/[escript]/branches/diaplayground/dudley/src/CPPAdapter/dudleycpp.cpp
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trunk/esys2/finley/src/CPPAdapter/finleycpp.cpp revision 108 by jgs, Thu Jan 27 06:21:59 2005 UTC trunk/dudley/src/CPPAdapter/dudleycpp.cpp revision 3981 by jfenwick, Fri Sep 21 02:47:54 2012 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) 2003-2012 by University of Queensland
5    * http://www.uq.edu.au
6    *
7    * Primary Business: Queensland, Australia
8    * Licensed under the Open Software License version 3.0
9    * http://www.opensource.org/licenses/osl-3.0.php
10    *
11    * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12    * Development since 2012 by School of Earth Sciences
13    *
14    *****************************************************************************/
15    
16    
17    #ifdef ESYS_MPI
18    #include "esysUtils/Esys_MPI.h"
19    #endif
20  extern "C" {  extern "C" {
21  #include "finley/finleyC/Finley.h"  #include "../Dudley.h"
22  }  }
 #include "finley/CPPAdapter/MeshAdapter.h"  
 #include "finley/CPPAdapter/MeshAdapterFactory.h"  
 #include "finley/CPPAdapter/SystemMatrixAdapter.h"  
23    
24  #include "esysUtils/EsysException.h"  #include <pasowrap/SystemMatrixAdapter.h>
25    #include <pasowrap/TransportProblemAdapter.h>
26    
27    #include "MeshAdapter.h"
28    #include "MeshAdapterFactory.h"
29    
30    #include "DudleyAdapterException.h"
31    // #include "esysUtils/EsysException.h"
32  #include "esysUtils/esysExceptionTranslator.h"  #include "esysUtils/esysExceptionTranslator.h"
33    
34  #include "escript/Data/AbstractContinuousDomain.h"  #include "escript/AbstractContinuousDomain.h"
35    
36  #include <boost/python.hpp>  #include <boost/python.hpp>
37  #include <boost/python/module.hpp>  #include <boost/python/module.hpp>
38  #include <boost/python/def.hpp>  #include <boost/python/def.hpp>
39  #include <boost/python/detail/defaults_gen.hpp>  #include <boost/python/detail/defaults_gen.hpp>
40    #include <boost/version.hpp>
41    
42  using namespace boost::python;  using namespace boost::python;
43    
44  /**  /**
45     @memo     \page dudley Dudley
46     finley is the python module name that contains the interfaces     Dudley is the python module name that contains the interfaces
47     to the C++ wrapper to finley.     to the C++ wrapper to dudley.
   
    @version 1.0.0  
48    
49     @doc     \version 1.0.0
50    
51     Class Description:     \section class_desc Class Description:
52     Data     Data
53    
54     Class Limitations:     \section class_limits Class Limitations:
55     None     None
56    
57     Class Conditions of Use:     \section class_conds Class Conditions of Use:
58     None     None
59    
60     Throws:     \section throws Throws:
61     None     None
62    
63  */  */
64    
65  //  BOOST_PYTHON_MODULE(dudleycpp)
 // The BOOST_PYTHON_FUNCTION_OVERLOADS macro generates function overloads for optional  
 // arguments to the respective finley functions.  
 // !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!  
 //  
 // NOTE: If the number of arguments to the finley functions change  
 // the magic numbers in the BOOST_PYTHON_FUNCTION_OVERLOADS call  
 // must change.  
 //  
 // !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!  
 // BOOST_PYTHON_FUNCTION_OVERLOADS(readMesh_overloads,finley::readMesh,1,2)  
 // BOOST_PYTHON_FUNCTION_OVERLOADS(brick_overloads,finley::brick,0,12)  
 // BOOST_PYTHON_FUNCTION_OVERLOADS(rectangle_overloads,finley::rectangle,0,9)  
 // BOOST_PYTHON_FUNCTION_OVERLOADS(interval_overloads,finley::interval,0,6)  
 // BOOST_PYTHON_FUNCTION_OVERLOADS(glueFaces_overloads,finley::glueFaces,1,3)  
 // BOOST_PYTHON_FUNCTION_OVERLOADS(joinFaces_overloads,finley::joinFaces,1,3)  
   
 BOOST_PYTHON_MODULE(finleycpp)  
66  {  {
67    // This feature was added in boost v1.34
68    #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
69      // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
70      docstring_options docopt(true, true, false);
71    #endif
72    
   // 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());  
73    //    //
74    // NOTE: The return_value_policy is necessary for functions that    // NOTE: The return_value_policy is necessary for functions that
75    // return pointers.    // return pointers.
76      //
77      register_exception_translator<dudley::DudleyAdapterException>(&(esysUtils::esysExceptionTranslator));
78    
79    def("ReadMesh",finley::readMesh,    def("LoadMesh",dudley::loadMesh,
80        (arg("fileName"),arg("integrationOrder")=-1),        (arg("fileName")="file.nc"),":rtype: `Domain`"
81        return_value_policy<manage_new_object>());  /*      ,return_value_policy<manage_new_object>());*/
82          );
83    
84      def("ReadMesh",dudley::readMesh,
85          (arg("fileName")="file.fly",arg("integrationOrder")=-1,  arg("reducedIntegrationOrder")=-1,  arg("optimize")=true)
86    /*      ,return_value_policy<manage_new_object>());*/
87        ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
88    ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
89    ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
90    ":type integrationOrder: ``int``\n"
91    ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
92    ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
93    
94      def("ReadGmsh",dudley::readGmsh,
95          (arg("fileName")="file.msh",
96           arg("numDim"),
97           arg("integrationOrder")=-1,
98           arg("reducedIntegrationOrder")=-1,
99           arg("optimize")=true,  
100           arg("useMacroElements")=false)
101    //       ,return_value_policy<manage_new_object>());
102    ,"Read a gmsh mesh file\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``\n"
108    ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
109    );
110    
111    def ("Brick",finley::brick,    def ("Brick",dudley::brick,
112        (arg("n0")=1,arg("n1")=1,arg("n2")=1,        (arg("n0")=1,arg("n1")=1,arg("n2")=1,
113        arg("order")=1,        arg("order")=1,
114        arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,        arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,
115        arg("periodic0")=false,arg("periodic1")=false,arg("periodic2")=false,        arg("periodic0")=false,arg("periodic1")=false,arg("periodic2")=false,
116        arg("integrationOrder")=-1,        arg("integrationOrder")=-1,  arg("reducedIntegrationOrder")=-1,
117        arg("useElementsOnFace")=false),        arg("useElementsOnFace")=false,
118        return_value_policy<manage_new_object>());        arg("useFullElementOrder")=false,
119          arg("optimize")=false)
120    ,"Creates a tetrahedral mesh by subdividing n0 x n1 x n2 rectangular elements over the brick [0,l0] x [0,l1] x [0,l2]."
121    "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
122    "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
123    ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
124    ":param l0: length of side 0\n:param l1:\n:param l2:\n"
125    ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
126    ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
127    ":param useElementsOnFace:  whether or not to use elements on face\n"
128    ":type useElementsOnFace: ``int``"
129    ":param periodic0:  whether or not boundary conditions are periodic\n"
130    ":param periodic1:\n:param periodic2:\n"
131    ":param useFullElementOrder:\n:param optimize:\n"
132    ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
133    );
134    
135    def ("Rectangle",finley::rectangle,    def ("Rectangle",dudley::rectangle,
136        (arg("n0")=1,arg("n1")=1,arg("order")=1,        (arg("n0")=1,arg("n1")=1,arg("order")=1,
137        arg("l0")=1.0,arg("l1")=1.0,        arg("l0")=1.0,arg("l1")=1.0,
138        arg("periodic0")=false,arg("periodic1")=false,        arg("periodic0")=false,arg("periodic1")=false,
139        arg("integrationOrder")=-1,        arg("integrationOrder")=-1,  arg("reducedIntegrationOrder")=-1,
140        arg("useElementsOnFace")=false),        arg("useElementsOnFace")=false,
141        return_value_policy<manage_new_object>());        arg("useFullElementOrder")=false,
142          arg("optimize")=false)
143    def("Interval",finley::interval,  ,"Creates a triangular mesh by subdividing n0 x n1 rectangular elements over the brick [0,l0] x [0,l1]."
144        (arg("n1")=1,arg("order")=1,  "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
145        arg("l1")=1.0,arg("periodic0")=false,  "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
146        arg("integrationOrder")=-1,  ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
147        arg("useElementsOnFace")=false),  ":param l0: length of side 0\n:param l1:\n"
148        return_value_policy<manage_new_object>());  ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
149    ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
150    def("GlueFaces",finley::glueFaces,  ":param useElementsOnFace:  whether or not to use elements on face\n"
151        (arg("safetyFactor")=0.2,  ":type useElementsOnFace: ``int``"
152        arg("tolerance")=std::numeric_limits<double>::epsilon()),  ":param periodic0:  whether or not boundary conditions are periodic\n"
153        return_value_policy<manage_new_object>());  ":param periodic1:\n"
154    ":param useFullElementOrder:\n:param optimize:\n"
155    def("JoinFaces",finley::joinFaces,  ":param useMacroElements: Enable the usage of first order macro elements.\n:type useMacroElements: ``bool``\n"
156        (arg("safetyFactor")=0.2,  ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
157        arg("tolerance")=std::numeric_limits<double>::epsilon()),  );
158        return_value_policy<manage_new_object>());  
159      class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
160    register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);        ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())
161          .def(init<const dudley::MeshAdapter&>())
162    class_<finley::MeshAdapter, bases<escript::AbstractContinuousDomain> >        .def("write",&dudley::MeshAdapter::write,args("filename"),
163        ("MeshAdapter",init<optional <Finley_Mesh*> >())  "Write the current mesh to a file with the given name.")
164        .def(init<const finley::MeshAdapter&>())        .def("print_mesh_info",&dudley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
165        .def("write",&finley::MeshAdapter::write)  ":param full:\n:type full: ``bool``")
166        .def("getDescription",&finley::MeshAdapter::getDescription)        .def("dump",&dudley::MeshAdapter::dump,args("fileName")
167        .def("getDim",&finley::MeshAdapter::getDim)  ,"dumps the mesh to a file with the given name.")
168        .def("getDataShape",&finley::MeshAdapter::getDataShape)        .def("getDescription",&dudley::MeshAdapter::getDescription,
169        .def("addPDEToSystem",&finley::MeshAdapter::addPDEToSystem)  ":return: a description for this domain\n:rtype: ``string``")
170        .def("addPDEToRHS",&finley::MeshAdapter::addPDEToRHS)        .def("getDim",&dudley::MeshAdapter::getDim,":rtype: ``int``")
171        .def("newOperator",&finley::MeshAdapter::newSystemMatrix)        .def("getDataShape",&dudley::MeshAdapter::getDataShape, args("functionSpaceCode"),
172        .def("getSystemMatrixTypeId",&finley::MeshAdapter::getSystemMatrixTypeId)  ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
173        .def("getX",&finley::MeshAdapter::getX)        .def("getNumDataPointsGlobal",&dudley::MeshAdapter::getNumDataPointsGlobal,
174        .def("getNormal",&finley::MeshAdapter::getNormal)  ":return: the number of data points summed across all MPI processes\n"
175        .def("getSize",&finley::MeshAdapter::getSize);  ":rtype: ``int``")
176          .def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
177    args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
178    class_<finley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >  "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
179        ("OperatorAdapter",no_init)  ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
180        .def("nullifyRowsAndCols",&finley::SystemMatrixAdapter::nullifyRowsAndCols)  ":param A:\n:type A: `Data`\n"
181        .def("setValue",&finley::SystemMatrixAdapter::setValue)  ":param B:\n:type B: `Data`\n"
182        .def("resetSolver",&finley::SystemMatrixAdapter::resetSolver)  ":param C:\n:type C: `Data`\n"
183        .def("saveMM",&finley::SystemMatrixAdapter::saveMM);  ":param D:\n:type D: `Data`\n"
184    ":param X:\n:type X: `Data`\n"
185    ":param Y:\n:type Y: `Data`\n"
186    ":param d:\n:type d: `Data`\n"
187    ":param d_contact:\n:type d_contact: `Data`\n"
188    ":param y_contact:\n:type y_contact: `Data`\n"
189    )
190          .def("addPDEToLumpedSystem",&dudley::MeshAdapter::addPDEToLumpedSystem,
191    args("mat", "D", "d"),
192    "adds a PDE onto the lumped stiffness matrix\n\n"
193    ":param mat:\n:type mat: `Data`\n"
194    ":param D:\n:type D: `Data`\n"
195    ":param d:\n:type d: `Data`\n"
196    ":param useHRZ:\n:type useHRZ: bool\n"
197    )
198          .def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,
199    args("rhs", "X", "Y", "y", "y_contact"),
200    "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
201    ":param rhs:\n:type rhs: `Data`\n"
202    ":param X:\n:type X: `Data`\n"
203    ":param Y:\n:type Y: `Data`\n"
204    ":param y:\n:type y: `Data`\n"
205    ":param y_contact:\n:type y_contact: `Data`"
206    )
207          .def("addPDEToTransportProblem",&dudley::MeshAdapter::addPDEToTransportProblem,
208    args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
209    ":param tp:\n:type tp: `TransportProblemAdapter`\n"
210    ":param source:\n:type source: `Data`\n"
211    ":param M:\n:type M: `Data`\n"
212    ":param A:\n:type A: `Data`\n"
213    ":param B:\n:type B: `Data`\n"
214    ":param C:\n:type C: `Data`\n"
215    ":param D:\n:type D: `Data`\n"
216    ":param X:\n:type X: `Data`\n"
217    ":param Y:\n:type Y: `Data`\n"
218    ":param d:\n:type d: `Data`\n"
219    ":param y:\n:type y: `Data`\n"
220    ":param d_contact:\n:type d_contact: `Data`\n"
221    ":param y_contact:\n:type y_contact: `Data`\n"
222    )
223          .def("newOperator",&dudley::MeshAdapter::newSystemMatrix,
224    args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
225    "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
226    ":param row_blocksize:\n:type row_blocksize: ``int``\n"
227    ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
228    ":param column_blocksize:\n:type column_blocksize: ``int``\n"
229    ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
230    ":param type:\n:type type: ``int``\n"
231    )
232          .def("newTransportProblem",&dudley::MeshAdapter::newTransportProblem,
233    args("theta", "blocksize", "functionspace", "type"),
234    "creates a TransportProblemAdapter\n\n"
235    ":param theta:\n:type theta: ``float``\n"
236    ":param blocksize:\n:type blocksize: ``int``\n"
237    ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
238    ":param type:\n:type type: ``int``\n"
239    )
240          .def("getSystemMatrixTypeId",&dudley::MeshAdapter::getSystemMatrixTypeId,
241    args("solver", "preconditioner", "package", "symmetry"),
242    ":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"
243    ":rtype: ``int``\n"
244    ":param solver:\n:type solver: ``int``\n"
245    ":param preconditioner:\n:type preconditioner: ``int``\n"
246    ":param package:\n:type package: ``int``\n"
247    ":param symmetry:\n:type symmetry: ``int``\n"
248    )
249          .def("getTransportTypeId",&dudley::MeshAdapter::getTransportTypeId,
250    args("solver", "preconditioner", "package", "symmetry"),
251    ":return: the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.\n"
252    ":rtype: ``int``\n"
253    ":param solver:\n:type solver: ``int``\n"
254    ":param preconditioner:\n:type preconditioner: ``int``\n"
255    ":param package:\n:type package: ``int``\n"
256    ":param symmetry:\n:type symmetry: ``int``\n"
257    )
258          .def("setX",&dudley::MeshAdapter::setNewX,
259    args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
260          .def("getX",&dudley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
261    ":rtype: `Data`")
262          .def("getNormal",&dudley::MeshAdapter::getNormal,
263    ":return: boundary normals at the quadrature point on the face elements\n"
264    ":rtype: `Data`")
265          .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
266    ":rtype: `Data`")
267          .def("saveDX",&dudley::MeshAdapter::saveDX,args("filename" ,"arg"),
268    "Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier"
269    "\n\n:param filename: \n:type filename: ``string``\n"
270    "\n:param arg: \n:type arg: ``dict``\n")
271          .def("saveVTK",&dudley::MeshAdapter::saveVTK,
272    args("filename" ,"arg",  "metadata", "metadata_schema"),
273    "Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier"
274    "\n\n:param filename:\n:type filename: ``string``\n"
275    ":param arg:\n:type arg: ``dict``\n"
276    ":param metadata:\n:type metadata: ``string``\n"
277    ":param metadata_schema:\n:type metadata_schema: ``string``\n"
278    )
279          .def("setTagMap",&dudley::MeshAdapter::setTagMap,args("name","tag"),
280    "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
281    ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
282          .def("getTag",&dudley::MeshAdapter::getTag,args("name"),":return: tag id for "
283    "``name``\n:rtype: ``string``")
284          .def("isValidTagName",&dudley::MeshAdapter::isValidTagName,args("name"),
285    ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
286          .def("showTagNames",&dudley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
287          .def("getMPISize",&dudley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
288          .def("getMPIRank",&dudley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
289          .def("MPIBarrier",&dudley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
290          .def("onMasterProcessor",&dudley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
291    
292  }  }

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