/[escript]/branches/diaplayground/dudley/src/CPPAdapter/dudleycpp.cpp
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trunk/finley/src/CPPAdapter/finleycpp.cpp revision 2064 by jfenwick, Thu Nov 20 04:06:34 2008 UTC branches/diaplayground/dudley/src/CPPAdapter/dudleycpp.cpp revision 5136 by caltinay, Tue Sep 9 07:13:55 2014 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*****************************************************************************
3  *  *
4  * Copyright (c) 2003-2008 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 > 33) || (BOOST_VERSION/100000 >1)  #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
47    // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures    // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
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")        (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"
69    ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
70    def("ReadGmsh",finley::readGmsh,  ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
71        (arg("fileName")="file.msh",arg("numDim"), arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)  ":type integrationOrder: ``int``\n"
72    ":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``");
74    
75      def("ReadGmsh",dudley::readGmsh,
76          (arg("fileName")="file.msh",
77           arg("numDim"),
78           arg("integrationOrder")=-1,
79           arg("reducedIntegrationOrder")=-1,
80           arg("optimize")=true,  
81           arg("useMacroElements")=false)
82  //       ,return_value_policy<manage_new_object>());  //       ,return_value_policy<manage_new_object>());
83      );  ,"Read a gmsh mesh file\n\n"
84    ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
85    def ("Brick",finley::brick,  ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
86    ":type integrationOrder: ``int``\n"
87    ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
88    ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``\n"
89    ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
90    );
91    
92      def ("__Brick_driver",dudley::brick_driver,
93          arg("args"),
94    /*      
95        (arg("n0")=1,arg("n1")=1,arg("n2")=1,        (arg("n0")=1,arg("n1")=1,arg("n2")=1,
96        arg("order")=1,        arg("order")=1,
97        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 115  BOOST_PYTHON_MODULE(finleycpp) Line 100  BOOST_PYTHON_MODULE(finleycpp)
100        arg("useElementsOnFace")=false,        arg("useElementsOnFace")=false,
101        arg("useFullElementOrder")=false,        arg("useFullElementOrder")=false,
102        arg("optimize")=false)        arg("optimize")=false)
103  //       ,return_value_policy<manage_new_object>());  */      
104      );  "Creates a tetrahedral mesh by subdividing n0 x n1 x n2 rectangular elements over the brick [0,l0] x [0,l1] x [0,l2]."
105    "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
106    def ("Rectangle",finley::rectangle,  "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
107    ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
108    ":param l0: length of side 0\n:param l1:\n:param l2:\n"
109    ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
110    ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
111    ":param useElementsOnFace:  whether or not to use elements on face\n"
112    ":type useElementsOnFace: ``int``"
113    ":param periodic0:  whether or not boundary conditions are periodic\n"
114    ":param periodic1:\n:param periodic2:\n"
115    ":param useFullElementOrder:\n:param optimize:\n"
116    ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
117    );
118    
119      def ("__Rectangle_driver",dudley::rectangle_driver,
120          arg("args"),
121    /*      
122        (arg("n0")=1,arg("n1")=1,arg("order")=1,        (arg("n0")=1,arg("n1")=1,arg("order")=1,
123        arg("l0")=1.0,arg("l1")=1.0,        arg("l0")=1.0,arg("l1")=1.0,
124        arg("periodic0")=false,arg("periodic1")=false,        arg("periodic0")=false,arg("periodic1")=false,
# Line 126  BOOST_PYTHON_MODULE(finleycpp) Line 126  BOOST_PYTHON_MODULE(finleycpp)
126        arg("useElementsOnFace")=false,        arg("useElementsOnFace")=false,
127        arg("useFullElementOrder")=false,        arg("useFullElementOrder")=false,
128        arg("optimize")=false)        arg("optimize")=false)
129  //       ,return_value_policy<manage_new_object>());  */      
130      );  "Creates a triangular mesh by subdividing n0 x n1 rectangular elements over the brick [0,l0] x [0,l1]."
131    "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
132    def("Merge",finley::meshMerge  "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
133  //       ,return_value_policy<manage_new_object>());  ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
134    );  ":param l0: length of side 0\n:param l1:\n"
135    ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
136    def("GlueFaces",finley::glueFaces,  ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
137        (arg("safetyFactor")=0.2,  ":param useElementsOnFace:  whether or not to use elements on face\n"
138        arg("tolerance")=1.e-8,  ":type useElementsOnFace: ``int``"
139        arg("optimize")=true)  ":param periodic0:  whether or not boundary conditions are periodic\n"
140  //       ,return_value_policy<manage_new_object>());  ":param periodic1:\n"
141      );  ":param useFullElementOrder:\n:param optimize:\n"
142    ":param useMacroElements: Enable the usage of first order macro elements.\n:type useMacroElements: ``bool``\n"
143    def("JoinFaces",finley::joinFaces,  ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
144        (arg("safetyFactor")=0.2,  );
145        arg("tolerance")=1.e-8,  
146        arg("optimize")=true)    class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
147  //       ,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*> >())
148      );        .def(init<const dudley::MeshAdapter&>())
149          .def("write",&dudley::MeshAdapter::write,args("filename"),
150    "Write the current mesh to a file with the given name.")
151          .def("print_mesh_info",&dudley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
152    ":param full:\n:type full: ``bool``")
153          .def("dump",&dudley::MeshAdapter::dump,args("fileName")
154    ,"dumps the mesh to a file with the given name.")
155          .def("getDescription",&dudley::MeshAdapter::getDescription,
156    ":return: a description for this domain\n:rtype: ``string``")
157          .def("getDim",&dudley::MeshAdapter::getDim,":rtype: ``int``")
158          .def("getDataShape",&dudley::MeshAdapter::getDataShape, args("functionSpaceCode"),
159    ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
160          .def("getNumDataPointsGlobal",&dudley::MeshAdapter::getNumDataPointsGlobal,
161    ":return: the number of data points summed across all MPI processes\n"
162    ":rtype: ``int``")
163          .def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
164    args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
165    "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
166    ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
167    ":param A:\n:type A: `Data`\n"
168    ":param B:\n:type B: `Data`\n"
169    ":param C:\n:type C: `Data`\n"
170    ":param D:\n:type D: `Data`\n"
171    ":param X:\n:type X: `Data`\n"
172    ":param Y:\n:type Y: `Data`\n"
173    ":param d:\n:type d: `Data`\n"
174    ":param d_contact:\n:type d_contact: `Data`\n"
175    ":param y_contact:\n:type y_contact: `Data`\n"
176    )
177          .def("addPDEToLumpedSystem",&dudley::MeshAdapter::addPDEToLumpedSystem,
178    args("mat", "D", "d"),
179    "adds a PDE onto the lumped stiffness matrix\n\n"
180    ":param mat:\n:type mat: `Data`\n"
181    ":param D:\n:type D: `Data`\n"
182    ":param d:\n:type d: `Data`\n"
183    ":param useHRZ:\n:type useHRZ: bool\n"
184    )
185          .def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,
186    args("rhs", "X", "Y", "y", "y_contact"),
187    "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
188    ":param rhs:\n:type rhs: `Data`\n"
189    ":param X:\n:type X: `Data`\n"
190    ":param Y:\n:type Y: `Data`\n"
191    ":param y:\n:type y: `Data`\n"
192    ":param y_contact:\n:type y_contact: `Data`"
193    )
194          .def("addPDEToTransportProblem",&dudley::MeshAdapter::addPDEToTransportProblem,
195    args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
196    ":param tp:\n:type tp: `TransportProblemAdapter`\n"
197    ":param source:\n:type source: `Data`\n"
198    ":param M:\n:type M: `Data`\n"
199    ":param A:\n:type A: `Data`\n"
200    ":param B:\n:type B: `Data`\n"
201    ":param C:\n:type C: `Data`\n"
202    ":param D:\n:type D: `Data`\n"
203    ":param X:\n:type X: `Data`\n"
204    ":param Y:\n:type Y: `Data`\n"
205    ":param d:\n:type d: `Data`\n"
206    ":param y:\n:type y: `Data`\n"
207    ":param d_contact:\n:type d_contact: `Data`\n"
208    ":param y_contact:\n:type y_contact: `Data`\n"
209    )
210          .def("newOperator",&dudley::MeshAdapter::newSystemMatrix,
211    args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
212    "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
213    ":param row_blocksize:\n:type row_blocksize: ``int``\n"
214    ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
215    ":param column_blocksize:\n:type column_blocksize: ``int``\n"
216    ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
217    ":param type:\n:type type: ``int``\n"
218    )
219          .def("newTransportProblem",&dudley::MeshAdapter::newTransportProblem,
220    args("theta", "blocksize", "functionspace", "type"),
221    "creates a TransportProblemAdapter\n\n"
222    ":param theta:\n:type theta: ``float``\n"
223    ":param blocksize:\n:type blocksize: ``int``\n"
224    ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
225    ":param type:\n:type type: ``int``\n"
226    )
227          .def("getSystemMatrixTypeId",&dudley::MeshAdapter::getSystemMatrixTypeId,
228    args("options"),
229    ":return: the identifier of the matrix type to be used for the global stiffness matrix when particular solver options are used.\n"
230    ":rtype: ``int``\n"
231    ":param options:\n:type options: `SolverBuddy`\n"
232    )
233          .def("getTransportTypeId",&dudley::MeshAdapter::getTransportTypeId,
234    args("solver", "preconditioner", "package", "symmetry"),
235    ":return: the identifier of the transport problem type to be used when a particular solver, preconditioner, package and symmetric matrix is used.\n"
236    ":rtype: ``int``\n"
237    ":param solver:\n:type solver: ``int``\n"
238    ":param preconditioner:\n:type preconditioner: ``int``\n"
239    ":param package:\n:type package: ``int``\n"
240    ":param symmetry:\n:type symmetry: ``int``\n"
241    )
242          .def("setX",&dudley::MeshAdapter::setNewX,
243    args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
244          .def("getX",&dudley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
245    ":rtype: `Data`")
246          .def("getNormal",&dudley::MeshAdapter::getNormal,
247    ":return: boundary normals at the quadrature point on the face elements\n"
248    ":rtype: `Data`")
249          .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
250    ":rtype: `Data`")
251          .def("setTagMap",&dudley::MeshAdapter::setTagMap,args("name","tag"),
252    "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
253    ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
254          .def("getTag",&dudley::MeshAdapter::getTag,args("name"),":return: tag id for "
255    "``name``\n:rtype: ``string``")
256          .def("isValidTagName",&dudley::MeshAdapter::isValidTagName,args("name"),
257    ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
258          .def("showTagNames",&dudley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
259          .def("getMPISize",&dudley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
260          .def("getMPIRank",&dudley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
261          .def("MPIBarrier",&dudley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
262          .def("onMasterProcessor",&dudley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
263    
   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)  
       .def("print_mesh_info",&finley::MeshAdapter::Print_Mesh_Info,(arg("full")=false))  
       .def("dump",&finley::MeshAdapter::dump)  
       .def("getDescription",&finley::MeshAdapter::getDescription)  
       .def("getDim",&finley::MeshAdapter::getDim)  
       .def("getDataShape",&finley::MeshAdapter::getDataShape)  
       .def("getNumDataPointsGlobal",&finley::MeshAdapter::getNumDataPointsGlobal)  
       .def("addPDEToSystem",&finley::MeshAdapter::addPDEToSystem)  
       .def("addPDEToLumpedSystem",&finley::MeshAdapter::addPDEToLumpedSystem)  
       .def("addPDEToRHS",&finley::MeshAdapter::addPDEToRHS)  
       .def("addPDEToTransportProblem",&finley::MeshAdapter::addPDEToTransportProblem)  
       .def("newOperator",&finley::MeshAdapter::newSystemMatrix)  
       .def("newTransportProblem",&finley::MeshAdapter::newTransportProblem)  
       .def("getSystemMatrixTypeId",&finley::MeshAdapter::getSystemMatrixTypeId)  
       .def("getTransportTypeId",&finley::MeshAdapter::getTransportTypeId)  
       .def("setX",&finley::MeshAdapter::setNewX)  
       .def("getX",&finley::MeshAdapter::getX)  
       .def("getNormal",&finley::MeshAdapter::getNormal)  
       .def("getSize",&finley::MeshAdapter::getSize)  
       .def("saveDX",&finley::MeshAdapter::saveDX)  
       .def("saveVTK",&finley::MeshAdapter::saveVTK)  
       .def("setTagMap",&finley::MeshAdapter::setTagMap)  
       .def("getTag",&finley::MeshAdapter::getTag)  
       .def("isValidTagName",&finley::MeshAdapter::isValidTagName)  
       .def("showTagNames",&finley::MeshAdapter::showTagNames)  
       .def("getMPISize",&finley::MeshAdapter::getMPISize)  
       .def("getMPIRank",&finley::MeshAdapter::getMPIRank)  
       .def("MPIBarrier",&finley::MeshAdapter::MPIBarrier)  
       .def("onMasterProcessor",&finley::MeshAdapter::onMasterProcessor);  
   
   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))  
       .def("nullifyRowsAndCols",&finley::SystemMatrixAdapter::nullifyRowsAndCols)  
       .def("resetValues",&finley::SystemMatrixAdapter::resetValues)  
       .def("saveMM",&finley::SystemMatrixAdapter::saveMM)  
       .def("saveHB",&finley::SystemMatrixAdapter::saveHB);  
   
   class_<finley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >  
       ("TransportProblemAdapter","",no_init)  
       .def("getSafeTimeStepSize",&finley::TransportProblemAdapter::getSafeTimeStepSize)  
       .def("getUnlimitedTimeStepSize",&finley::TransportProblemAdapter::getUnlimitedTimeStepSize)  
       .def("resetTransport",&finley::TransportProblemAdapter::resetTransport);  
264  }  }

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