/[escript]/trunk/escript/src/escriptcpp.cpp
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revision 3059 by jfenwick, Tue Jul 6 03:31:48 2010 UTC revision 3506 by jfenwick, Wed May 11 01:59:45 2011 UTC
# Line 22  Line 22 
22  #include "AbstractSystemMatrix.h"  #include "AbstractSystemMatrix.h"
23  #include "AbstractTransportProblem.h"  #include "AbstractTransportProblem.h"
24  #include "DataVector.h"  #include "DataVector.h"
25  #include "paso/Paso_MPI.h"  #include "esysUtils/Esys_MPI.h"
26  #include "EscriptParams.h"  #include "EscriptParams.h"
27  #include "TestDomain.h"  #include "TestDomain.h"
28    
# Line 52  using namespace boost::python; Line 52  using namespace boost::python;
52   *   *
53   * - \ref esys_exception "Esys Exception"   * - \ref esys_exception "Esys Exception"
54   *   *
55   * - \ref finley   * - \ref dudley
56   *   *
57   * - <a href="../../epydoc/index.html">Python module documentation (epydoc generated)</a>   * - <a href="../../epydoc/index.html">Python module documentation (epydoc generated)</a>
58   *   *
# Line 115  BOOST_PYTHON_MODULE(escriptcpp) Line 115  BOOST_PYTHON_MODULE(escriptcpp)
115  "The keys given in the dictionary will be used to name columns.\n"  "The keys given in the dictionary will be used to name columns.\n"
116  "Then the data will be output, one line per sample (for all data).\n"  "Then the data will be output, one line per sample (for all data).\n"
117  "That is, items in each column will be printed in the same order.\n"  "That is, items in each column will be printed in the same order.\n"
118  "So you can be sure that values in the same row correspond to the same input value.\n"  "So you can be sure that values in the same row correspond to the same input value.\n\n"
119  "\n:param filename:\n:type filename: ``string``\n"  "\n:param filename:\n:type filename: ``string``\n"
120  ":param arg: dictionary of named `Data` objects. If one is called ``mask`` it must be scalar data."  ":param arg: dictionary of named `Data` objects. If one is called ``mask`` it must be scalar data.\n"
121  "\n:type arg: ``dict``\n"  ":type arg: ``dict``\n"
122  ":param sep:separator for columns (defaults to \", \"\n:type sep:``string``\n"  ":param sep: separator for columns (defaults to ',')\n"
123  ":param csep:separator for fields within data object (defaults to \"_\"\n:type csep:``string``\n"  ":type sep: ``string``\n"
124    ":param csep: separator for fields within data object (defaults to \"_\")\n:type csep: ``string``\n"
125  ":param append: If True, write to the end of ``filename``\n:type append: ``string``\n");  ":param append: If True, write to the end of ``filename``\n:type append: ``string``\n");
126    
127    
# Line 155  BOOST_PYTHON_MODULE(escriptcpp) Line 156  BOOST_PYTHON_MODULE(escriptcpp)
156       .def("getMPIRank",&escript::AbstractDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")       .def("getMPIRank",&escript::AbstractDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
157       .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier,"Wait until all processes have reached this point")       .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier,"Wait until all processes have reached this point")
158       .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")       .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")
159         .def("supportsContactElements", &escript::AbstractDomain::supportsContactElements,"Does this domain support contact elements.")
160       .def(self == self)       .def(self == self)
161       .def(self != self);       .def(self != self);
162    
# Line 169  args("solver", "preconditioner", "packag Line 170  args("solver", "preconditioner", "packag
170  "when a particular solver package and symmetric matrix is used.\n"  "when a particular solver package and symmetric matrix is used.\n"
171  ":rtype: int")  ":rtype: int")
172         .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId,         .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId,
173  args("solver", "preconditioner", "package", "symmetry"));  args("solver", "preconditioner", "package", "symmetry"))
174    
175          .def("addPDEToSystem",&escript::AbstractContinuousDomain::addPDEToSystem,
176    args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
177    "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
178    ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
179    ":param A:\n:type A: `Data`\n"
180    ":param B:\n:type B: `Data`\n"
181    ":param C:\n:type C: `Data`\n"
182    ":param D:\n:type D: `Data`\n"
183    ":param X:\n:type X: `Data`\n"
184    ":param Y:\n:type Y: `Data`\n"
185    ":param d:\n:type d: `Data`\n"
186    ":param d_contact:\n:type d_contact: `Data`\n"
187    ":param y_contact:\n:type y_contact: `Data`\n"
188    )
189          .def("addPDEToRHS",&escript::AbstractContinuousDomain::addPDEToRHS,
190    args("rhs", "X", "Y", "y", "y_contact"),
191    "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
192    ":param rhs:\n:type rhs: `Data`\n"
193    ":param X:\n:type X: `Data`\n"
194    ":param Y:\n:type Y: `Data`\n"
195    ":param y:\n:type y: `Data`\n"
196    ":param y_contact:\n:type y_contact: `Data`"
197    )
198          .def("addPDEToTransportProblem",&escript::AbstractContinuousDomain::addPDEToTransportProblem,
199    args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
200    ":param tp:\n:type tp: `TransportProblemAdapter`\n"
201    ":param source:\n:type source: `Data`\n"
202    ":param M:\n:type M: `Data`\n"
203    ":param A:\n:type A: `Data`\n"
204    ":param B:\n:type B: `Data`\n"
205    ":param C:\n:type C: `Data`\n"
206    ":param D:\n:type D: `Data`\n"
207    ":param X:\n:type X: `Data`\n"
208    ":param Y:\n:type Y: `Data`\n"
209    ":param d:\n:type d: `Data`\n"
210    ":param y:\n:type y: `Data`\n"
211    ":param d_contact:\n:type d_contact: `Data`\n"
212    ":param y_contact:\n:type y_contact: `Data`\n"
213    )
214          .def("newOperator",&escript::AbstractContinuousDomain::newSystemMatrix,
215    args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
216    "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
217    ":param row_blocksize:\n:type row_blocksize: ``int``\n"
218    ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
219    ":param column_blocksize:\n:type column_blocksize: ``int``\n"
220    ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
221    ":param type:\n:type type: ``int``\n"
222    )
223          .def("newTransportProblem",&escript::AbstractContinuousDomain::newTransportProblem,
224    args("theta", "blocksize", "functionspace", "type"),
225    "creates a TransportProblemAdapter\n\n"
226    ":param theta:\n:type theta: ``float``\n"
227    ":param blocksize:\n:type blocksize: ``int``\n"
228    ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
229    ":param type:\n:type type: ``int``\n"
230    )
231          .def("getDataShape",&escript::AbstractContinuousDomain::getDataShape, args("functionSpaceCode"),
232    ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
233          .def("print_mesh_info",&escript::AbstractContinuousDomain::Print_Mesh_Info,(arg("full")=false),
234    ":param full:\n:type full: ``bool``")
235          .def("getDescription",&escript::AbstractContinuousDomain::getDescription,
236    ":return: a description for this domain\n:rtype: ``string``")
237          .def("setX",&escript::AbstractContinuousDomain::setNewX,
238    args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
239          .def("getNumDataPointsGlobal",&escript::AbstractContinuousDomain::getNumDataPointsGlobal,
240    ":return: the number of data points summed across all MPI processes\n"
241    ":rtype: ``int``");
242    
243    
244    
245    
246    //    //
# Line 194  args("solver", "preconditioner", "packag Line 265  args("solver", "preconditioner", "packag
265    fs_definer.def("getNormal",&escript::FunctionSpace::getNormal,":return: the surface normal field.\n\n:rtype: `Data`");    fs_definer.def("getNormal",&escript::FunctionSpace::getNormal,":return: the surface normal field.\n\n:rtype: `Data`");
266    fs_definer.def("getSize",&escript::FunctionSpace::getSize,":return: sample size\n:rtype: `Data`");    fs_definer.def("getSize",&escript::FunctionSpace::getSize,":return: sample size\n:rtype: `Data`");
267    fs_definer.def("setTags",&escript::FunctionSpace::setTags,args("newtag","mask"),    fs_definer.def("setTags",&escript::FunctionSpace::setTags,args("newtag","mask"),
268  "Set tags according to a mask\n\n:param newtag: tag number to set\n:type newtag: non-zero ``int``\n:param mask: Samples which correspond to positive values in the mask will be set to ``newtag``.\n:type mask: scalar `Data`");  "Set tags according to a mask\n\n:param newtag: tag number to set\n:type newtag: string, non-zero ``int``\n:param mask: Samples which correspond to positive values in the mask will be set to ``newtag``.\n:type mask: scalar `Data`");
269    fs_definer.def("setTags",&escript::FunctionSpace::setTagsByString,args("newtag","mask"),    fs_definer.def("setTags",&escript::FunctionSpace::setTagsByString,args("newtag","mask"));
 "Set tags according to a mask\n\n:param newtag: tag name to set\n:type newtag: string\n:param mask: Samples which correspond to positive values in the mask will be set to ``newtag``.\n:type mask: scalar `Data`");  
270    fs_definer.def("getTagFromDataPointNo",    fs_definer.def("getTagFromDataPointNo",
271                   &escript::FunctionSpace::getTagFromDataPointNo,":return: the tag associated with the given sample number.\n:rtype: int");                   &escript::FunctionSpace::getTagFromDataPointNo,":return: the tag associated with the given sample number.\n:rtype: int");
272    fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo,args("dataPointNo"),":return: the reference number associated with ``dataPointNo``\n:rtype: int ");    fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo,args("dataPointNo"),":return: the reference number associated with ``dataPointNo``\n:rtype: int ");
# Line 208  args("solver", "preconditioner", "packag Line 278  args("solver", "preconditioner", "packag
278    //    //
279    // Interface for Data    // Interface for Data
280    //    //
281    class_<escript::Data>("Data","Represents a collection of datapoints. It is used to store the values of a function. For more details please consult the c++ class documentation.",init<>() )    class_<escript::Data>("Data"/*,shared_ptr<Data>*/, "Represents a collection of datapoints. It is used to store the values of a function. For more details please consult the c++ class documentation.",init<>() )
282      // various constructors for Data objects      // various constructors for Data objects
283      .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))      .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
284      .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))      .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))
# Line 263  args("solver", "preconditioner", "packag Line 333  args("solver", "preconditioner", "packag
333  "\n:param dataPointNo: datapoint to access\n:type dataPointNo: int")  "\n:param dataPointNo: datapoint to access\n:type dataPointNo: int")
334      .def("setToZero",&escript::Data::setToZero,"After this call the object will store values of the same shape as before but all components will be zero.")      .def("setToZero",&escript::Data::setToZero,"After this call the object will store values of the same shape as before but all components will be zero.")
335      .def("interpolate",&escript::Data::interpolate,args("functionspace"),"Interpolate this object's values into a new functionspace.")      .def("interpolate",&escript::Data::interpolate,args("functionspace"),"Interpolate this object's values into a new functionspace.")
336        .def("_interpolateTable3d", &escript::Data::interpolateFromTable3DP,
337    (arg("table"),arg("Amin"),arg("Astep"), arg("B"), arg("Bmin"), arg("Bstep"), arg("C"), arg("Cmin"), arg("Cstep"), arg("undef")=1.e50, arg("check_boundaries")=false, "For internal use only. Please use the interpolateTable function.")
338    )
339    
340      .def("interpolateTable", &escript::Data::interpolateFromTable2DP,      .def("interpolateTable", &escript::Data::interpolateFromTable2DP,
341  (arg("table"),arg("Amin"),arg("Astep"), arg("B"), arg("Bmin"), arg("Bstep"), arg("undef")=1.e50, arg("check_boundaries")=false),  (arg("table"),arg("Amin"),arg("Astep"), arg("B"), arg("Bmin"), arg("Bstep"), arg("undef")=1.e50, arg("check_boundaries")=false),
342  "Creates a new Data object by interpolating using the source data (which are\n"  "Creates a new Data object by interpolating using the source data (which are\n"
# Line 280  args("solver", "preconditioner", "packag Line 354  args("solver", "preconditioner", "packag
354  "\n:rtype: `Data`"  "\n:rtype: `Data`"
355  )  )
356      .def("interpolateTable", &escript::Data::interpolateFromTable1DP,      .def("interpolateTable", &escript::Data::interpolateFromTable1DP,
357  (arg("table"),arg("Amin"),arg("Astep"), arg("undef")=1.e50, arg("check_boundaries")=false),  (arg("table"),arg("Amin"),arg("Astep"), arg("undef")=1.e50, arg("check_boundaries")=false)/*,
358  "Creates a new Data object by interpolating using the source data (which are\n"  "Creates a new Data object by interpolating using the source data (which are\n"
359  "looked up in ``table``)\n\n"  "looked up in ``table``)\n\n"
360  ":param table: one dimensional collection of values\n"  ":param table: one dimensional collection of values\n"
# Line 290  args("solver", "preconditioner", "packag Line 364  args("solver", "preconditioner", "packag
364  ":param check_boundaries: if true, then values outside the boundaries will be rejected. If false, then boundary values will be used.\n"  ":param check_boundaries: if true, then values outside the boundaries will be rejected. If false, then boundary values will be used.\n"
365  ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"  ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"
366  "\n:rtype: `Data`"  "\n:rtype: `Data`"
367    */
368  )  )
369    
370    
# Line 349  args("solver", "preconditioner", "packag Line 424  args("solver", "preconditioner", "packag
424      .def("__neg__",&escript::Data::neg, ":return: negation of the values in this object\n:rtype: `Data`")      .def("__neg__",&escript::Data::neg, ":return: negation of the values in this object\n:rtype: `Data`")
425      // following implements the python "+" identity operator      // following implements the python "+" identity operator
426      .def("__pos__",&escript::Data::pos, "\nThe unary + operator\n\n:rtype: `Data`")      .def("__pos__",&escript::Data::pos, "\nThe unary + operator\n\n:rtype: `Data`")
427      // following two functions implement the python [] operator      // following three functions implement the python [] operator
428      .def("__getitem__",&escript::Data::getItem,"Used by the python [] operator\n\n:rtype: `Data`")      .def("__getitem__",&escript::Data::getItem,"Used by the python [] operator\n\n:rtype: `Data`")
429      .def("__setitem__",&escript::Data::setItemO,"Used by the python [] operator")      .def("__setitem__",&escript::Data::setItemO,"Used by the python [] operator")
430      .def("__setitem__",&escript::Data::setItemD,"Used by the python [] operator")      .def("__setitem__",&escript::Data::setItemD,"Used by the python [] operator")
431      // following two functions implement the python ** operator      // following three functions implement the python ** operator
432      .def("__pow__",&escript::Data::powO,"Used by the python ** operator\n\n:rtype: `Data`")      .def("__pow__",&escript::Data::powO,"Used by the python ** operator\n\n:rtype: `Data`")
433      .def("__pow__",&escript::Data::powD)      .def("__pow__",&escript::Data::powD)
434      .def("__rpow__",&escript::Data::rpowO,"\nUsed by the python ** operator\n\n:rtype: `Data`")      .def("__rpow__",&escript::Data::rpowO,"\nUsed by the python ** operator\n\n:rtype: `Data`")
435        // following two functions implement the newer python / operator
436        .def("__truediv__",&escript::Data::truedivD)
437        .def("__truediv__",&escript::Data::truedivO)
438      // NOTE:: The order of these declarations is important. Anything      // NOTE:: The order of these declarations is important. Anything
439      // declared before the generic declaration isn't found so the generic      // declared before the generic declaration isn't found so the generic
440      // version will be called.      // version will be called.
441      .def(self + other<object>())  //    .def(self + other<object>())
442      .def(other<object>() + self)  //    .def(other<object>() + self)
443      .def(self + self)  //    .def(self + self)
444      .def(self += other<object>())      .def(self += other<object>())
445      .def(self += self)      .def(self += self)
446    
447      .def(self - other<object>())  //     .def(self - other<object>())
448      .def(other<object>() - self)  //     .def(other<object>() - self)
449      .def(self - self)  //     .def(self - self)
450      .def(self -= other<object>())      .def(self -= other<object>())
451      .def(self -= self)      .def(self -= self)
452    
453      .def(self * other<object>())  //     .def(self * other<object>())
454      .def(other<object>() * self)  //     .def(other<object>() * self)
455      .def(self * self)  //     .def(self * self)
456      .def(self *= other<object>())      .def(self *= other<object>())
457      .def(self *= self)      .def(self *= self)
458    
459      .def(self / other<object>())  //     .def(self / other<object>())
460      .def(other<object>() / self)  //     .def(other<object>() / self)
461      .def(self / self)  //     .def(self / self)
462      .def(self /= other<object>())      .def(self /= other<object>())
463      .def(self /= self)      .def(self /= self)
464      // Need scope resolution due to a bug either in the compiler or      // Need scope resolution due to a bug either in the compiler or
465      // the boost code. This calls operator << for Data.      // the boost code. This calls operator << for Data.
466      .def(self_ns::str(self))      .def(self_ns::str(self))
467      .def("_inverse", &escript::Data::matrixInverse, ":return: inverse of square matricies\n");      .def("_inverse", &escript::Data::matrixInverse, ":return: inverse of square matricies\n")
468    //    .def("__add__", &escript::Data::addOperatorD)
469        .def("__add__", &escript::Data::__add__)
470        .def("__radd__", &escript::Data::__add__)  // its the same coz + is commutative
471        .def("__sub__", &escript::Data::__sub__)
472        .def("__rsub__", &escript::Data::__rsub__)
473        .def("__mul__", &escript::Data::__mul__)  
474        .def("__rmul__", &escript::Data::__mul__)   // commutative
475        .def("__div__", &escript::Data::__div__)  
476        .def("__rdiv__", &escript::Data::__rdiv__)   // commutative
477        
478        ;
479    
480    //    //
481    // Factory methods for function space    // Factory methods for function space
# Line 484  args("solver", "preconditioner", "packag Line 572  args("solver", "preconditioner", "packag
572      arg("what")=escript::FunctionSpace(),      arg("what")=escript::FunctionSpace(),
573      arg("expanded")=false));      arg("expanded")=false));
574    
575    
576     def("RandomData", escript::randomData, (arg("shape"), arg("fs"), arg("seed")=0),
577    "Creates a new expanded Data object containing (not very) random values.\n\n"
578    ":param shape: datapoint shape\n:type shape: tuple\n"
579    ":param fs: function space for data object.\n:type fs: `FunctionSpace`\n"
580    ":param seed: seed for random number generator.\n:type seed: long\n");
581    
582    //    //
583    // Binary operators    // Binary operators
584    //    //
# Line 500  args("solver", "preconditioner", "packag Line 595  args("solver", "preconditioner", "packag
595    //    //
596    // Interface for AbstractSystemMatrix    // Interface for AbstractSystemMatrix
597    //    //
598    class_<escript::AbstractSystemMatrix>("Operator","",init<>())    // Doco goes in the empty string param    class_<escript::AbstractSystemMatrix,escript::ASM_ptr>("Operator","",init<>())    // Doco goes in the empty string param
599       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty,":rtype: ``bool``\n"       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty,":rtype: ``bool``\n"
600  ":return: True if matrix is empty")  ":return: True if matrix is empty")
601       .def("solve",&escript::AbstractSystemMatrix::solve, args("in","options"),       .def("solve",&escript::AbstractSystemMatrix::solve, args("in","options"),
# Line 516  args("solver", "preconditioner", "packag Line 611  args("solver", "preconditioner", "packag
611    //    //
612    // Interface for AbstractTransportProblem    // Interface for AbstractTransportProblem
613    //    //
614    class_<escript::AbstractTransportProblem>("TransportProblem","",init<>())    // Doco goes in the empty string param    class_<escript::AbstractTransportProblem, escript::ATP_ptr>("TransportProblem","",init<>())    // Doco goes in the empty string param
615       .def("isEmpty",&escript::AbstractTransportProblem::isEmpty,":rtype: ``int``")       .def("isEmpty",&escript::AbstractTransportProblem::isEmpty,":rtype: ``int``")
616       .def("solve",&escript::AbstractTransportProblem::solve, args("u0","source","dt", "options"),       .def("solve",&escript::AbstractTransportProblem::solve, args("u0","source","dt", "options"),
617  "returns the solution *u* for a time step *dt>0* with initial value u0\n\n:rtype: `Data`\n"  "returns the solution *u* for a time step *dt>0* with initial value u0\n\n:rtype: `Data`\n"

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