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branches/domexper/dudley/src/CPPAdapter/finleycpp.cpp revision 3080 by jfenwick, Tue Aug 3 04:28:03 2010 UTC trunk/dudley/src/CPPAdapter/dudleycpp.cpp revision 4821 by sshaw, Tue Apr 1 04:58:33 2014 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*****************************************************************************
3  *  *
4  * Copyright (c) 2003-2010 by University of Queensland  * Copyright (c) 2003-2014 by University of Queensland
5  * Earth Systems Science Computational Center (ESSCC)  * http://www.uq.edu.au
 * http://www.uq.edu.au/esscc  
6  *  *
7  * Primary Business: Queensland, Australia  * Primary Business: Queensland, Australia
8  * Licensed under the Open Software License version 3.0  * Licensed under the Open Software License version 3.0
9  * http://www.opensource.org/licenses/osl-3.0.php  * http://www.opensource.org/licenses/osl-3.0.php
10  *  *
11  *******************************************************/  * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12    * Development 2012-2013 by School of Earth Sciences
13    * Development from 2014 by Centre for Geoscience Computing (GeoComp)
14    *
15    *****************************************************************************/
16    
17    
18  #ifdef PASO_MPI  #ifdef ESYS_MPI
19  #include <mpi.h>  #include "esysUtils/Esys_MPI.h"
 #include "paso/Paso_MPI.h"  
20  #endif  #endif
21  extern "C" {  #include "../Dudley.h"
22  #include "../Finley.h"  
23  }  #include <pasowrap/SystemMatrixAdapter.h>
24    #include <pasowrap/TransportProblemAdapter.h>
25    
26  #include "MeshAdapter.h"  #include "MeshAdapter.h"
27  #include "MeshAdapterFactory.h"  #include "MeshAdapterFactory.h"
 #include "SystemMatrixAdapter.h"  
 #include "TransportProblemAdapter.h"  
28    
29  #include "FinleyAdapterException.h"  #include "DudleyAdapterException.h"
30  // #include "esysUtils/EsysException.h"  // #include "esysUtils/EsysException.h"
31  #include "esysUtils/esysExceptionTranslator.h"  #include "esysUtils/esysExceptionTranslator.h"
32    
# Line 39  extern "C" { Line 40  extern "C" {
40    
41  using namespace boost::python;  using namespace boost::python;
42    
43  /**  BOOST_PYTHON_MODULE(dudleycpp)
    \page finley Finley  
    Finley is the python module name that contains the interfaces  
    to the C++ wrapper to finley.  
   
    \version 1.0.0  
   
    \section class_desc Class Description:  
    Data  
   
    \section class_limits Class Limitations:  
    None  
   
    \section class_conds Class Conditions of Use:  
    None  
   
    \section throws Throws:  
    None  
   
 */  
   
 //  
 // 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)  
44  {  {
45  // This feature was added in boost v1.34  // This feature was added in boost v1.34
46  #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)  #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
# Line 85  BOOST_PYTHON_MODULE(finleycpp) Line 48  BOOST_PYTHON_MODULE(finleycpp)
48    docstring_options docopt(true, true, false);    docstring_options docopt(true, true, false);
49  #endif  #endif
50    
51      scope().attr("__doc__") = "To use this module, please import esys.dudley";  
52      
53      
54    //    //
55    // NOTE: The return_value_policy is necessary for functions that    // NOTE: The return_value_policy is necessary for functions that
56    // return pointers.    // return pointers.
57    //    //
58    register_exception_translator<finley::FinleyAdapterException>(&(esysUtils::esysExceptionTranslator));    register_exception_translator<dudley::DudleyAdapterException>(&(esysUtils::RuntimeErrorTranslator));
59    
60    def("LoadMesh",finley::loadMesh,    def("LoadMesh",dudley::loadMesh,
61        (arg("fileName")="file.nc"),":rtype: `Domain`"        (arg("fileName")="file.nc"),":rtype: `Domain`"
62  /*      ,return_value_policy<manage_new_object>());*/  /*      ,return_value_policy<manage_new_object>());*/
63        );        );
64    
65    def("ReadMesh",finley::readMesh,    def("ReadMesh",dudley::readMesh,
66        (arg("fileName")="file.fly",arg("integrationOrder")=-1,  arg("reducedIntegrationOrder")=-1,  arg("optimize")=true)        (arg("fileName")="file.fly",arg("integrationOrder")=-1,  arg("reducedIntegrationOrder")=-1,  arg("optimize")=true)
67  /*      ,return_value_policy<manage_new_object>());*/  /*      ,return_value_policy<manage_new_object>());*/
68      ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"      ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
# Line 106  BOOST_PYTHON_MODULE(finleycpp) Line 72  BOOST_PYTHON_MODULE(finleycpp)
72  ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"  ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
73  ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");  ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
74    
75    def("ReadGmsh",finley::readGmsh,    def("ReadGmsh",dudley::readGmsh,
76        (arg("fileName")="file.msh",        (arg("fileName")="file.msh",
77         arg("numDim"),         arg("numDim"),
78         arg("integrationOrder")=-1,         arg("integrationOrder")=-1,
# Line 123  BOOST_PYTHON_MODULE(finleycpp) Line 89  BOOST_PYTHON_MODULE(finleycpp)
89  ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"  ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
90  );  );
91    
92    def ("Brick",finley::brick,    def ("Brick",dudley::brick,
93        (arg("n0")=1,arg("n1")=1,arg("n2")=1,        (arg("n0")=1,arg("n1")=1,arg("n2")=1,
94        arg("order")=1,        arg("order")=1,
95        arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,        arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,
# Line 132  BOOST_PYTHON_MODULE(finleycpp) Line 98  BOOST_PYTHON_MODULE(finleycpp)
98        arg("useElementsOnFace")=false,        arg("useElementsOnFace")=false,
99        arg("useFullElementOrder")=false,        arg("useFullElementOrder")=false,
100        arg("optimize")=false)        arg("optimize")=false)
101          ,"Creates a tetrahedral mesh by subdividing n0 x n1 x n2 rectangular elements over the brick [0,l0] x [0,l1] x [0,l2]."
102  //       ,return_value_policy<manage_new_object>());  "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
 ,"Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2]."  
103  "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"  "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
104  ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"  ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
105  ":param l0: length of side 0\n:param l1:\n:param l2:\n"  ":param l0: length of side 0\n:param l1:\n:param l2:\n"
# Line 148  BOOST_PYTHON_MODULE(finleycpp) Line 113  BOOST_PYTHON_MODULE(finleycpp)
113  ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"  ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
114  );  );
115    
116    def ("Rectangle",finley::rectangle,    def ("Rectangle",dudley::rectangle,
117        (arg("n0")=1,arg("n1")=1,arg("order")=1,        (arg("n0")=1,arg("n1")=1,arg("order")=1,
118        arg("l0")=1.0,arg("l1")=1.0,        arg("l0")=1.0,arg("l1")=1.0,
119        arg("periodic0")=false,arg("periodic1")=false,        arg("periodic0")=false,arg("periodic1")=false,
# Line 156  BOOST_PYTHON_MODULE(finleycpp) Line 121  BOOST_PYTHON_MODULE(finleycpp)
121        arg("useElementsOnFace")=false,        arg("useElementsOnFace")=false,
122        arg("useFullElementOrder")=false,        arg("useFullElementOrder")=false,
123        arg("optimize")=false)        arg("optimize")=false)
124  //       ,return_value_policy<manage_new_object>());  ,"Creates a triangular mesh by subdividing n0 x n1 rectangular elements over the brick [0,l0] x [0,l1]."
125  ,"Creates a rectangular mesh with n0 x n1 elements over the brick [0,l0] x [0,l1]."  "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
126  "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"  "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
127  ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"  ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
128  ":param l0: length of side 0\n:param l1:\n"  ":param l0: length of side 0\n:param l1:\n"
# Line 172  BOOST_PYTHON_MODULE(finleycpp) Line 137  BOOST_PYTHON_MODULE(finleycpp)
137  ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"  ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
138  );  );
139    
140    def("Merge",finley::meshMerge,args("meshList")    class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
141  //       ,return_value_policy<manage_new_object>());        ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())
142  ,"Merges a list of meshes into one mesh.\n\n:rtype: `Domain`"        .def(init<const dudley::MeshAdapter&>())
143    );        .def("write",&dudley::MeshAdapter::write,args("filename"),
   
   def("GlueFaces",finley::glueFaces,  
       (arg("meshList"),arg("safetyFactor")=0.2,  
       arg("tolerance")=1.e-8,  
       arg("optimize")=true)  
 //       ,return_value_policy<manage_new_object>());  
 ,"Detects matching faces in the mesh, removes them from the mesh and joins the elements touched by the face elements."  
     );  
   
   def("JoinFaces",finley::joinFaces,  
       (arg("meshList"), arg("safetyFactor")=0.2,  
       arg("tolerance")=1.e-8,  
       arg("optimize")=true)  
 //       ,return_value_policy<manage_new_object>());  
 ,"Detects matching faces in the mesh and replaces them by joint elements."  
     );  
   
   
   class_<finley::MeshAdapter, bases<escript::AbstractContinuousDomain> >  
       ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Finley_Mesh*> >())  
       .def(init<const finley::MeshAdapter&>())  
       .def("write",&finley::MeshAdapter::write,args("filename"),  
144  "Write the current mesh to a file with the given name.")  "Write the current mesh to a file with the given name.")
145        .def("print_mesh_info",&finley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),        .def("print_mesh_info",&dudley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
146  ":param full:\n:type full: ``bool``")  ":param full:\n:type full: ``bool``")
147        .def("dump",&finley::MeshAdapter::dump,args("fileName")        .def("dump",&dudley::MeshAdapter::dump,args("fileName")
148  ,"dumps the mesh to a file with the given name.")  ,"dumps the mesh to a file with the given name.")
149        .def("getDescription",&finley::MeshAdapter::getDescription,        .def("getDescription",&dudley::MeshAdapter::getDescription,
150  ":return: a description for this domain\n:rtype: ``string``")  ":return: a description for this domain\n:rtype: ``string``")
151        .def("getDim",&finley::MeshAdapter::getDim,":rtype: ``int``")        .def("getDim",&dudley::MeshAdapter::getDim,":rtype: ``int``")
152        .def("getDataShape",&finley::MeshAdapter::getDataShape, args("functionSpaceCode"),        .def("getDataShape",&dudley::MeshAdapter::getDataShape, args("functionSpaceCode"),
153  ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")  ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
154        .def("getNumDataPointsGlobal",&finley::MeshAdapter::getNumDataPointsGlobal,        .def("getNumDataPointsGlobal",&dudley::MeshAdapter::getNumDataPointsGlobal,
155  ":return: the number of data points summed across all MPI processes\n"  ":return: the number of data points summed across all MPI processes\n"
156  ":rtype: ``int``")  ":rtype: ``int``")
157        .def("addPDEToSystem",&finley::MeshAdapter::addPDEToSystem,        .def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
158  args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),  args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
159  "adds a PDE onto the stiffness matrix mat and a rhs\n\n"  "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
160  ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"  ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
# Line 225  args("mat", "rhs","A", "B", "C", "D", "X Line 168  args("mat", "rhs","A", "B", "C", "D", "X
168  ":param d_contact:\n:type d_contact: `Data`\n"  ":param d_contact:\n:type d_contact: `Data`\n"
169  ":param y_contact:\n:type y_contact: `Data`\n"  ":param y_contact:\n:type y_contact: `Data`\n"
170  )  )
171        .def("addPDEToLumpedSystem",&finley::MeshAdapter::addPDEToLumpedSystem,        .def("addPDEToLumpedSystem",&dudley::MeshAdapter::addPDEToLumpedSystem,
172  args("mat", "D", "d"),  args("mat", "D", "d"),
173  "adds a PDE onto the lumped stiffness matrix\n\n"  "adds a PDE onto the lumped stiffness matrix\n\n"
174  ":param mat:\n:type mat: `Data`\n"  ":param mat:\n:type mat: `Data`\n"
175  ":param D:\n:type D: `Data`\n"  ":param D:\n:type D: `Data`\n"
176  ":param d:\n:type d: `Data`\n")  ":param d:\n:type d: `Data`\n"
177        .def("addPDEToRHS",&finley::MeshAdapter::addPDEToRHS,  ":param useHRZ:\n:type useHRZ: bool\n"
178    )
179          .def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,
180  args("rhs", "X", "Y", "y", "y_contact"),  args("rhs", "X", "Y", "y", "y_contact"),
181  "adds a PDE onto the stiffness matrix mat and a rhs\n\n"  "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
182  ":param rhs:\n:type rhs: `Data`\n"  ":param rhs:\n:type rhs: `Data`\n"
# Line 240  args("rhs", "X", "Y", "y", "y_contact"), Line 185  args("rhs", "X", "Y", "y", "y_contact"),
185  ":param y:\n:type y: `Data`\n"  ":param y:\n:type y: `Data`\n"
186  ":param y_contact:\n:type y_contact: `Data`"  ":param y_contact:\n:type y_contact: `Data`"
187  )  )
188        .def("addPDEToTransportProblem",&finley::MeshAdapter::addPDEToTransportProblem,        .def("addPDEToTransportProblem",&dudley::MeshAdapter::addPDEToTransportProblem,
189  args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),  args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
190  ":param tp:\n:type tp: `TransportProblemAdapter`\n"  ":param tp:\n:type tp: `TransportProblemAdapter`\n"
191  ":param source:\n:type source: `Data`\n"  ":param source:\n:type source: `Data`\n"
# Line 256  args( "tp", "source", "M", "A", "B", "C" Line 201  args( "tp", "source", "M", "A", "B", "C"
201  ":param d_contact:\n:type d_contact: `Data`\n"  ":param d_contact:\n:type d_contact: `Data`\n"
202  ":param y_contact:\n:type y_contact: `Data`\n"  ":param y_contact:\n:type y_contact: `Data`\n"
203  )  )
204        .def("newOperator",&finley::MeshAdapter::newSystemMatrix,        .def("newOperator",&dudley::MeshAdapter::newSystemMatrix,
205  args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),  args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
206  "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"  "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
207  ":param row_blocksize:\n:type row_blocksize: ``int``\n"  ":param row_blocksize:\n:type row_blocksize: ``int``\n"
# Line 265  args("row_blocksize", "row_functionspace Line 210  args("row_blocksize", "row_functionspace
210  ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"  ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
211  ":param type:\n:type type: ``int``\n"  ":param type:\n:type type: ``int``\n"
212  )  )
213        .def("newTransportProblem",&finley::MeshAdapter::newTransportProblem,        .def("newTransportProblem",&dudley::MeshAdapter::newTransportProblem,
214  args("theta", "blocksize", "functionspace", "type"),  args("theta", "blocksize", "functionspace", "type"),
215  "creates a TransportProblemAdapter\n\n"  "creates a TransportProblemAdapter\n\n"
216  ":param theta:\n:type theta: ``float``\n"  ":param theta:\n:type theta: ``float``\n"
# Line 273  args("theta", "blocksize", "functionspac Line 218  args("theta", "blocksize", "functionspac
218  ":param functionspace:\n:type functionspace: `FunctionSpace`\n"  ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
219  ":param type:\n:type type: ``int``\n"  ":param type:\n:type type: ``int``\n"
220  )  )
221        .def("getSystemMatrixTypeId",&finley::MeshAdapter::getSystemMatrixTypeId,        .def("getSystemMatrixTypeId",&dudley::MeshAdapter::getSystemMatrixTypeId,
222  args("solver", "preconditioner", "package", "symmetry"),  args("solver", "preconditioner", "package", "symmetry"),
223  ":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"  ":return: the identifier of the matrix type to be used for the global stiffness matrix when a particular solver, package, preconditioner, and symmetric matrix is used.\n"
224  ":rtype: ``int``\n"  ":rtype: ``int``\n"
225  ":param solver:\n:type solver: ``int``\n"  ":param solver:\n:type solver: ``int``\n"
226  ":param preconditioner:\n:type preconditioner: ``int``\n"  ":param preconditioner:\n:type preconditioner: ``int``\n"
227  ":param package:\n:type package: ``int``\n"  ":param package:\n:type package: ``int``\n"
228  ":param symmetry:\n:type symmetry: ``int``\n"  ":param symmetry:\n:type symmetry: ``int``\n"
229  )  )
230        .def("getTransportTypeId",&finley::MeshAdapter::getTransportTypeId,        .def("getTransportTypeId",&dudley::MeshAdapter::getTransportTypeId,
231  args("solver", "preconditioner", "package", "symmetry"),  args("solver", "preconditioner", "package", "symmetry"),
232  ":return: the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.\n"  ":return: the identifier of the transport problem type to be used when a particular solver, preconditioner, package and symmetric matrix is used.\n"
233  ":rtype: ``int``\n"  ":rtype: ``int``\n"
234  ":param solver:\n:type solver: ``int``\n"  ":param solver:\n:type solver: ``int``\n"
235  ":param preconditioner:\n:type preconditioner: ``int``\n"  ":param preconditioner:\n:type preconditioner: ``int``\n"
236  ":param package:\n:type package: ``int``\n"  ":param package:\n:type package: ``int``\n"
237  ":param symmetry:\n:type symmetry: ``int``\n"  ":param symmetry:\n:type symmetry: ``int``\n"
238  )  )
239        .def("setX",&finley::MeshAdapter::setNewX,        .def("setX",&dudley::MeshAdapter::setNewX,
240  args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")  args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
241        .def("getX",&finley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"        .def("getX",&dudley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
242  ":rtype: `Data`")  ":rtype: `Data`")
243        .def("getNormal",&finley::MeshAdapter::getNormal,        .def("getNormal",&dudley::MeshAdapter::getNormal,
244  ":return: boundary normals at the quadrature point on the face elements\n"  ":return: boundary normals at the quadrature point on the face elements\n"
245  ":rtype: `Data`")  ":rtype: `Data`")
246        .def("getSize",&finley::MeshAdapter::getSize,":return: the element size\n"        .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
247  ":rtype: `Data`")  ":rtype: `Data`")
248        .def("saveDX",&finley::MeshAdapter::saveDX,args("filename" ,"arg"),        .def("setTagMap",&dudley::MeshAdapter::setTagMap,args("name","tag"),
 "Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier"  
 "\n\n:param filename: \n:type filename: ``string``\n"  
 "\n:param arg: \n:type arg: ``dict``\n")  
       .def("saveVTK",&finley::MeshAdapter::saveVTK,  
 args("filename" ,"arg",  "metadata", "metadata_schema"),  
 "Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier"  
 "\n\n:param filename:\n:type filename: ``string``\n"  
 ":param arg:\n:type arg: ``dict``\n"  
 ":param metadata:\n:type metadata: ``string``\n"  
 ":param metadata_schema:\n:type metadata_schema: ``string``\n"  
 )  
       .def("setTagMap",&finley::MeshAdapter::setTagMap,args("name","tag"),  
249  "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"  "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
250  ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")  ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
251        .def("getTag",&finley::MeshAdapter::getTag,args("name"),":return: tag id for "        .def("getTag",&dudley::MeshAdapter::getTag,args("name"),":return: tag id for "
252  "``name``\n:rtype: ``string``")  "``name``\n:rtype: ``string``")
253        .def("isValidTagName",&finley::MeshAdapter::isValidTagName,args("name"),        .def("isValidTagName",&dudley::MeshAdapter::isValidTagName,args("name"),
254  ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")  ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
255        .def("showTagNames",&finley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")        .def("showTagNames",&dudley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
256        .def("getMPISize",&finley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")        .def("getMPISize",&dudley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
257        .def("getMPIRank",&finley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")        .def("getMPIRank",&dudley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
258        .def("MPIBarrier",&finley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")        .def("MPIBarrier",&dudley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
259        .def("onMasterProcessor",&finley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");        .def("onMasterProcessor",&dudley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
260    
   class_<finley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >  
       ("OperatorAdapter","A concrete class representing an operator. For more details, please see the c++ documentation.", no_init)  
       .def("print_matrix_info",&finley::SystemMatrixAdapter::Print_Matrix_Info,(arg("full")=false),"prints information about a system matrix")  
       .def("nullifyRowsAndCols",&finley::SystemMatrixAdapter::nullifyRowsAndCols)  
       .def("resetValues",&finley::SystemMatrixAdapter::resetValues, "resets the matrix entries")  
       .def("saveMM",&finley::SystemMatrixAdapter::saveMM,args("fileName"),  
 "writes the matrix to a file using the Matrix Market file format")  
       .def("saveHB",&finley::SystemMatrixAdapter::saveHB, args("filename"),  
 "writes the matrix to a file using the Harwell-Boeing file format");  
   
   class_<finley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >  
       ("TransportProblemAdapter","",no_init)  
       .def("getSafeTimeStepSize",&finley::TransportProblemAdapter::getSafeTimeStepSize)  
       .def("getUnlimitedTimeStepSize",&finley::TransportProblemAdapter::getUnlimitedTimeStepSize)  
       .def("resetTransport",&finley::TransportProblemAdapter::resetTransport,  
 "resets the transport operator typically as they have been updated");  
261  }  }

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