/[escript]/trunk/escript/py_src/util.py
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revision 378 by gross, Fri Dec 16 09:02:28 2005 UTC revision 528 by gross, Wed Feb 15 02:20:33 2006 UTC
# Line 30  __date__="$Date$" Line 30  __date__="$Date$"
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 clip(arg,minval,maxval)  
   
 # 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 126  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 148  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 164  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 179  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 192  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 364  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.
363        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.         return not Lsup(arg)>0.
369      except TypeError:      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 826  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 876  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 908  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 994  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 1080  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 1114  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 1150  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 1237  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 2878  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    
3281    def inverse(arg):
3282        """
3283        returns the inverse of the square matrix arg.
3284    
3285        @param arg: square matrix. Must have rank 2 and the first and second dimension must be equal.
3286        @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
3287        @return: inverse arg_inv of the argument. It will be matrixmul(inverse(arg),arg) almost equal to kronecker(arg.getShape()[0])
3288        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
3289        @remark: for L{escript.Data} objects the dimension is restricted to 3.
3290        """
3291        if isinstance(arg,numarray.NumArray):
3292          return numarray.linear_algebra.inverse(arg)
3293        elif isinstance(arg,escript.Data):
3294          return escript_inverse(arg)
3295        elif isinstance(arg,float):
3296          return 1./arg
3297        elif isinstance(arg,int):
3298          return 1./float(arg)
3299        elif isinstance(arg,Symbol):
3300          return Inverse_Symbol(arg)
3301        else:
3302          raise TypeError,"inverse: Unknown argument type."
3303    
3304    def escript_inverse(arg): # this should be escript._inverse and use LAPACK
3305          "arg is a Data objects!!!"
3306          if not arg.getRank()==2:
3307            raise ValueError,"escript_inverse: argument must have rank 2"
3308          s=arg.getShape()      
3309          if not s[0] == s[1]:
3310            raise ValueError,"escript_inverse: argument must be a square matrix."
3311          out=escript.Data(0.,s,arg.getFunctionSpace())
3312          if s[0]==1:
3313              if inf(abs(arg[0,0]))==0: # in c this should be done point wise as abs(arg[0,0](i))<=0.
3314                  raise ZeroDivisionError,"escript_inverse: argument not invertible"
3315              out[0,0]=1./arg[0,0]
3316          elif s[0]==2:
3317              A11=arg[0,0]
3318              A12=arg[0,1]
3319              A21=arg[1,0]
3320              A22=arg[1,1]
3321              D = A11*A22-A12*A21
3322              if inf(abs(D))==0: # in c this should be done point wise as abs(D(i))<=0.
3323                  raise ZeroDivisionError,"escript_inverse: argument not invertible"
3324              D=1./D
3325              out[0,0]= A22*D
3326              out[1,0]=-A21*D
3327              out[0,1]=-A12*D
3328              out[1,1]= A11*D
3329          elif s[0]==3:
3330              A11=arg[0,0]
3331              A21=arg[1,0]
3332              A31=arg[2,0]
3333              A12=arg[0,1]
3334              A22=arg[1,1]
3335              A32=arg[2,1]
3336              A13=arg[0,2]
3337              A23=arg[1,2]
3338              A33=arg[2,2]
3339              D  =  A11*(A22*A33-A23*A32)+ A12*(A31*A23-A21*A33)+A13*(A21*A32-A31*A22)
3340              if inf(abs(D))==0: # in c this should be done point wise as abs(D(i))<=0.
3341                  raise ZeroDivisionError,"escript_inverse: argument not invertible"
3342              D=1./D
3343              out[0,0]=(A22*A33-A23*A32)*D
3344              out[1,0]=(A31*A23-A21*A33)*D
3345              out[2,0]=(A21*A32-A31*A22)*D
3346              out[0,1]=(A13*A32-A12*A33)*D
3347              out[1,1]=(A11*A33-A31*A13)*D
3348              out[2,1]=(A12*A31-A11*A32)*D
3349              out[0,2]=(A12*A23-A13*A22)*D
3350              out[1,2]=(A13*A21-A11*A23)*D
3351              out[2,2]=(A11*A22-A12*A21)*D
3352          else:
3353             raise TypeError,"escript_inverse: only matrix dimensions 1,2,3 are supported right now."
3354          return out
3355    
3356    class Inverse_Symbol(DependendSymbol):
3357       """
3358       L{Symbol} representing the result of the inverse function
3359       """
3360       def __init__(self,arg):
3361          """
3362          initialization of inverse L{Symbol} with argument arg
3363          @param arg: argument of function
3364          @type arg: L{Symbol}.
3365          """
3366          if not arg.getRank()==2:
3367            raise ValueError,"Inverse_Symbol:: argument must have rank 2"
3368          s=arg.getShape()
3369          if not s[0] == s[1]:
3370            raise ValueError,"Inverse_Symbol:: argument must be a square matrix."
3371          super(Inverse_Symbol,self).__init__(args=[arg],shape=s,dim=arg.getDim())
3372    
3373       def getMyCode(self,argstrs,format="escript"):
3374          """
3375          returns a program code that can be used to evaluate the symbol.
3376    
3377          @param argstrs: gives for each argument a string representing the argument for the evaluation.
3378          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
3379          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
3380          @type format: C{str}
3381          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3382          @rtype: C{str}
3383          @raise: NotImplementedError: if the requested format is not available
3384          """
3385          if format=="escript" or format=="str"  or format=="text":
3386             return "inverse(%s)"%argstrs[0]
3387          else:
3388             raise NotImplementedError,"Inverse_Symbol does not provide program code for format %s."%format
3389    
3390       def substitute(self,argvals):
3391          """
3392          assigns new values to symbols in the definition of the symbol.
3393          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
3394    
3395          @param argvals: new values assigned to symbols
3396          @type argvals: C{dict} with keywords of type L{Symbol}.
3397          @return: result of the substitution process. Operations are executed as much as possible.
3398          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
3399          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
3400          """
3401          if argvals.has_key(self):
3402             arg=argvals[self]
3403             if self.isAppropriateValue(arg):
3404                return arg
3405             else:
3406                raise TypeError,"%s: new value is not appropriate."%str(self)
3407          else:
3408             arg=self.getSubstitutedArguments(argvals)
3409             return inverse(arg[0])
3410    
3411       def diff(self,arg):
3412          """
3413          differential of this object
3414    
3415          @param arg: the derivative is calculated with respect to arg
3416          @type arg: L{escript.Symbol}
3417          @return: derivative with respect to C{arg}
3418          @rtype: typically L{Symbol} but other types such as C{float}, L{escript.Data}, L{numarray.NumArray}  are possible.
3419          """
3420          if arg==self:
3421             return identity(self.getShape())
3422          else:
3423             return -matrixmult(matrixmult(self,self.getDifferentiatedArguments(arg)[0]),self)
3424    
3425    def eigenvalues(arg):
3426        """
3427        returns the eigenvalues of the square matrix arg.
3428    
3429        @param arg: square matrix. Must have rank 2 and the first and second dimension must be equal.
3430                    arg must be symmetric, ie. transpose(arg)==arg (this is not checked).
3431        @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol},L {float} or L{int}
3432        @return: the list of the eigenvalues in increasing order.
3433        @rtype: C{list} of L{float}, L{escript.Data}, L{Symbol} depending on the input.
3434        @remark: for L{escript.Data} and L{Symbol} objects the dimension is restricted to 3.
3435        """
3436        if isinstance(arg,numarray.NumArray):
3437          if not arg.rank==2:
3438            raise ValueError,"eigenvalues: argument must have rank 2"
3439          s=arg.shape      
3440          if not s[0] == s[1]:
3441            raise ValueError,"eigenvalues: argument must be a square matrix."
3442          out=numarray.linear_algebra.eigenvalues((arg+numarray.transpose(arg))/2.)
3443          out.sort()
3444          return numarray.array2list(out)
3445        elif isinstance(arg,escript.Data) or isinstance(arg,Symbol):
3446          if not arg.getRank()==2:
3447            raise ValueError,"eigenvalues: argument must have rank 2"
3448          s=arg.getShape()      
3449          if not s[0] == s[1]:
3450            raise ValueError,"eigenvalues: argument must be a square matrix."
3451          if s[0]==1:
3452              return [arg[0,0]]
3453          elif s[0]==2:
3454              A11=arg[0,0]
3455              A12=arg[0,1]
3456              A22=arg[1,1]
3457              trA=(A11+A22)/2.
3458              A11-=trA
3459              A22-=trA
3460              s=sqrt(A12**2-A11*A22)
3461              return [trA-s,trA+s]
3462          elif s[0]==3:
3463              A11=arg[0,0]
3464              A12=arg[0,1]
3465              A22=arg[1,1]
3466              A13=arg[0,2]
3467              A23=arg[1,2]
3468              A33=arg[2,2]
3469              trA=(A11+A22+A22)/3.
3470              A11-=trA
3471              A22-=trA
3472              A33-=trA
3473              A13_2=A13**2
3474              A23_2=A23**2
3475              A12_2=A12**2
3476              p=A13_2+A_23_2+A12_2+(A11**2+A22**2+A33**2)/2.
3477              q=A13_2*A22+A_23_2*A11+A12_2*A33-A11*A22*A33-2*A12*A23*A13
3478              sq_p=sqrt(p/3.)
3479              alpha_3=acos(-q/sq_p**(1./3.)/2.)/3.
3480              sq_p*=2.
3481              return [trA+sq_p*cos(alpha_3),trA-sq_p*cos(alpha_3+numarray.pi/3.),trA-sq_p*cos(alpha_3-numarray.pi/3.)]
3482          else:
3483             raise TypeError,"eigenvalues: only matrix dimensions 1,2,3 are supported right now."
3484        elif isinstance(arg,float):
3485          return [arg]
3486        elif isinstance(arg,int):
3487          return [float(arg)]
3488        else:
3489          raise TypeError,"eigenvalues: Unknown argument type."
3490  #=======================================================  #=======================================================
3491  #  Binary operations:  #  Binary operations:
3492  #=======================================================  #=======================================================
# Line 3305  def maximum(*args): Line 3914  def maximum(*args):
3914         if out==None:         if out==None:
3915            out=a            out=a
3916         else:         else:
3917            m=whereNegative(out-a)            diff=add(a,-out)
3918            out=m*a+(1.-m)*out            out=add(out,mult(wherePositive(diff),diff))
3919      return out      return out
3920        
3921  def minimum(*arg):  def minimum(*args):
3922      """      """
3923      the minimum over arguments args      the minimum over arguments args
3924    
# Line 3323  def minimum(*arg): Line 3932  def minimum(*arg):
3932         if out==None:         if out==None:
3933            out=a            out=a
3934         else:         else:
3935            m=whereNegative(out-a)            diff=add(a,-out)
3936            out=m*out+(1.-m)*a            out=add(out,mult(whereNegative(diff),diff))
3937      return out      return out
3938    
3939  def clip(arg,minval=0.,maxval=1.):  def clip(arg,minval=0.,maxval=1.):
# Line 3335  def clip(arg,minval=0.,maxval=1.): Line 3944  def clip(arg,minval=0.,maxval=1.):
3944      @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float}      @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float}
3945      @param minval: lower range      @param minval: lower range
3946      @type arg: C{float}      @type arg: C{float}
3947      @param maxval: uper range      @param maxval: upper range
3948      @type arg: C{float}      @type arg: C{float}
3949      @return: is on object with all its value between minval and maxval. value of the argument that greater then minval and      @return: is on object with all its value between minval and maxval. value of the argument that greater then minval and
3950               less then maxval are unchanged.               less then maxval are unchanged.
3951      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float} depending on the input      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float} depending on the input
3952        @raise ValueError: if minval>maxval
3953      """      """
3954      if minval>maxval:      if minval>maxval:
3955         raise ValueError,"minval = %s must be less then maxval %s"%(minval,maxval)         raise ValueError,"minval = %s must be less then maxval %s"%(minval,maxval)
# Line 3368  def inner(arg0,arg1): Line 3978  def inner(arg0,arg1):
3978      sh1=pokeShape(arg1)      sh1=pokeShape(arg1)
3979      if not sh0==sh1:      if not sh0==sh1:
3980          raise ValueError,"inner: shape of arguments does not match"          raise ValueError,"inner: shape of arguments does not match"
3981      return generalTensorProduct(arg0,arg1,offset=len(sh0))      return generalTensorProduct(arg0,arg1,axis_offset=len(sh0))
3982    
3983  def matrixmult(arg0,arg1):  def matrixmult(arg0,arg1):
3984      """      """
# Line 3396  def matrixmult(arg0,arg1): Line 4006  def matrixmult(arg0,arg1):
4006          raise ValueError,"first argument must have rank 2"          raise ValueError,"first argument must have rank 2"
4007      if not len(sh1)==2 and not len(sh1)==1:      if not len(sh1)==2 and not len(sh1)==1:
4008          raise ValueError,"second argument must have rank 1 or 2"          raise ValueError,"second argument must have rank 1 or 2"
4009      return generalTensorProduct(arg0,arg1,offset=1)      return generalTensorProduct(arg0,arg1,axis_offset=1)
4010    
4011  def outer(arg0,arg1):  def outer(arg0,arg1):
4012      """      """
# Line 3414  def outer(arg0,arg1): Line 4024  def outer(arg0,arg1):
4024      @return: the outer product of arg0 and arg1 at each data point      @return: the outer product of arg0 and arg1 at each data point
4025      @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
4026      """      """
4027      return generalTensorProduct(arg0,arg1,offset=0)      return generalTensorProduct(arg0,arg1,axis_offset=0)
4028    
4029    
4030  def tensormult(arg0,arg1):  def tensormult(arg0,arg1):
# Line 3456  def tensormult(arg0,arg1): Line 4066  def tensormult(arg0,arg1):
4066      sh0=pokeShape(arg0)      sh0=pokeShape(arg0)
4067      sh1=pokeShape(arg1)      sh1=pokeShape(arg1)
4068      if len(sh0)==2 and ( len(sh1)==2 or len(sh1)==1 ):      if len(sh0)==2 and ( len(sh1)==2 or len(sh1)==1 ):
4069         return generalTensorProduct(arg0,arg1,offset=1)         return generalTensorProduct(arg0,arg1,axis_offset=1)
4070      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):
4071         return generalTensorProduct(arg0,arg1,offset=2)         return generalTensorProduct(arg0,arg1,axis_offset=2)
4072      else:      else:
4073          raise ValueError,"tensormult: first argument must have rank 2 or 4"          raise ValueError,"tensormult: first argument must have rank 2 or 4"
4074    
4075  def generalTensorProduct(arg0,arg1,offset=0):  def generalTensorProduct(arg0,arg1,axis_offset=0):
4076      """      """
4077      generalized tensor product      generalized tensor product
4078    
4079      out[s,t]=S{Sigma}_r arg0[s,r]*arg1[r,t]      out[s,t]=S{Sigma}_r arg0[s,r]*arg1[r,t]
4080    
4081      where s runs through arg0.Shape[:arg0.Rank-offset]      where s runs through arg0.Shape[:arg0.Rank-axis_offset]
4082            r runs trough arg0.Shape[:offset]            r runs trough arg0.Shape[:axis_offset]
4083            t runs through arg1.Shape[offset:]            t runs through arg1.Shape[axis_offset:]
4084    
4085      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  
4086      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 3487  def generalTensorProduct(arg0,arg1,offse Line 4097  def generalTensorProduct(arg0,arg1,offse
4097      # 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
4098      if isinstance(arg0,numarray.NumArray):      if isinstance(arg0,numarray.NumArray):
4099         if isinstance(arg1,Symbol):         if isinstance(arg1,Symbol):
4100             return GeneralTensorProduct_Symbol(arg0,arg1,offset)             return GeneralTensorProduct_Symbol(arg0,arg1,axis_offset)
4101         else:         else:
4102             if not arg0.shape[arg0.rank-offset:]==arg1.shape[:offset]:             if not arg0.shape[arg0.rank-axis_offset:]==arg1.shape[:axis_offset]:
4103                 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)
4104             arg0_c=arg0.copy()             arg0_c=arg0.copy()
4105             arg1_c=arg1.copy()             arg1_c=arg1.copy()
4106             sh0,sh1=arg0.shape,arg1.shape             sh0,sh1=arg0.shape,arg1.shape
4107             d0,d1,d01=1,1,1             d0,d1,d01=1,1,1
4108             for i in sh0[:arg0.rank-offset]: d0*=i             for i in sh0[:arg0.rank-axis_offset]: d0*=i
4109             for i in sh1[offset:]: d1*=i             for i in sh1[axis_offset:]: d1*=i
4110             for i in sh1[:offset]: d01*=i             for i in sh1[:axis_offset]: d01*=i
4111             arg0_c.resize((d0,d01))             arg0_c.resize((d0,d01))
4112             arg1_c.resize((d01,d1))             arg1_c.resize((d01,d1))
4113             out=numarray.zeros((d0,d1),numarray.Float)             out=numarray.zeros((d0,d1),numarray.Float)
4114             for i0 in range(d0):             for i0 in range(d0):
4115                      for i1 in range(d1):                      for i1 in range(d1):
4116                           out[i0,i1]=numarray.sum(arg0_c[i0,:]*arg1_c[:,i1])                           out[i0,i1]=numarray.sum(arg0_c[i0,:]*arg1_c[:,i1])
4117             out.resize(sh0[:arg0.rank-offset]+sh1[offset:])             out.resize(sh0[:arg0.rank-axis_offset]+sh1[axis_offset:])
4118             return out             return out
4119      elif isinstance(arg0,escript.Data):      elif isinstance(arg0,escript.Data):
4120         if isinstance(arg1,Symbol):         if isinstance(arg1,Symbol):
4121             return GeneralTensorProduct_Symbol(arg0,arg1,offset)             return GeneralTensorProduct_Symbol(arg0,arg1,axis_offset)
4122         else:         else:
4123             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)
4124      else:            else:      
4125         return GeneralTensorProduct_Symbol(arg0,arg1,offset)         return GeneralTensorProduct_Symbol(arg0,arg1,axis_offset)
4126                                    
4127  class GeneralTensorProduct_Symbol(DependendSymbol):  class GeneralTensorProduct_Symbol(DependendSymbol):
4128     """     """
4129     Symbol representing the quotient of two arguments.     Symbol representing the quotient of two arguments.
4130     """     """
4131     def __init__(self,arg0,arg1,offset=0):     def __init__(self,arg0,arg1,axis_offset=0):
4132         """         """
4133         initialization of L{Symbol} representing the quotient of two arguments         initialization of L{Symbol} representing the quotient of two arguments
4134    
# Line 3531  class GeneralTensorProduct_Symbol(Depend Line 4141  class GeneralTensorProduct_Symbol(Depend
4141         """         """
4142         sh_arg0=pokeShape(arg0)         sh_arg0=pokeShape(arg0)
4143         sh_arg1=pokeShape(arg1)         sh_arg1=pokeShape(arg1)
4144         sh0=sh_arg0[:len(sh_arg0)-offset]         sh0=sh_arg0[:len(sh_arg0)-axis_offset]
4145         sh01=sh_arg0[len(sh_arg0)-offset:]         sh01=sh_arg0[len(sh_arg0)-axis_offset:]
4146         sh10=sh_arg1[:offset]         sh10=sh_arg1[:axis_offset]
4147         sh1=sh_arg1[offset:]         sh1=sh_arg1[axis_offset:]
4148         if not sh01==sh10:         if not sh01==sh10:
4149             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)
4150         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])
4151    
4152     def getMyCode(self,argstrs,format="escript"):     def getMyCode(self,argstrs,format="escript"):
4153        """        """
# Line 3552  class GeneralTensorProduct_Symbol(Depend Line 4162  class GeneralTensorProduct_Symbol(Depend
4162        @raise: NotImplementedError: if the requested format is not available        @raise: NotImplementedError: if the requested format is not available
4163        """        """
4164        if format=="escript" or format=="str" or format=="text":        if format=="escript" or format=="str" or format=="text":
4165           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])
4166        else:        else:
4167           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)
4168    
# Line 3577  class GeneralTensorProduct_Symbol(Depend Line 4187  class GeneralTensorProduct_Symbol(Depend
4187           args=self.getSubstitutedArguments(argvals)           args=self.getSubstitutedArguments(argvals)
4188           return generalTensorProduct(args[0],args[1],args[2])           return generalTensorProduct(args[0],args[1],args[2])
4189    
4190  def escript_generalTensorProduct(arg0,arg1,offset): # this should be escript._generalTensorProduct  def escript_generalTensorProduct(arg0,arg1,axis_offset): # this should be escript._generalTensorProduct
4191      "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!!!"
4192      # calculate the return shape:      # calculate the return shape:
4193      shape0=arg0.getShape()[:arg0.getRank()-offset]      shape0=arg0.getShape()[:arg0.getRank()-axis_offset]
4194      shape01=arg0.getShape()[arg0.getRank()-offset:]      shape01=arg0.getShape()[arg0.getRank()-axis_offset:]
4195      shape10=arg1.getShape()[:offset]      shape10=arg1.getShape()[:axis_offset]
4196      shape1=arg1.getShape()[offset:]      shape1=arg1.getShape()[axis_offset:]
4197      if not shape01==shape10:      if not shape01==shape10:
4198          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)
4199    
4200        # whatr function space should be used? (this here is not good!)
4201        fs=(escript.Scalar(0.,arg0.getFunctionSpace())+escript.Scalar(0.,arg1.getFunctionSpace())).getFunctionSpace()
4202      # create return value:      # create return value:
4203      out=escript.Data(0.,tuple(shape0+shape1),arg0.getFunctionSpace())      out=escript.Data(0.,tuple(shape0+shape1),fs)
4204      #      #
4205      s0=[[]]      s0=[[]]
4206      for k in shape0:      for k in shape0:
# Line 3611  def escript_generalTensorProduct(arg0,ar Line 4223  def escript_generalTensorProduct(arg0,ar
4223    
4224      for i0 in s0:      for i0 in s0:
4225         for i1 in s1:         for i1 in s1:
4226           s=escript.Scalar(0.,arg0.getFunctionSpace())           s=escript.Scalar(0.,fs)
4227           for i01 in s01:           for i01 in s01:
4228              s+=arg0.__getitem__(tuple(i0+i01))*arg1.__getitem__(tuple(i01+i1))              s+=arg0.__getitem__(tuple(i0+i01))*arg1.__getitem__(tuple(i01+i1))
4229           out.__setitem__(tuple(i0+i1),s)           out.__setitem__(tuple(i0+i1),s)
4230      return out      return out
4231    
4232    
4233  #=========================================================  #=========================================================
4234  #   some little helpers  #  functions dealing with spatial dependency
4235  #=========================================================  #=========================================================
4236  def grad(arg,where=None):  def grad(arg,where=None):
4237      """      """
4238      Returns the spatial gradient of arg at where.      Returns the spatial gradient of arg at where.
4239    
4240        If C{g} is the returned object, then
4241    
4242      @param arg:   Data object representing the function which gradient        - if C{arg} is rank 0 C{g[s]} is the derivative of C{arg} with respect to the C{s}-th spatial dimension.
4243                    to be calculated.        - 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.
4244          - 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.
4245          - 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.
4246    
4247        @param arg: function which gradient to be calculated. Its rank has to be less than 3.
4248        @type arg: L{escript.Data} or L{Symbol}
4249      @param where: FunctionSpace in which the gradient will be calculated.      @param where: FunctionSpace in which the gradient will be calculated.
4250                    If not present or C{None} an appropriate default is used.                    If not present or C{None} an appropriate default is used.
4251        @type where: C{None} or L{escript.FunctionSpace}
4252        @return: gradient of arg.
4253        @rtype:  L{escript.Data} or L{Symbol}
4254      """      """
4255      if isinstance(arg,Symbol):      if isinstance(arg,Symbol):
4256         return Grad_Symbol(arg,where)         return Grad_Symbol(arg,where)
# Line 3637  def grad(arg,where=None): Line 4260  def grad(arg,where=None):
4260         else:         else:
4261            return arg._grad(where)            return arg._grad(where)
4262      else:      else:
4263        raise TypeError,"grad: Unknown argument type."         raise TypeError,"grad: Unknown argument type."
4264    
4265    class Grad_Symbol(DependendSymbol):
4266       """
4267       L{Symbol} representing the result of the gradient operator
4268       """
4269       def __init__(self,arg,where=None):
4270          """
4271          initialization of gradient L{Symbol} with argument arg
4272          @param arg: argument of function
4273          @type arg: L{Symbol}.
4274          @param where: FunctionSpace in which the gradient will be calculated.
4275                      If not present or C{None} an appropriate default is used.
4276          @type where: C{None} or L{escript.FunctionSpace}
4277          """
4278          d=arg.getDim()
4279          if d==None:
4280             raise ValueError,"argument must have a spatial dimension"
4281          super(Grad_Symbol,self).__init__(args=[arg,where],shape=arg.getShape()+(d,),dim=d)
4282    
4283       def getMyCode(self,argstrs,format="escript"):
4284          """
4285          returns a program code that can be used to evaluate the symbol.
4286    
4287          @param argstrs: gives for each argument a string representing the argument for the evaluation.
4288          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
4289          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
4290          @type format: C{str}
4291          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4292          @rtype: C{str}
4293          @raise: NotImplementedError: if the requested format is not available
4294          """
4295          if format=="escript" or format=="str"  or format=="text":
4296             return "grad(%s,where=%s)"%(argstrs[0],argstrs[1])
4297          else:
4298             raise NotImplementedError,"Trace_Symbol does not provide program code for format %s."%format
4299    
4300       def substitute(self,argvals):
4301          """
4302          assigns new values to symbols in the definition of the symbol.
4303          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
4304    
4305          @param argvals: new values assigned to symbols
4306          @type argvals: C{dict} with keywords of type L{Symbol}.
4307          @return: result of the substitution process. Operations are executed as much as possible.
4308          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
4309          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
4310          """
4311          if argvals.has_key(self):
4312             arg=argvals[self]
4313             if self.isAppropriateValue(arg):
4314                return arg
4315             else:
4316                raise TypeError,"%s: new value is not appropriate."%str(self)
4317          else:
4318             arg=self.getSubstitutedArguments(argvals)
4319             return grad(arg[0],where=arg[1])
4320    
4321       def diff(self,arg):
4322          """
4323          differential of this object
4324    
4325          @param arg: the derivative is calculated with respect to arg
4326          @type arg: L{escript.Symbol}
4327          @return: derivative with respect to C{arg}
4328          @rtype: typically L{Symbol} but other types such as C{float}, L{escript.Data}, L{numarray.NumArray}  are possible.
4329          """
4330          if arg==self:
4331             return identity(self.getShape())
4332          else:
4333             return grad(self.getDifferentiatedArguments(arg)[0],where=self.getArgument()[1])
4334    
4335  def integrate(arg,where=None):  def integrate(arg,where=None):
4336      """      """
4337      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}
4338      its domain.      before integration.
4339    
4340      @param arg:   Data object representing the function which is integrated.      @param arg:   the function which is integrated.
4341        @type arg: L{escript.Data} or L{Symbol}
4342      @param where: FunctionSpace in which the integral is calculated.      @param where: FunctionSpace in which the integral is calculated.
4343                    If not present or C{None} an appropriate default is used.                    If not present or C{None} an appropriate default is used.
4344        @type where: C{None} or L{escript.FunctionSpace}
4345        @return: integral of arg.
4346        @rtype:  C{float}, C{numarray.NumArray} or L{Symbol}
4347      """      """
4348      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):  
4349         return Integrate_Symbol(arg,where)         return Integrate_Symbol(arg,where)
4350      elif isinstance(arg,escript.Data):      elif isinstance(arg,escript.Data):
4351         if not where==None: arg=escript.Data(arg,where)         if not where==None: arg=escript.Data(arg,where)
# Line 3674  def integrate(arg,where=None): Line 4356  def integrate(arg,where=None):
4356      else:      else:
4357        raise TypeError,"integrate: Unknown argument type."        raise TypeError,"integrate: Unknown argument type."
4358    
4359    class Integrate_Symbol(DependendSymbol):
4360       """
4361       L{Symbol} representing the result of the spatial integration operator
4362       """
4363       def __init__(self,arg,where=None):
4364          """
4365          initialization of integration L{Symbol} with argument arg
4366          @param arg: argument of the integration
4367          @type arg: L{Symbol}.
4368          @param where: FunctionSpace in which the integration will be calculated.
4369                      If not present or C{None} an appropriate default is used.
4370          @type where: C{None} or L{escript.FunctionSpace}
4371          """
4372          super(Integrate_Symbol,self).__init__(args=[arg,where],shape=arg.getShape(),dim=arg.getDim())
4373    
4374       def getMyCode(self,argstrs,format="escript"):
4375          """
4376          returns a program code that can be used to evaluate the symbol.
4377    
4378          @param argstrs: gives for each argument a string representing the argument for the evaluation.
4379          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
4380          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
4381          @type format: C{str}
4382          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4383          @rtype: C{str}
4384          @raise: NotImplementedError: if the requested format is not available
4385          """
4386          if format=="escript" or format=="str"  or format=="text":
4387             return "integrate(%s,where=%s)"%(argstrs[0],argstrs[1])
4388          else:
4389             raise NotImplementedError,"Trace_Symbol does not provide program code for format %s."%format
4390    
4391       def substitute(self,argvals):
4392          """
4393          assigns new values to symbols in the definition of the symbol.
4394          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
4395    
4396          @param argvals: new values assigned to symbols
4397          @type argvals: C{dict} with keywords of type L{Symbol}.
4398          @return: result of the substitution process. Operations are executed as much as possible.
4399          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
4400          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
4401          """
4402          if argvals.has_key(self):
4403             arg=argvals[self]
4404             if self.isAppropriateValue(arg):
4405                return arg
4406             else:
4407                raise TypeError,"%s: new value is not appropriate."%str(self)
4408          else:
4409             arg=self.getSubstitutedArguments(argvals)
4410             return integrate(arg[0],where=arg[1])
4411    
4412       def diff(self,arg):
4413          """
4414          differential of this object
4415    
4416          @param arg: the derivative is calculated with respect to arg
4417          @type arg: L{escript.Symbol}
4418          @return: derivative with respect to C{arg}
4419          @rtype: typically L{Symbol} but other types such as C{float}, L{escript.Data}, L{numarray.NumArray}  are possible.
4420          """
4421          if arg==self:
4422             return identity(self.getShape())
4423          else:
4424             return integrate(self.getDifferentiatedArguments(arg)[0],where=self.getArgument()[1])
4425    
4426    
4427  def interpolate(arg,where):  def interpolate(arg,where):
4428      """      """
4429      Interpolates the function into the FunctionSpace where.      interpolates the function into the FunctionSpace where.
4430    
4431      @param arg:    interpolant      @param arg: interpolant
4432      @param where:  FunctionSpace to interpolate to      @type arg: L{escript.Data} or L{Symbol}
4433        @param where: FunctionSpace to be interpolated to
4434        @type where: L{escript.FunctionSpace}
4435        @return: interpolated argument
4436        @rtype:  C{escript.Data} or L{Symbol}
4437      """      """
4438      if isinstance(arg,Symbol):      if isinstance(arg,Symbol):
4439         return Interpolated_Symbol(arg,where)         return Interpolate_Symbol(arg,where)
4440      else:      else:
4441         return escript.Data(arg,where)         return escript.Data(arg,where)
4442    
4443  def div(arg,where=None):  class Interpolate_Symbol(DependendSymbol):
4444      """     """
4445      Returns the divergence of arg at where.     L{Symbol} representing the result of the interpolation operator
4446       """
4447       def __init__(self,arg,where):
4448          """
4449          initialization of interpolation L{Symbol} with argument arg
4450          @param arg: argument of the interpolation
4451          @type arg: L{Symbol}.
4452          @param where: FunctionSpace into which the argument is interpolated.
4453          @type where: L{escript.FunctionSpace}
4454          """
4455          super(Interpolate_Symbol,self).__init__(args=[arg,where],shape=arg.getShape(),dim=arg.getDim())
4456    
4457      @param arg:   Data object representing the function which gradient to     def getMyCode(self,argstrs,format="escript"):
4458                    be calculated.        """
4459      @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)  
4460    
4461  def jump(arg):        @param argstrs: gives for each argument a string representing the argument for the evaluation.
4462      """        @type argstrs: C{str} or a C{list} of length 1 of C{str}.
4463      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.
4464          @type format: C{str}
4465          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4466          @rtype: C{str}
4467          @raise: NotImplementedError: if the requested format is not available
4468          """
4469          if format=="escript" or format=="str"  or format=="text":
4470             return "interpolate(%s,where=%s)"%(argstrs[0],argstrs[1])
4471          else:
4472             raise NotImplementedError,"Trace_Symbol does not provide program code for format %s."%format
4473    
4474      @param arg:   Data object representing the function which gradient     def substitute(self,argvals):
4475                    to be calculated.        """
4476      """        assigns new values to symbols in the definition of the symbol.
4477      d=arg.getDomain()        The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
     return arg.interpolate(escript.FunctionOnContactOne(d))-arg.interpolate(escript.FunctionOnContactZero(d))  
4478    
4479  #=============================        @param argvals: new values assigned to symbols
4480  #        @type argvals: C{dict} with keywords of type L{Symbol}.
4481  # 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.
4482  # 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
4483  # numarray function is called.        @raise TypeError: if a value for a L{Symbol} cannot be substituted.
4484          """
4485          if argvals.has_key(self):
4486             arg=argvals[self]
4487             if self.isAppropriateValue(arg):
4488                return arg
4489             else:
4490                raise TypeError,"%s: new value is not appropriate."%str(self)
4491          else:
4492             arg=self.getSubstitutedArguments(argvals)
4493             return interpolate(arg[0],where=arg[1])
4494    
4495       def diff(self,arg):
4496          """
4497          differential of this object
4498    
4499          @param arg: the derivative is calculated with respect to arg
4500          @type arg: L{escript.Symbol}
4501          @return: derivative with respect to C{arg}
4502          @rtype: L{Symbol} but other types such as L{escript.Data}, L{numarray.NumArray}  are possible.
4503          """
4504          if arg==self:
4505             return identity(self.getShape())
4506          else:
4507             return interpolate(self.getDifferentiatedArguments(arg)[0],where=self.getArgument()[1])
4508    
 # functions involving the underlying Domain:  
4509    
4510  def transpose(arg,axis=None):  def div(arg,where=None):
4511      """      """
4512      Returns the transpose of the Data object arg.      returns the divergence of arg at where.
4513    
4514      @param arg:      @param arg: function which divergence to be calculated. Its shape has to be (d,) where d is the spatial dimension.
4515        @type arg: L{escript.Data} or L{Symbol}
4516        @param where: FunctionSpace in which the divergence will be calculated.
4517                      If not present or C{None} an appropriate default is used.
4518        @type where: C{None} or L{escript.FunctionSpace}
4519        @return: divergence of arg.
4520        @rtype:  L{escript.Data} or L{Symbol}
4521      """      """
     if axis==None:  
        r=0  
        if hasattr(arg,"getRank"): r=arg.getRank()  
        if hasattr(arg,"rank"): r=arg.rank  
        axis=r/2  
4522      if isinstance(arg,Symbol):      if isinstance(arg,Symbol):
4523         return Transpose_Symbol(arg,axis=r)          dim=arg.getDim()
4524      if isinstance(arg,escript.Data):      elif isinstance(arg,escript.Data):
4525         # 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)  
4526      else:      else:
4527         return numarray.transpose(arg,axis=axis)          raise TypeError,"div: argument type not supported"
4528        if not arg.getShape()==(dim,):
4529          raise ValueError,"div: expected shape is (%s,)"%dim
4530        return trace(grad(arg,where))
4531    
4532  def trace(arg,axis0=0,axis1=1):  def jump(arg,domain=None):
4533      """      """
4534      Return      returns the jump of arg across the continuity of the domain
4535    
4536      @param arg:      @param arg: argument
4537        @type arg: L{escript.Data} or L{Symbol}
4538        @param domain: the domain where the discontinuity is located. If domain is not present or equal to C{None}
4539                       the domain of arg is used. If arg is a L{Symbol} the domain must be present.
4540        @type domain: C{None} or L{escript.Domain}
4541        @return: jump of arg
4542        @rtype:  L{escript.Data} or L{Symbol}
4543      """      """
4544      if isinstance(arg,Symbol):      if domain==None: domain=arg.getDomain()
4545         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)  
4546    
4547    def L2(arg):
4548        """
4549        returns the L2 norm of arg at where
4550        
4551        @param arg: function which L2 to be calculated.
4552        @type arg: L{escript.Data} or L{Symbol}
4553        @return: L2 norm of arg.
4554        @rtype:  L{float} or L{Symbol}
4555        @note: L2(arg) is equivalent to sqrt(integrate(inner(arg,arg)))
4556        """
4557        return sqrt(integrate(inner(arg,arg)))
4558    #=============================
4559    #
4560    
4561  def reorderComponents(arg,index):  def reorderComponents(arg,index):
4562      """      """
4563      resorts the component of arg according to index      resorts the component of arg according to index
4564    
4565      """      """
4566      pass      raise NotImplementedError
4567  #  #
4568  # $Log: util.py,v $  # $Log: util.py,v $
4569  # 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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