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branches/domexper/dudley/src/CPPAdapter/dudleycpp.cpp revision 3114 by jfenwick, Fri Aug 27 05:26:25 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
 extern "C" {  
21  #include "../Dudley.h"  #include "../Dudley.h"
22  }  
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 "DudleyAdapterException.h"  #include "DudleyAdapterException.h"
30  // #include "esysUtils/EsysException.h"  // #include "esysUtils/EsysException.h"
# Line 39  extern "C" { Line 40  extern "C" {
40    
41  using namespace boost::python;  using namespace boost::python;
42    
 /**  
    \page dudley Dudley  
    Dudley is the python module name that contains the interfaces  
    to the C++ wrapper to dudley.  
   
    \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  
   
 */  
   
43  BOOST_PYTHON_MODULE(dudleycpp)  BOOST_PYTHON_MODULE(dudleycpp)
44  {  {
45  // This feature was added in boost v1.34  // This feature was added in boost v1.34
# Line 68  BOOST_PYTHON_MODULE(dudleycpp) Line 48  BOOST_PYTHON_MODULE(dudleycpp)
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<dudley::DudleyAdapterException>(&(esysUtils::esysExceptionTranslator));    register_exception_translator<dudley::DudleyAdapterException>(&(esysUtils::RuntimeErrorTranslator));
59    
60    def("LoadMesh",dudley::loadMesh,    def("LoadMesh",dudley::loadMesh,
61        (arg("fileName")="file.nc"),":rtype: `Domain`"        (arg("fileName")="file.nc"),":rtype: `Domain`"
# Line 115  BOOST_PYTHON_MODULE(dudleycpp) Line 98  BOOST_PYTHON_MODULE(dudleycpp)
98        arg("useElementsOnFace")=false,        arg("useElementsOnFace")=false,
99        arg("useFullElementOrder")=false,        arg("useFullElementOrder")=false,
100        arg("optimize")=false)        arg("optimize")=false)
101  ,"Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2]."  ,"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    "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
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 137  BOOST_PYTHON_MODULE(dudleycpp) Line 121  BOOST_PYTHON_MODULE(dudleycpp)
121        arg("useElementsOnFace")=false,        arg("useElementsOnFace")=false,
122        arg("useFullElementOrder")=false,        arg("useFullElementOrder")=false,
123        arg("optimize")=false)        arg("optimize")=false)
124  ,"Creates a rectangular mesh with n0 x n1 elements over the brick [0,l0] x [0,l1]."  ,"Creates a triangular mesh by subdividing n0 x n1 rectangular elements over the brick [0,l0] x [0,l1]."
125    "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 152  BOOST_PYTHON_MODULE(dudleycpp) Line 137  BOOST_PYTHON_MODULE(dudleycpp)
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    
   def("Merge",dudley::meshMerge,args("meshList")  
 //       ,return_value_policy<manage_new_object>());  
 ,"Merges a list of meshes into one mesh.\n\n:rtype: `Domain`"  
   );  
   
   def("GlueFaces",dudley::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",dudley::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."  
     );  
   
   
140    class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >    class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
141        ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())        ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())
142        .def(init<const dudley::MeshAdapter&>())        .def(init<const dudley::MeshAdapter&>())
# Line 192  BOOST_PYTHON_MODULE(dudleycpp) Line 155  BOOST_PYTHON_MODULE(dudleycpp)
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",&dudley::MeshAdapter::addPDEToSystem,        .def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
158  args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y"),  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"
161  ":param A:\n:type A: `Data`\n"  ":param A:\n:type A: `Data`\n"
# Line 202  args("mat", "rhs","A", "B", "C", "D", "X Line 165  args("mat", "rhs","A", "B", "C", "D", "X
165  ":param X:\n:type X: `Data`\n"  ":param X:\n:type X: `Data`\n"
166  ":param Y:\n:type Y: `Data`\n"  ":param Y:\n:type Y: `Data`\n"
167  ":param d:\n:type d: `Data`\n"  ":param d:\n:type d: `Data`\n"
168    ":param d_contact:\n:type d_contact: `Data`\n"
169    ":param y_contact:\n:type y_contact: `Data`\n"
170  )  )
171        .def("addPDEToLumpedSystem",&dudley::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    ":param useHRZ:\n:type useHRZ: bool\n"
178    )
179        .def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,        .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"
# Line 253  args("theta", "blocksize", "functionspac Line 220  args("theta", "blocksize", "functionspac
220  )  )
221        .def("getSystemMatrixTypeId",&dudley::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"
# Line 262  args("solver", "preconditioner", "packag Line 229  args("solver", "preconditioner", "packag
229  )  )
230        .def("getTransportTypeId",&dudley::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"
# Line 278  args("arg"), "assigns new location to th Line 245  args("arg"), "assigns new location to th
245  ":rtype: `Data`")  ":rtype: `Data`")
246        .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"        .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
247  ":rtype: `Data`")  ":rtype: `Data`")
       .def("saveDX",&dudley::MeshAdapter::saveDX,args("filename" ,"arg"),  
 "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",&dudley::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"  
 )  
248        .def("setTagMap",&dudley::MeshAdapter::setTagMap,args("name","tag"),        .def("setTagMap",&dudley::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")
# Line 303  args("filename" ,"arg",  "metadata", "me Line 258  args("filename" ,"arg",  "metadata", "me
258        .def("MPIBarrier",&dudley::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",&dudley::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_<dudley::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",&dudley::SystemMatrixAdapter::Print_Matrix_Info,(arg("full")=false),"prints information about a system matrix")  
       .def("nullifyRowsAndCols",&dudley::SystemMatrixAdapter::nullifyRowsAndCols)  
       .def("resetValues",&dudley::SystemMatrixAdapter::resetValues, "resets the matrix entries")  
       .def("saveMM",&dudley::SystemMatrixAdapter::saveMM,args("fileName"),  
 "writes the matrix to a file using the Matrix Market file format")  
       .def("saveHB",&dudley::SystemMatrixAdapter::saveHB, args("filename"),  
 "writes the matrix to a file using the Harwell-Boeing file format");  
   
   class_<dudley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >  
       ("TransportProblemAdapter","",no_init)  
       .def("getSafeTimeStepSize",&dudley::TransportProblemAdapter::getSafeTimeStepSize)  
       .def("getUnlimitedTimeStepSize",&dudley::TransportProblemAdapter::getUnlimitedTimeStepSize)  
       .def("resetTransport",&dudley::TransportProblemAdapter::resetTransport,  
 "resets the transport operator typically as they have been updated");  
261  }  }

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