/[escript]/trunk/dudley/src/CPPAdapter/dudleycpp.cpp
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revision 155 by jgs, Wed Nov 9 02:02:19 2005 UTC revision 2625 by jfenwick, Fri Aug 21 06:30:25 2009 UTC
# Line 1  Line 1 
 // $Id$  
 /*  
  ******************************************************************************  
  *                                                                            *  
  *       COPYRIGHT ACcESS 2004 -  All Rights Reserved                         *  
  *                                                                            *  
  * This software is the property of ACcESS.  No part of this code             *  
  * may be copied in any form or by any means without the expressed written    *  
  * consent of ACcESS.  Copying, use or modification of this software          *  
  * by any unauthorised person is illegal unless that                          *  
  * person has a software license agreement with ACcESS.                       *  
  *                                                                            *  
  ******************************************************************************  
   
 ******************************************************************************/  
1    
2    /*******************************************************
3    *
4    * Copyright (c) 2003-2009 by University of Queensland
5    * Earth Systems Science Computational Center (ESSCC)
6    * http://www.uq.edu.au/esscc
7    *
8    * Primary Business: Queensland, Australia
9    * Licensed under the Open Software License version 3.0
10    * http://www.opensource.org/licenses/osl-3.0.php
11    *
12    *******************************************************/
13    
14    
15    #ifdef PASO_MPI
16    #include <mpi.h>
17    #include "paso/Paso_MPI.h"
18    #endif
19  extern "C" {  extern "C" {
20  #include "finley/finleyC/Finley.h"  #include "../Finley.h"
21  }  }
 #include "finley/CPPAdapter/MeshAdapter.h"  
 #include "finley/CPPAdapter/MeshAdapterFactory.h"  
 #include "finley/CPPAdapter/SystemMatrixAdapter.h"  
22    
23  #include "esysUtils/EsysException.h"  #include "MeshAdapter.h"
24    #include "MeshAdapterFactory.h"
25    #include "SystemMatrixAdapter.h"
26    #include "TransportProblemAdapter.h"
27    
28    #include "FinleyAdapterException.h"
29    // #include "esysUtils/EsysException.h"
30  #include "esysUtils/esysExceptionTranslator.h"  #include "esysUtils/esysExceptionTranslator.h"
31    
32  #include "escript/Data/AbstractContinuousDomain.h"  #include "escript/AbstractContinuousDomain.h"
33    
34  #include <boost/python.hpp>  #include <boost/python.hpp>
35  #include <boost/python/module.hpp>  #include <boost/python/module.hpp>
36  #include <boost/python/def.hpp>  #include <boost/python/def.hpp>
37  #include <boost/python/detail/defaults_gen.hpp>  #include <boost/python/detail/defaults_gen.hpp>
38    #include <boost/version.hpp>
39    
40  using namespace boost::python;  using namespace boost::python;
41    
# Line 73  using namespace boost::python; Line 79  using namespace boost::python;
79    
80  BOOST_PYTHON_MODULE(finleycpp)  BOOST_PYTHON_MODULE(finleycpp)
81  {  {
82    // This feature was added in boost v1.34
83    #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
84      // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
85      docstring_options docopt(true, true, false);
86    #endif
87    
   // def("ReadMesh",finley::readMesh,readMesh_overloads());  
   // def("Brick",finley::brick,brick_overloads());  
   // def("Rectangle",finley::rectangle,rectangle_overloads());  
   // def("Interval",finley::interval,interval_overloads());  
   // def("GlueFaces",finley::glueFaces,glueFaces_overloads());  
   // def("JoinFaces",finley::joinFaces,joinFaces_overloads());  
88    //    //
89    // NOTE: The return_value_policy is necessary for functions that    // NOTE: The return_value_policy is necessary for functions that
90    // return pointers.    // return pointers.
91      //
92      register_exception_translator<finley::FinleyAdapterException>(&(esysUtils::esysExceptionTranslator));
93    
94      def("LoadMesh",finley::loadMesh,
95          (arg("fileName")="file.nc"),":rtype: `Domain`"
96    /*      ,return_value_policy<manage_new_object>());*/
97          );
98    
99    def("ReadMesh",finley::readMesh,    def("ReadMesh",finley::readMesh,
100        (arg("fileName"),arg("integrationOrder")=-1),        (arg("fileName")="file.fly",arg("integrationOrder")=-1,  arg("reducedIntegrationOrder")=-1,  arg("optimize")=true)
101        return_value_policy<manage_new_object>());  /*      ,return_value_policy<manage_new_object>());*/
102        ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
103    ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
104    ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
105    ":type integrationOrder: ``int``\n"
106    ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
107    ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
108    
109      def("ReadGmsh",finley::readGmsh,
110          (arg("fileName")="file.msh",arg("numDim"), arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)
111    //       ,return_value_policy<manage_new_object>());
112    ,"Read a gmsh mesh file\n\n"
113    ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
114    ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
115    ":type integrationOrder: ``int``\n"
116    ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
117    ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
118    
119    def ("Brick",finley::brick,    def ("Brick",finley::brick,
120        (arg("n0")=1,arg("n1")=1,arg("n2")=1,        (arg("n0")=1,arg("n1")=1,arg("n2")=1,
121        arg("order")=1,        arg("order")=1,
122        arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,        arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,
123        arg("periodic0")=false,arg("periodic1")=false,arg("periodic2")=false,        arg("periodic0")=false,arg("periodic1")=false,arg("periodic2")=false,
124        arg("integrationOrder")=-1,        arg("integrationOrder")=-1,  arg("reducedIntegrationOrder")=-1,
125        arg("useElementsOnFace")=false),        arg("useElementsOnFace")=false,
126        return_value_policy<manage_new_object>());        arg("useFullElementOrder")=false,
127          arg("optimize")=false)
128    //       ,return_value_policy<manage_new_object>());
129    ,"Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2]."
130    "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
131    ":param order: =1 or =2 gives the order of shape function\n"
132    ":param l0: length of side 0\n:param l1:\n:param l2:\n"
133    ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
134    ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
135    ":param useElementsOnFace:  whether or not to use elements on face\n"
136    ":type useElementsOnFace: ``int``"
137    ":param periodic0:  whether or not boundary conditions are periodic\n"
138    ":param periodic1:\n:param periodic2:\n"
139    ":param useFullElementOrder:\n:param optimize:\n"
140    );
141    
142    def ("Rectangle",finley::rectangle,    def ("Rectangle",finley::rectangle,
143        (arg("n0")=1,arg("n1")=1,arg("order")=1,        (arg("n0")=1,arg("n1")=1,arg("order")=1,
144        arg("l0")=1.0,arg("l1")=1.0,        arg("l0")=1.0,arg("l1")=1.0,
145        arg("periodic0")=false,arg("periodic1")=false,        arg("periodic0")=false,arg("periodic1")=false,
146        arg("integrationOrder")=-1,        arg("integrationOrder")=-1,  arg("reducedIntegrationOrder")=-1,
147        arg("useElementsOnFace")=false),        arg("useElementsOnFace")=false,
148        return_value_policy<manage_new_object>());        arg("useFullElementOrder")=false,
149          arg("optimize")=false)
150    def("Interval",finley::interval,  //       ,return_value_policy<manage_new_object>());
151        (arg("n1")=1,arg("order")=1,  ,"Creates a rectangular mesh with n0 x n1 elements over the brick [0,l0] x [0,l1]."
152        arg("l1")=1.0,arg("periodic0")=false,  "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
153        arg("integrationOrder")=-1,  ":param order: =1 or =2 gives the order of shape function\n"
154        arg("useElementsOnFace")=false),  ":param l0: length of side 0\n:param l1:\n"
155        return_value_policy<manage_new_object>());  ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
156    ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
157    def("Merge",finley::meshMerge,  ":param useElementsOnFace:  whether or not to use elements on face\n"
158        return_value_policy<manage_new_object>());  ":type useElementsOnFace: ``int``"
159    ":param periodic0:  whether or not boundary conditions are periodic\n"
160    ":param periodic1:\n"
161    ":param useFullElementOrder:\n:param optimize:\n");
162    
163      def("Merge",finley::meshMerge,args("meshList")
164    //       ,return_value_policy<manage_new_object>());
165    ,"Merges a list of meshes into one mesh.\n\n:rtype: `Domain`"
166      );
167    
168    def("GlueFaces",finley::glueFaces,    def("GlueFaces",finley::glueFaces,
169        (arg("safetyFactor")=0.2,        (arg("meshList"),arg("safetyFactor")=0.2,
170        arg("tolerance")=std::numeric_limits<double>::epsilon()),        arg("tolerance")=1.e-8,
171        return_value_policy<manage_new_object>());        arg("optimize")=true)
172    //       ,return_value_policy<manage_new_object>());
173    ,"Detects matching faces in the mesh, removes them from the mesh and joins the elements touched by the face elements."
174        );
175    
176    def("JoinFaces",finley::joinFaces,    def("JoinFaces",finley::joinFaces,
177        (arg("safetyFactor")=0.2,        (arg("meshList"), arg("safetyFactor")=0.2,
178        arg("tolerance")=std::numeric_limits<double>::epsilon()),        arg("tolerance")=1.e-8,
179        return_value_policy<manage_new_object>());        arg("optimize")=true)
180    //       ,return_value_policy<manage_new_object>());
181    ,"Detects matching faces in the mesh and replaces them by joint elements."
182        );
183    
   register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);  
184    
185    class_<finley::MeshAdapter, bases<escript::AbstractContinuousDomain> >    class_<finley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
186        ("MeshAdapter",init<optional <Finley_Mesh*> >())        ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Finley_Mesh*> >())
187        .def(init<const finley::MeshAdapter&>())        .def(init<const finley::MeshAdapter&>())
188        .def("write",&finley::MeshAdapter::write)        .def("write",&finley::MeshAdapter::write,args("filename"),
189        .def("getDescription",&finley::MeshAdapter::getDescription)  "Write the current mesh to a file with the given name.")
190        .def("getDim",&finley::MeshAdapter::getDim)        .def("print_mesh_info",&finley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
191        .def("getDataShape",&finley::MeshAdapter::getDataShape)  ":param full:\n:type full: ``bool``")
192        .def("addPDEToSystem",&finley::MeshAdapter::addPDEToSystem)        .def("dump",&finley::MeshAdapter::dump,args("fileName")
193        .def("addPDEToRHS",&finley::MeshAdapter::addPDEToRHS)  ,"dumps the mesh to a file with the given name.")
194        .def("newOperator",&finley::MeshAdapter::newSystemMatrix)        .def("getDescription",&finley::MeshAdapter::getDescription,
195        .def("getSystemMatrixTypeId",&finley::MeshAdapter::getSystemMatrixTypeId)  ":return: a description for this domain\n:rtype: ``string``")
196        .def("setX",&finley::MeshAdapter::setNewX)        .def("getDim",&finley::MeshAdapter::getDim,":rtype: ``int``")
197        .def("getX",&finley::MeshAdapter::getX)        .def("getDataShape",&finley::MeshAdapter::getDataShape, args("functionSpaceCode"),
198        .def("getNormal",&finley::MeshAdapter::getNormal)  ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
199        .def("getSize",&finley::MeshAdapter::getSize)        .def("getNumDataPointsGlobal",&finley::MeshAdapter::getNumDataPointsGlobal,
200        .def("saveDX",&finley::MeshAdapter::saveDX)  ":return: the number of data points summed across all MPI processes\n"
201        .def("saveVTK",&finley::MeshAdapter::saveVTK);  ":rtype: ``int``")
202          .def("addPDEToSystem",&finley::MeshAdapter::addPDEToSystem,
203    args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
204    "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
205    ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
206    ":param A:\n:type A: `Data`\n"
207    ":param B:\n:type B: `Data`\n"
208    ":param C:\n:type C: `Data`\n"
209    ":param D:\n:type D: `Data`\n"
210    ":param X:\n:type X: `Data`\n"
211    ":param Y:\n:type Y: `Data`\n"
212    ":param d:\n:type d: `Data`\n"
213    ":param d_contact:\n:type d_contact: `Data`\n"
214    ":param y_contact:\n:type y_contact: `Data`\n"
215    )
216          .def("addPDEToLumpedSystem",&finley::MeshAdapter::addPDEToLumpedSystem,
217    args("mat", "D", "d"),
218    "adds a PDE onto the lumped stiffness matrix\n\n"
219    ":param mat:\n:type mat: `Data`\n"
220    ":param D:\n:type D: `Data`\n"
221    ":param d:\n:type d: `Data`\n")
222          .def("addPDEToRHS",&finley::MeshAdapter::addPDEToRHS,
223    args("rhs", "X", "Y", "y", "y_contact"),
224    "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
225    ":param rhs:\n:type rhs: `Data`\n"
226    ":param X:\n:type X: `Data`\n"
227    ":param Y:\n:type Y: `Data`\n"
228    ":param y:\n:type y: `Data`\n"
229    ":param y_contact:\n:type y_contact: `Data`"
230    )
231          .def("addPDEToTransportProblem",&finley::MeshAdapter::addPDEToTransportProblem,
232    args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
233    ":param tp:\n:type tp: `TransportProblemAdapter`\n"
234    ":param source:\n:type source: `Data`\n"
235    ":param M:\n:type M: `Data`\n"
236    ":param A:\n:type A: `Data`\n"
237    ":param B:\n:type B: `Data`\n"
238    ":param C:\n:type C: `Data`\n"
239    ":param D:\n:type D: `Data`\n"
240    ":param X:\n:type X: `Data`\n"
241    ":param Y:\n:type Y: `Data`\n"
242    ":param d:\n:type d: `Data`\n"
243    ":param y:\n:type y: `Data`\n"
244    ":param d_contact:\n:type d_contact: `Data`\n"
245    ":param y_contact:\n:type y_contact: `Data`\n"
246    )
247          .def("newOperator",&finley::MeshAdapter::newSystemMatrix,
248    args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
249    "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
250    ":param row_blocksize:\n:type row_blocksize: ``int``\n"
251    ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
252    ":param column_blocksize:\n:type column_blocksize: ``int``\n"
253    ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
254    ":param type:\n:type type: ``int``\n"
255    )
256          .def("newTransportProblem",&finley::MeshAdapter::newTransportProblem,
257    args("theta", "blocksize", "functionspace", "type"),
258    "creates a TransportProblemAdapter\n\n"
259    ":param theta:\n:type theta: ``float``\n"
260    ":param blocksize:\n:type blocksize: ``int``\n"
261    ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
262    ":param type:\n:type type: ``int``\n"
263    )
264          .def("getSystemMatrixTypeId",&finley::MeshAdapter::getSystemMatrixTypeId,
265    args("solver", "preconditioner", "package", "symmetry"),
266    ":return: the identifier of the matrix type to be used for the global stiffness matrix when a particular solver, package, perconditioner, and symmetric matrix is used.\n"
267    ":rtype: ``int``\n"
268    ":param solver:\n:type solver: ``int``\n"
269    ":param preconditioner:\n:type preconditioner: ``int``\n"
270    ":param package:\n:type package: ``int``\n"
271    ":param symmetry:\n:type symmetry: ``int``\n"
272    )
273          .def("getTransportTypeId",&finley::MeshAdapter::getTransportTypeId,
274    args("solver", "preconditioner", "package", "symmetry"),
275    ":return: the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.\n"
276    ":rtype: ``int``\n"
277    ":param solver:\n:type solver: ``int``\n"
278    ":param preconditioner:\n:type preconditioner: ``int``\n"
279    ":param package:\n:type package: ``int``\n"
280    ":param symmetry:\n:type symmetry: ``int``\n"
281    )
282          .def("setX",&finley::MeshAdapter::setNewX,
283    args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
284          .def("getX",&finley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
285    ":rtype: `Data`")
286          .def("getNormal",&finley::MeshAdapter::getNormal,
287    ":return: boundary normals at the quadrature point on the face elements\n"
288    ":rtype: `Data`")
289          .def("getSize",&finley::MeshAdapter::getSize,":return: the element size\n"
290    ":rtype: `Data`")
291          .def("saveDX",&finley::MeshAdapter::saveDX,args("filename" ,"arg"),
292    "Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier"
293    "\n\n:param filename: \n:type filename: ``string``\n"
294    "\n:param arg: \n:type arg: ``dict``\n")
295          .def("saveVTK",&finley::MeshAdapter::saveVTK,
296    args("filename" ,"arg",  "metadata", "metadata_schema"),
297    "Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier"
298    "\n\n:param filename:\n:type filename: ``string``\n"
299    ":param arg:\n:type arg: ``dict``\n"
300    ":param metadata:\n:type metadata: ``string``\n"
301    ":param metadata_schema:\n:type metadata_schema: ``string``\n"
302    )
303          .def("setTagMap",&finley::MeshAdapter::setTagMap,args("name","tag"),
304    "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
305    ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
306          .def("getTag",&finley::MeshAdapter::getTag,args("name"),":return: tag id for "
307    "``name``\n:rtype: ``string``")
308          .def("isValidTagName",&finley::MeshAdapter::isValidTagName,args("name"),
309    ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
310          .def("showTagNames",&finley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
311          .def("getMPISize",&finley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
312          .def("getMPIRank",&finley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
313          .def("MPIBarrier",&finley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
314          .def("onMasterProcessor",&finley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
315    
316    class_<finley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >    class_<finley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >
317        ("OperatorAdapter",no_init)        ("OperatorAdapter","A concrete class representing an operator. For more details, please see the c++ documentation.", no_init)
318          .def("print_matrix_info",&finley::SystemMatrixAdapter::Print_Matrix_Info,(arg("full")=false),"prints information about a system matrix")
319        .def("nullifyRowsAndCols",&finley::SystemMatrixAdapter::nullifyRowsAndCols)        .def("nullifyRowsAndCols",&finley::SystemMatrixAdapter::nullifyRowsAndCols)
320        .def("resetValues",&finley::SystemMatrixAdapter::resetValues)        .def("resetValues",&finley::SystemMatrixAdapter::resetValues, "resets the matrix entries")
321        .def("saveMM",&finley::SystemMatrixAdapter::saveMM)        .def("saveMM",&finley::SystemMatrixAdapter::saveMM,args("fileName"),
322        .def("saveHB",&finley::SystemMatrixAdapter::saveHB);  "writes the matrix to a file using the Matrix Market file format")
323          .def("saveHB",&finley::SystemMatrixAdapter::saveHB, args("filename"),
324    "writes the matrix to a file using the Harwell-Boeing file format");
325    
326      class_<finley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >
327          ("TransportProblemAdapter","",no_init)
328          .def("getSafeTimeStepSize",&finley::TransportProblemAdapter::getSafeTimeStepSize)
329          .def("getUnlimitedTimeStepSize",&finley::TransportProblemAdapter::getUnlimitedTimeStepSize)
330          .def("resetTransport",&finley::TransportProblemAdapter::resetTransport,
331    "resets the transport operator typically as they have been updated");
332  }  }

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