sq_p=sqrt(p/3.)
3599              alpha_3=acos(-q*sq_p**(-3.)/2.)/3.
3600              sq_p*=2.
3601              f=cos(alpha_3)               *numarray.array([0.,0.,1.]) \
3602               -cos(alpha_3+numarray.pi/3.)*numarray.array([0.,1.,0.]) \
3603               -cos(alpha_3-numarray.pi/3.)*numarray.array([1.,0.,0.])
3604              return trA+sq_p*f
3605          else:
3606             raise TypeError,"eigenvalues: only matrix dimensions 1,2,3 are supported right now."
3607        elif isinstance(arg,float):
3608          return arg
3609        elif isinstance(arg,int):
3610          return float(arg)
3611        else:
3612          raise TypeError,"eigenvalues: Unknown argument type."
3613    
3614    def escript_eigenvalues(arg): # this should be implemented in C++ arg and LAPACK is data object
3615          if not arg.getRank()==2:
3616            raise ValueError,"eigenvalues: argument must have rank 2"
3617          s=arg.getShape()      
3618          if not s[0] == s[1]:
3619            raise ValueError,"eigenvalues: argument must be a square matrix."
3620          if s[0]==1:
3621              return arg[0]
3622          elif s[0]==2:
3623              A11=arg[0,0]
3624              A12=arg[0,1]
3625              A22=arg[1,1]
3626              trA=(A11+A22)/2.
3627              A11-=trA
3628              A22-=trA
3629              s=sqrt(A12**2-A11*A22)
3630              return trA+s*numarray.array([-1.,1.])
3631          elif s[0]==3:
3632              A11=arg[0,0]
3633              A12=arg[0,1]
3634              A22=arg[1,1]
3635              A13=arg[0,2]
3636              A23=arg[1,2]
3637              A33=arg[2,2]
3638              trA=(A11+A22+A33)/3.
3639              A11-=trA
3640              A22-=trA
3641              A33-=trA
3642              A13_2=A13**2
3643              A23_2=A23**2
3644              A12_2=A12**2
3645              p=A13_2+A23_2+A12_2+(A11**2+A22**2+A33**2)/2.
3646              q=A13_2*A22+A23_2*A11+A12_2*A33-A11*A22*A33-2*A12*A23*A13
3647              sq_p=sqrt(p/3.)
3648              alpha_3=acos(-q*sq_p**(-3.)/2.)/3.
3649              sq_p*=2.
3650              f=escript.Data(0.,(3,),arg.getFunctionSpace())
3651              f[0]=-cos(alpha_3-numarray.pi/3.)
3652              f[1]=-cos(alpha_3+numarray.pi/3.)
3653              f[2]=cos(alpha_3)
3654              return trA+sq_p*f
3655          else:
3656             raise TypeError,"eigenvalues: only matrix dimensions 1,2,3 are supported right now."
3657  #=======================================================  #=======================================================
3658  #  Binary operations:  #  Binary operations:
3659  #=======================================================  #=======================================================
# Line 3304  def maximum(*args): Line 4081  def maximum(*args):
4081         if out==None:         if out==None:
4082            out=a            out=a
4083         else:         else:
4084            m=whereNegative(out-a)            diff=add(a,-out)
4085            out=m*a+(1.-m)*out            out=add(out,mult(wherePositive(diff),diff))
4086      return out      return out
4087        
4088  def minimum(*arg):  def minimum(*args):
4089      """      """
4090      the minimum over arguments args      the minimum over arguments args
4091    
# Line 3322  def minimum(*arg): Line 4099  def minimum(*arg):
4099         if out==None:         if out==None:
4100            out=a            out=a
4101         else:         else:
4102            m=whereNegative(out-a)            diff=add(a,-out)
4103            out=m*out+(1.-m)*a            out=add(out,mult(whereNegative(diff),diff))
4104      return out      return out
4105    
4106    def clip(arg,minval=0.,maxval=1.):
4107        """
4108        cuts the values of arg between minval and maxval
4109    
4110        @param arg: argument
4111        @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float}
4112        @param minval: lower range
4113        @type arg: C{float}
4114        @param maxval: upper range
4115        @type arg: C{float}
4116        @return: is on object with all its value between minval and maxval. value of the argument that greater then minval and
4117                 less then maxval are unchanged.
4118        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float} depending on the input
4119        @raise ValueError: if minval>maxval
4120        """
4121        if minval>maxval:
4122           raise ValueError,"minval = %s must be less then maxval %s"%(minval,maxval)
4123        return minimum(maximum(minval,arg),maxval)
4124    
4125        
4126  def inner(arg0,arg1):  def inner(arg0,arg1):
4127      """      """
# Line 3348  def inner(arg0,arg1): Line 4145  def inner(arg0,arg1):
4145      sh1=pokeShape(arg1)      sh1=pokeShape(arg1)
4146      if not sh0==sh1:      if not sh0==sh1:
4147          raise ValueError,"inner: shape of arguments does not match"          raise ValueError,"inner: shape of arguments does not match"
4148      return generalTensorProduct(arg0,arg1,offset=len(sh0))      return generalTensorProduct(arg0,arg1,axis_offset=len(sh0))
4149    
4150  def matrixmult(arg0,arg1):  def matrixmult(arg0,arg1):
4151      """      """
# Line 3376  def matrixmult(arg0,arg1): Line 4173  def matrixmult(arg0,arg1):
4173          raise ValueError,"first argument must have rank 2"          raise ValueError,"first argument must have rank 2"
4174      if not len(sh1)==2 and not len(sh1)==1:      if not len(sh1)==2 and not len(sh1)==1:
4175          raise ValueError,"second argument must have rank 1 or 2"          raise ValueError,"second argument must have rank 1 or 2"
4176      return generalTensorProduct(arg0,arg1,offset=1)      return generalTensorProduct(arg0,arg1,axis_offset=1)
4177    
4178  def outer(arg0,arg1):  def outer(arg0,arg1):
4179      """      """
# Line 3394  def outer(arg0,arg1): Line 4191  def outer(arg0,arg1):
4191      @return: the outer product of arg0 and arg1 at each data point      @return: the outer product of arg0 and arg1 at each data point
4192      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
4193      """      """
4194      return generalTensorProduct(arg0,arg1,offset=0)      return generalTensorProduct(arg0,arg1,axis_offset=0)
4195    
4196    
4197  def tensormult(arg0,arg1):  def tensormult(arg0,arg1):
# Line 3436  def tensormult(arg0,arg1): Line 4233  def tensormult(arg0,arg1):
4233      sh0=pokeShape(arg0)      sh0=pokeShape(arg0)
4234      sh1=pokeShape(arg1)      sh1=pokeShape(arg1)
4235      if len(sh0)==2 and ( len(sh1)==2 or len(sh1)==1 ):      if len(sh0)==2 and ( len(sh1)==2 or len(sh1)==1 ):
4236         return generalTensorProduct(arg0,arg1,offset=1)         return generalTensorProduct(arg0,arg1,axis_offset=1)
4237      elif len(sh0)==4 and (len(sh1)==2 or len(sh1)==3 or len(sh1)==4):      elif len(sh0)==4 and (len(sh1)==2 or len(sh1)==3 or len(sh1)==4):
4238         return generalTensorProduct(arg0,arg1,offset=2)         return generalTensorProduct(arg0,arg1,axis_offset=2)
4239      else:      else:
4240          raise ValueError,"tensormult: first argument must have rank 2 or 4"          raise ValueError,"tensormult: first argument must have rank 2 or 4"
4241    
4242  def generalTensorProduct(arg0,arg1,offset=0):  def generalTensorProduct(arg0,arg1,axis_offset=0):
4243      """      """
4244      generalized tensor product      generalized tensor product
4245    
4246      out[s,t]=S{Sigma}_r arg0[s,r]*arg1[r,t]      out[s,t]=S{Sigma}_r arg0[s,r]*arg1[r,t]
4247    
4248      where s runs through arg0.Shape[:arg0.Rank-offset]      where s runs through arg0.Shape[:arg0.Rank-axis_offset]
4249            r runs trough arg0.Shape[:offset]            r runs trough arg0.Shape[:axis_offset]
4250            t runs through arg1.Shape[offset:]            t runs through arg1.Shape[axis_offset:]
4251    
4252      In the first case the the second dimension of arg0 and the length of arg1 must match and        In the first case the the second dimension of arg0 and the length of arg1 must match and  
4253      in the second case the two last dimensions of arg0 must match the shape of arg1.      in the second case the two last dimensions of arg0 must match the shape of arg1.
# Line 3467  def generalTensorProduct(arg0,arg1,offse Line 4264  def generalTensorProduct(arg0,arg1,offse
4264      # at this stage arg0 and arg0 are both numarray.NumArray or escript.Data or Symbols      # at this stage arg0 and arg0 are both numarray.NumArray or escript.Data or Symbols
4265      if isinstance(arg0,numarray.NumArray):      if isinstance(arg0,numarray.NumArray):
4266         if isinstance(arg1,Symbol):         if isinstance(arg1,Symbol):
4267             return GeneralTensorProduct_Symbol(arg0,arg1,offset)             return GeneralTensorProduct_Symbol(arg0,arg1,axis_offset)
4268         else:         else:
4269             if not arg0.shape[arg0.rank-offset:]==arg1.shape[:offset]:             if not arg0.shape[arg0.rank-axis_offset:]==arg1.shape[:axis_offset]:
4270                 raise ValueError,"generalTensorProduct: dimensions of last %s components in left argument don't match the first %s components in the right argument."%(offset,offset)                 raise ValueError,"generalTensorProduct: dimensions of last %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4271             arg0_c=arg0.copy()             arg0_c=arg0.copy()
4272             arg1_c=arg1.copy()             arg1_c=arg1.copy()
4273             sh0,sh1=arg0.shape,arg1.shape             sh0,sh1=arg0.shape,arg1.shape
4274             d0,d1,d01=1,1,1             d0,d1,d01=1,1,1
4275             for i in sh0[:arg0.rank-offset]: d0*=i             for i in sh0[:arg0.rank-axis_offset]: d0*=i
4276             for i in sh1[offset:]: d1*=i             for i in sh1[axis_offset:]: d1*=i
4277             for i in sh1[:offset]: d01*=i             for i in sh1[:axis_offset]: d01*=i
4278             arg0_c.resize((d0,d01))             arg0_c.resize((d0,d01))
4279             arg1_c.resize((d01,d1))             arg1_c.resize((d01,d1))
4280             out=numarray.zeros((d0,d1),numarray.Float)             out=numarray.zeros((d0,d1),numarray.Float)
4281             for i0 in range(d0):             for i0 in range(d0):
4282                      for i1 in range(d1):                      for i1 in range(d1):
4283                           out[i0,i1]=numarray.sum(arg0_c[i0,:]*arg1_c[:,i1])                           out[i0,i1]=numarray.sum(arg0_c[i0,:]*arg1_c[:,i1])
4284             out.resize(sh0[:arg0.rank-offset]+sh1[offset:])             out.resize(sh0[:arg0.rank-axis_offset]+sh1[axis_offset:])
4285             return out             return out
4286      elif isinstance(arg0,escript.Data):      elif isinstance(arg0,escript.Data):
4287         if isinstance(arg1,Symbol):         if isinstance(arg1,Symbol):
4288             return GeneralTensorProduct_Symbol(arg0,arg1,offset)             return GeneralTensorProduct_Symbol(arg0,arg1,axis_offset)
4289         else:         else:
4290             return escript_generalTensorProduct(arg0,arg1,offset) # this calls has to be replaced by escript._generalTensorProduct(arg0,arg1,offset)             return escript_generalTensorProduct(arg0,arg1,axis_offset) # this calls has to be replaced by escript._generalTensorProduct(arg0,arg1,axis_offset)
4291      else:            else:      
4292         return GeneralTensorProduct_Symbol(arg0,arg1,offset)         return GeneralTensorProduct_Symbol(arg0,arg1,axis_offset)
4293                                    
4294  class GeneralTensorProduct_Symbol(DependendSymbol):  class GeneralTensorProduct_Symbol(DependendSymbol):
4295     """     """
4296     Symbol representing the quotient of two arguments.     Symbol representing the quotient of two arguments.
4297     """     """
4298     def __init__(self,arg0,arg1,offset=0):     def __init__(self,arg0,arg1,axis_offset=0):
4299         """         """
4300         initialization of L{Symbol} representing the quotient of two arguments         initialization of L{Symbol} representing the quotient of two arguments
4301    
# Line 3511  class GeneralTensorProduct_Symbol(Depend Line 4308  class GeneralTensorProduct_Symbol(Depend
4308         """         """
4309         sh_arg0=pokeShape(arg0)         sh_arg0=pokeShape(arg0)
4310         sh_arg1=pokeShape(arg1)         sh_arg1=pokeShape(arg1)
4311         sh0=sh_arg0[:len(sh_arg0)-offset]         sh0=sh_arg0[:len(sh_arg0)-axis_offset]
4312         sh01=sh_arg0[len(sh_arg0)-offset:]         sh01=sh_arg0[len(sh_arg0)-axis_offset:]
4313         sh10=sh_arg1[:offset]         sh10=sh_arg1[:axis_offset]
4314         sh1=sh_arg1[offset:]         sh1=sh_arg1[axis_offset:]
4315         if not sh01==sh10:         if not sh01==sh10:
4316             raise ValueError,"dimensions of last %s components in left argument don't match the first %s components in the right argument."%(offset,offset)             raise ValueError,"dimensions of last %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4317         DependendSymbol.__init__(self,dim=commonDim(arg0,arg1),shape=sh0+sh1,args=[arg0,arg1,offset])         DependendSymbol.__init__(self,dim=commonDim(arg0,arg1),shape=sh0+sh1,args=[arg0,arg1,axis_offset])
4318    
4319     def getMyCode(self,argstrs,format="escript"):     def getMyCode(self,argstrs,format="escript"):
4320        """        """
# Line 3532  class GeneralTensorProduct_Symbol(Depend Line 4329  class GeneralTensorProduct_Symbol(Depend
4329        @raise: NotImplementedError: if the requested format is not available        @raise: NotImplementedError: if the requested format is not available
4330        """        """
4331        if format=="escript" or format=="str" or format=="text":        if format=="escript" or format=="str" or format=="text":
4332           return "generalTensorProduct(%s,%s,offset=%s)"%(argstrs[0],argstrs[1],argstrs[2])           return "generalTensorProduct(%s,%s,axis_offset=%s)"%(argstrs[0],argstrs[1],argstrs[2])
4333        else:        else:
4334           raise NotImplementedError,"%s does not provide program code for format %s."%(str(self),format)           raise NotImplementedError,"%s does not provide program code for format %s."%(str(self),format)
4335    
# Line 3557  class GeneralTensorProduct_Symbol(Depend Line 4354  class GeneralTensorProduct_Symbol(Depend
4354           args=self.getSubstitutedArguments(argvals)           args=self.getSubstitutedArguments(argvals)
4355           return generalTensorProduct(args[0],args[1],args[2])           return generalTensorProduct(args[0],args[1],args[2])
4356    
4357  def escript_generalTensorProduct(arg0,arg1,offset): # this should be escript._generalTensorProduct  def escript_generalTensorProduct(arg0,arg1,axis_offset): # this should be escript._generalTensorProduct
4358      "arg0 and arg1 are both Data objects but not neccesrily on the same function space. they could be identical!!!"      "arg0 and arg1 are both Data objects but not neccesrily on the same function space. they could be identical!!!"
4359      # calculate the return shape:      # calculate the return shape:
4360      shape0=arg0.getShape()[:arg0.getRank()-offset]      shape0=arg0.getShape()[:arg0.getRank()-axis_offset]
4361      shape01=arg0.getShape()[arg0.getRank()-offset:]      shape01=arg0.getShape()[arg0.getRank()-axis_offset:]
4362      shape10=arg1.getShape()[:offset]      shape10=arg1.getShape()[:axis_offset]
4363      shape1=arg1.getShape()[offset:]      shape1=arg1.getShape()[axis_offset:]
4364      if not shape01==shape10:      if not shape01==shape10:
4365          raise ValueError,"dimensions of last %s components in left argument don't match the first %s components in the right argument."%(offset,offset)          raise ValueError,"dimensions of last %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4366    
4367        # whatr function space should be used? (this here is not good!)
4368        fs=(escript.Scalar(0.,arg0.getFunctionSpace())+escript.Scalar(0.,arg1.getFunctionSpace())).getFunctionSpace()
4369      # create return value:      # create return value:
4370      out=escript.Data(0.,tuple(shape0+shape1),arg0.getFunctionSpace())      out=escript.Data(0.,tuple(shape0+shape1),fs)
4371      #      #
4372      s0=[[]]      s0=[[]]
4373      for k in shape0:      for k in shape0:
# Line 3591  def escript_generalTensorProduct(arg0,ar Line 4390  def escript_generalTensorProduct(arg0,ar
4390    
4391      for i0 in s0:      for i0 in s0:
4392         for i1 in s1:         for i1 in s1:
4393           s=escript.Scalar(0.,arg0.getFunctionSpace())           s=escript.Scalar(0.,fs)
4394           for i01 in s01:           for i01 in s01:
4395              s+=arg0.__getitem__(tuple(i0+i01))*arg1.__getitem__(tuple(i01+i1))              s+=arg0.__getitem__(tuple(i0+i01))*arg1.__getitem__(tuple(i01+i1))
4396           out.__setitem__(tuple(i0+i1),s)           out.__setitem__(tuple(i0+i1),s)
4397      return out      return out
4398    
4399    
4400  #=========================================================  #=========================================================
4401  #   some little helpers  #  functions dealing with spatial dependency
4402  #=========================================================  #=========================================================
4403  def grad(arg,where=None):  def grad(arg,where=None):
4404      """      """
4405      Returns the spatial gradient of arg at where.      Returns the spatial gradient of arg at where.
4406    
4407      @param arg:   Data object representing the function which gradient      If C{g} is the returned object, then
4408                    to be calculated.  
4409          - if C{arg} is rank 0 C{g[s]} is the derivative of C{arg} with respect to the C{s}-th spatial dimension.
4410          - if C{arg} is rank 1 C{g[i,s]} is the derivative of C{arg[i]} with respect to the C{s}-th spatial dimension.
4411          - if C{arg} is rank 2 C{g[i,j,s]} is the derivative of C{arg[i,j]} with respect to the C{s}-th spatial dimension.
4412          - if C{arg} is rank 3 C{g[i,j,k,s]} is the derivative of C{arg[i,j,k]} with respect to the C{s}-th spatial dimension.
4413    
4414        @param arg: function which gradient to be calculated. Its rank has to be less than 3.
4415        @type arg: L{escript.Data} or L{Symbol}
4416      @param where: FunctionSpace in which the gradient will be calculated.      @param where: FunctionSpace in which the gradient will be calculated.
4417                    If not present or C{None} an appropriate default is used.                    If not present or C{None} an appropriate default is used.
4418        @type where: C{None} or L{escript.FunctionSpace}
4419        @return: gradient of arg.
4420        @rtype:  L{escript.Data} or L{Symbol}
4421      """      """
4422      if isinstance(arg,Symbol):      if isinstance(arg,Symbol):
4423         return Grad_Symbol(arg,where)         return Grad_Symbol(arg,where)
# Line 3617  def grad(arg,where=None): Line 4427  def grad(arg,where=None):
4427         else:         else:
4428            return arg._grad(where)            return arg._grad(where)
4429      else:      else:
4430        raise TypeError,"grad: Unknown argument type."         raise TypeError,"grad: Unknown argument type."
4431    
4432    class Grad_Symbol(DependendSymbol):
4433       """
4434       L{Symbol} representing the result of the gradient operator
4435       """
4436       def __init__(self,arg,where=None):
4437          """
4438          initialization of gradient L{Symbol} with argument arg
4439          @param arg: argument of function
4440          @type arg: L{Symbol}.
4441          @param where: FunctionSpace in which the gradient will be calculated.
4442                      If not present or C{None} an appropriate default is used.
4443          @type where: C{None} or L{escript.FunctionSpace}
4444          """
4445          d=arg.getDim()
4446          if d==None:
4447             raise ValueError,"argument must have a spatial dimension"
4448          super(Grad_Symbol,self).__init__(args=[arg,where],shape=arg.getShape()+(d,),dim=d)
4449    
4450       def getMyCode(self,argstrs,format="escript"):
4451          """
4452          returns a program code that can be used to evaluate the symbol.
4453    
4454          @param argstrs: gives for each argument a string representing the argument for the evaluation.
4455          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
4456          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
4457          @type format: C{str}
4458          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4459          @rtype: C{str}
4460          @raise: NotImplementedError: if the requested format is not available
4461          """
4462          if format=="escript" or format=="str"  or format=="text":
4463             return "grad(%s,where=%s)"%(argstrs[0],argstrs[1])
4464          else:
4465             raise NotImplementedError,"Trace_Symbol does not provide program code for format %s."%format
4466    
4467       def substitute(self,argvals):
4468          """
4469          assigns new values to symbols in the definition of the symbol.
4470          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
4471    
4472          @param argvals: new values assigned to symbols
4473          @type argvals: C{dict} with keywords of type L{Symbol}.
4474          @return: result of the substitution process. Operations are executed as much as possible.
4475          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
4476          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
4477          """
4478          if argvals.has_key(self):
4479             arg=argvals[self]
4480             if self.isAppropriateValue(arg):
4481                return arg
4482             else:
4483                raise TypeError,"%s: new value is not appropriate."%str(self)
4484          else:
4485             arg=self.getSubstitutedArguments(argvals)
4486             return grad(arg[0],where=arg[1])
4487    
4488       def diff(self,arg):
4489          """
4490          differential of this object
4491    
4492          @param arg: the derivative is calculated with respect to arg
4493          @type arg: L{escript.Symbol}
4494          @return: derivative with respect to C{arg}
4495          @rtype: typically L{Symbol} but other types such as C{float}, L{escript.Data}, L{numarray.NumArray}  are possible.
4496          """
4497          if arg==self:
4498             return identity(self.getShape())
4499          else:
4500             return grad(self.getDifferentiatedArguments(arg)[0],where=self.getArgument()[1])
4501    
4502  def integrate(arg,where=None):  def integrate(arg,where=None):
4503      """      """
4504      Return the integral if the function represented by Data object arg over      Return the integral of the function C{arg} over its domain. If C{where} is present C{arg} is interpolated to C{where}
4505      its domain.      before integration.
4506    
4507      @param arg:   Data object representing the function which is integrated.      @param arg:   the function which is integrated.
4508        @type arg: L{escript.Data} or L{Symbol}
4509      @param where: FunctionSpace in which the integral is calculated.      @param where: FunctionSpace in which the integral is calculated.
4510                    If not present or C{None} an appropriate default is used.                    If not present or C{None} an appropriate default is used.
4511        @type where: C{None} or L{escript.FunctionSpace}
4512        @return: integral of arg.
4513        @rtype:  C{float}, C{numarray.NumArray} or L{Symbol}
4514      """      """
4515      if isinstance(arg,numarray.NumArray):      if isinstance(arg,Symbol):
         if checkForZero(arg):  
            return arg  
         else:  
            raise TypeError,"integrate: cannot intergrate argument"  
     elif isinstance(arg,float):  
         if checkForZero(arg):  
            return arg  
         else:  
            raise TypeError,"integrate: cannot intergrate argument"  
     elif isinstance(arg,int):  
         if checkForZero(arg):  
            return float(arg)  
         else:  
            raise TypeError,"integrate: cannot intergrate argument"  
     elif isinstance(arg,Symbol):  
4516         return Integrate_Symbol(arg,where)         return Integrate_Symbol(arg,where)
4517      elif isinstance(arg,escript.Data):      elif isinstance(arg,escript.Data):
4518         if not where==None: arg=escript.Data(arg,where)         if not where==None: arg=escript.Data(arg,where)
# Line 3654  def integrate(arg,where=None): Line 4523  def integrate(arg,where=None):
4523      else:      else:
4524        raise TypeError,"integrate: Unknown argument type."        raise TypeError,"integrate: Unknown argument type."
4525    
4526    class Integrate_Symbol(DependendSymbol):
4527       """
4528       L{Symbol} representing the result of the spatial integration operator
4529       """
4530       def __init__(self,arg,where=None):
4531          """
4532          initialization of integration L{Symbol} with argument arg
4533          @param arg: argument of the integration
4534          @type arg: L{Symbol}.
4535          @param where: FunctionSpace in which the integration will be calculated.
4536                      If not present or C{None} an appropriate default is used.
4537          @type where: C{None} or L{escript.FunctionSpace}
4538          """
4539          super(Integrate_Symbol,self).__init__(args=[arg,where],shape=arg.getShape(),dim=arg.getDim())
4540    
4541       def getMyCode(self,argstrs,format="escript"):
4542          """
4543          returns a program code that can be used to evaluate the symbol.
4544    
4545          @param argstrs: gives for each argument a string representing the argument for the evaluation.
4546          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
4547          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
4548          @type format: C{str}
4549          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4550          @rtype: C{str}
4551          @raise: NotImplementedError: if the requested format is not available
4552          """
4553          if format=="escript" or format=="str"  or format=="text":
4554             return "integrate(%s,where=%s)"%(argstrs[0],argstrs[1])
4555          else:
4556             raise NotImplementedError,"Trace_Symbol does not provide program code for format %s."%format
4557    
4558       def substitute(self,argvals):
4559          """
4560          assigns new values to symbols in the definition of the symbol.
4561          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
4562    
4563          @param argvals: new values assigned to symbols
4564          @type argvals: C{dict} with keywords of type L{Symbol}.
4565          @return: result of the substitution process. Operations are executed as much as possible.
4566          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
4567          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
4568          """
4569          if argvals.has_key(self):
4570             arg=argvals[self]
4571             if self.isAppropriateValue(arg):
4572                return arg
4573             else:
4574                raise TypeError,"%s: new value is not appropriate."%str(self)
4575          else:
4576             arg=self.getSubstitutedArguments(argvals)
4577             return integrate(arg[0],where=arg[1])
4578    
4579       def diff(self,arg):
4580          """
4581          differential of this object
4582    
4583          @param arg: the derivative is calculated with respect to arg
4584          @type arg: L{escript.Symbol}
4585          @return: derivative with respect to C{arg}
4586          @rtype: typically L{Symbol} but other types such as C{float}, L{escript.Data}, L{numarray.NumArray}  are possible.
4587          """
4588          if arg==self:
4589             return identity(self.getShape())
4590          else:
4591             return integrate(self.getDifferentiatedArguments(arg)[0],where=self.getArgument()[1])
4592    
4593    
4594  def interpolate(arg,where):  def interpolate(arg,where):
4595      """      """
4596      Interpolates the function into the FunctionSpace where.      interpolates the function into the FunctionSpace where.
4597    
4598      @param arg:    interpolant      @param arg: interpolant
4599      @param where:  FunctionSpace to interpolate to      @type arg: L{escript.Data} or L{Symbol}
4600        @param where: FunctionSpace to be interpolated to
4601        @type where: L{escript.FunctionSpace}
4602        @return: interpolated argument
4603        @rtype:  C{escript.Data} or L{Symbol}
4604      """      """
4605      if testForZero(arg):      if isinstance(arg,Symbol):
4606        return 0         return Interpolate_Symbol(arg,where)
     elif isinstance(arg,Symbol):  
        return Interpolated_Symbol(arg,where)  
4607      else:      else:
4608         return escript.Data(arg,where)         return escript.Data(arg,where)
4609    
4610  def div(arg,where=None):  class Interpolate_Symbol(DependendSymbol):
4611      """     """
4612      Returns the divergence of arg at where.     L{Symbol} representing the result of the interpolation operator
4613       """
4614       def __init__(self,arg,where):
4615          """
4616          initialization of interpolation L{Symbol} with argument arg
4617          @param arg: argument of the interpolation
4618          @type arg: L{Symbol}.
4619          @param where: FunctionSpace into which the argument is interpolated.
4620          @type where: L{escript.FunctionSpace}
4621          """
4622          super(Interpolate_Symbol,self).__init__(args=[arg,where],shape=arg.getShape(),dim=arg.getDim())
4623    
4624      @param arg:   Data object representing the function which gradient to     def getMyCode(self,argstrs,format="escript"):
4625                    be calculated.        """
4626      @param where: FunctionSpace in which the gradient will be calculated.        returns a program code that can be used to evaluate the symbol.
                   If not present or C{None} an appropriate default is used.  
     """  
     g=grad(arg,where)  
     return trace(g,axis0=g.getRank()-2,axis1=g.getRank()-1)  
4627    
4628  def jump(arg):        @param argstrs: gives for each argument a string representing the argument for the evaluation.
4629      """        @type argstrs: C{str} or a C{list} of length 1 of C{str}.
4630      Returns the jump of arg across a continuity.        @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
4631          @type format: C{str}
4632          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4633          @rtype: C{str}
4634          @raise: NotImplementedError: if the requested format is not available
4635          """
4636          if format=="escript" or format=="str"  or format=="text":
4637             return "interpolate(%s,where=%s)"%(argstrs[0],argstrs[1])
4638          else:
4639             raise NotImplementedError,"Trace_Symbol does not provide program code for format %s."%format
4640    
4641      @param arg:   Data object representing the function which gradient     def substitute(self,argvals):
4642                    to be calculated.        """
4643      """        assigns new values to symbols in the definition of the symbol.
4644      d=arg.getDomain()        The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
     return arg.interpolate(escript.FunctionOnContactOne())-arg.interpolate(escript.FunctionOnContactZero())  
4645    
4646  #=============================        @param argvals: new values assigned to symbols
4647  #        @type argvals: C{dict} with keywords of type L{Symbol}.
4648  # wrapper for various functions: if the argument has attribute the function name        @return: result of the substitution process. Operations are executed as much as possible.
4649  # as an argument it calls the corresponding methods. Otherwise the corresponding        @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
4650  # numarray function is called.        @raise TypeError: if a value for a L{Symbol} cannot be substituted.
4651          """
4652          if argvals.has_key(self):
4653             arg=argvals[self]
4654             if self.isAppropriateValue(arg):
4655                return arg
4656             else:
4657                raise TypeError,"%s: new value is not appropriate."%str(self)
4658          else:
4659             arg=self.getSubstitutedArguments(argvals)
4660             return interpolate(arg[0],where=arg[1])
4661    
4662       def diff(self,arg):
4663          """
4664          differential of this object
4665    
4666          @param arg: the derivative is calculated with respect to arg
4667          @type arg: L{escript.Symbol}
4668          @return: derivative with respect to C{arg}
4669          @rtype: L{Symbol} but other types such as L{escript.Data}, L{numarray.NumArray}  are possible.
4670          """
4671          if arg==self:
4672             return identity(self.getShape())
4673          else:
4674             return interpolate(self.getDifferentiatedArguments(arg)[0],where=self.getArgument()[1])
4675    
 # functions involving the underlying Domain:  
4676    
4677  def transpose(arg,axis=None):  def div(arg,where=None):
4678      """      """
4679      Returns the transpose of the Data object arg.      returns the divergence of arg at where.
4680    
4681      @param arg:      @param arg: function which divergence to be calculated. Its shape has to be (d,) where d is the spatial dimension.
4682        @type arg: L{escript.Data} or L{Symbol}
4683        @param where: FunctionSpace in which the divergence will be calculated.
4684                      If not present or C{None} an appropriate default is used.
4685        @type where: C{None} or L{escript.FunctionSpace}
4686        @return: divergence of arg.
4687        @rtype:  L{escript.Data} or L{Symbol}
4688      """      """
     if axis==None:  
        r=0  
        if hasattr(arg,"getRank"): r=arg.getRank()  
        if hasattr(arg,"rank"): r=arg.rank  
        axis=r/2  
4689      if isinstance(arg,Symbol):      if isinstance(arg,Symbol):
4690         return Transpose_Symbol(arg,axis=r)          dim=arg.getDim()
4691      if isinstance(arg,escript.Data):      elif isinstance(arg,escript.Data):
4692         # hack for transpose          dim=arg.getDomain().getDim()
        r=arg.getRank()  
        if r!=2: raise ValueError,"Tranpose only avalaible for rank 2 objects"  
        s=arg.getShape()  
        out=escript.Data(0.,(s[1],s[0]),arg.getFunctionSpace())  
        for i in range(s[0]):  
           for j in range(s[1]):  
              out[j,i]=arg[i,j]  
        return out  
        # end hack for transpose  
        return arg.transpose(axis)  
4693      else:      else:
4694         return numarray.transpose(arg,axis=axis)          raise TypeError,"div: argument type not supported"
4695        if not arg.getShape()==(dim,):
4696          raise ValueError,"div: expected shape is (%s,)"%dim
4697        return trace(grad(arg,where))
4698    
4699  def trace(arg,axis0=0,axis1=1):  def jump(arg,domain=None):
4700      """      """
4701      Return      returns the jump of arg across the continuity of the domain
4702    
4703      @param arg:      @param arg: argument
4704        @type arg: L{escript.Data} or L{Symbol}
4705        @param domain: the domain where the discontinuity is located. If domain is not present or equal to C{None}
4706                       the domain of arg is used. If arg is a L{Symbol} the domain must be present.
4707        @type domain: C{None} or L{escript.Domain}
4708        @return: jump of arg
4709        @rtype:  L{escript.Data} or L{Symbol}
4710      """      """
4711      if isinstance(arg,Symbol):      if domain==None: domain=arg.getDomain()
4712         s=list(arg.getShape())              return interpolate(arg,escript.FunctionOnContactOne(domain))-interpolate(arg,escript.FunctionOnContactZero(domain))
        s=tuple(s[0:axis0]+s[axis0+1:axis1]+s[axis1+1:])  
        return Trace_Symbol(arg,axis0=axis0,axis1=axis1)  
     elif isinstance(arg,escript.Data):  
        # hack for trace  
        s=arg.getShape()  
        if s[axis0]!=s[axis1]:  
            raise ValueError,"illegal axis in trace"  
        out=escript.Scalar(0.,arg.getFunctionSpace())  
        for i in range(s[axis0]):  
           out+=arg[i,i]  
        return out  
        # end hack for trace  
     else:  
        return numarray.trace(arg,axis0=axis0,axis1=axis1)  
4713    
4714    def L2(arg):
4715        """
4716        returns the L2 norm of arg at where
4717        
4718        @param arg: function which L2 to be calculated.
4719        @type arg: L{escript.Data} or L{Symbol}
4720        @return: L2 norm of arg.
4721        @rtype:  L{float} or L{Symbol}
4722        @note: L2(arg) is equivalent to sqrt(integrate(inner(arg,arg)))
4723        """
4724        return sqrt(integrate(inner(arg,arg)))
4725    #=============================
4726    #
4727    
4728  def reorderComponents(arg,index):  def reorderComponents(arg,index):
4729      """      """
4730      resorts the component of arg according to index      resorts the component of arg according to index
4731    
4732      """      """
4733      pass      raise NotImplementedError
4734  #  #
4735  # $Log: util.py,v $  # $Log: util.py,v $
4736  # Revision 1.14.2.16  2005/10/19 06:09:57  gross  # Revision 1.14.2.16  2005/10/19 06:09:57  gross

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