/[escript]/branches/diaplayground/finley/src/CPPAdapter/finleycpp.cpp
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Revision 5136 - (hide annotations)
Tue Sep 9 07:13:55 2014 UTC (4 years, 6 months ago) by caltinay
File size: 16837 byte(s)
ripley now supports paso solvers again and returns an appropriate matrix type
id. Changed the getSystemMatrixTypeId() method to take a full SolverBuddy
instance and made some other simplifications.

1 jgs 102
2 jfenwick 3981 /*****************************************************************************
3 ksteube 1811 *
4 jfenwick 4657 * Copyright (c) 2003-2014 by University of Queensland
5 jfenwick 3981 * http://www.uq.edu.au
6 ksteube 1811 *
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 jfenwick 3981 * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12 jfenwick 4657 * Development 2012-2013 by School of Earth Sciences
13     * Development from 2014 by Centre for Geoscience Computing (GeoComp)
14 jfenwick 3981 *
15     *****************************************************************************/
16 ksteube 1312
17 ksteube 1811
18 jfenwick 3259 #ifdef ESYS_MPI
19     #include "esysUtils/Esys_MPI.h"
20 ksteube 817 #endif
21 robwdcock 682 #include "../Finley.h"
22 jgs 472
23 jfenwick 3675 #include <pasowrap/SystemMatrixAdapter.h>
24     #include <pasowrap/TransportProblemAdapter.h>
25    
26    
27 jgs 203 #include "MeshAdapter.h"
28     #include "MeshAdapterFactory.h"
29 jfenwick 3675 // #include "SystemMatrixAdapter.h"
30     // #include "TransportProblemAdapter.h"
31 jgs 102
32 gross 727 #include "FinleyAdapterException.h"
33     // #include "esysUtils/EsysException.h"
34 robwdcock 682 #include "esysUtils/esysExceptionTranslator.h"
35 jgs 102
36 robwdcock 682 #include "escript/AbstractContinuousDomain.h"
37 jgs 102
38     #include <boost/python.hpp>
39     #include <boost/python/module.hpp>
40     #include <boost/python/def.hpp>
41     #include <boost/python/detail/defaults_gen.hpp>
42 jfenwick 2064 #include <boost/version.hpp>
43 jgs 102
44     using namespace boost::python;
45    
46     //
47     // The BOOST_PYTHON_FUNCTION_OVERLOADS macro generates function overloads for optional
48     // arguments to the respective finley functions.
49     // !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
50     //
51     // NOTE: If the number of arguments to the finley functions change
52     // the magic numbers in the BOOST_PYTHON_FUNCTION_OVERLOADS call
53     // must change.
54     //
55     // !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
56     // BOOST_PYTHON_FUNCTION_OVERLOADS(readMesh_overloads,finley::readMesh,1,2)
57     // BOOST_PYTHON_FUNCTION_OVERLOADS(brick_overloads,finley::brick,0,12)
58     // BOOST_PYTHON_FUNCTION_OVERLOADS(rectangle_overloads,finley::rectangle,0,9)
59     // BOOST_PYTHON_FUNCTION_OVERLOADS(interval_overloads,finley::interval,0,6)
60     // BOOST_PYTHON_FUNCTION_OVERLOADS(glueFaces_overloads,finley::glueFaces,1,3)
61     // BOOST_PYTHON_FUNCTION_OVERLOADS(joinFaces_overloads,finley::joinFaces,1,3)
62    
63     BOOST_PYTHON_MODULE(finleycpp)
64     {
65 jfenwick 2064 // This feature was added in boost v1.34
66 phornby 2076 #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
67 jfenwick 2061 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
68     docstring_options docopt(true, true, false);
69 jfenwick 2064 #endif
70 jgs 102
71 jfenwick 3994 scope().attr("__doc__") = "To use this module, please import esys.finley";
72    
73    
74 jgs 102 //
75     // NOTE: The return_value_policy is necessary for functions that
76     // return pointers.
77 gross 1382 //
78 sshaw 4821 register_exception_translator<finley::FinleyAdapterException>(&(esysUtils::RuntimeErrorTranslator));
79 jgs 102
80 ksteube 1345 def("LoadMesh",finley::loadMesh,
81 jfenwick 2625 (arg("fileName")="file.nc"),":rtype: `Domain`"
82 jfenwick 1872 /* ,return_value_policy<manage_new_object>());*/
83     );
84    
85 caltinay 4949
86     def("__ReadMesh_driver", finley::readMesh_driver,
87     (arg("params"))
88     // def("ReadMesh",finley::readMesh,
89     // (arg("fileName")="file.fly",arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)
90 jfenwick 2625 ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
91     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
92     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
93     ":type integrationOrder: ``int``\n"
94     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
95     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
96 jgs 102
97 caltinay 4949 def("__ReadGmsh_driver", finley::readGmsh_driver,
98     (arg("params"))
99     // def("ReadGmsh",finley::readGmsh,
100     // (arg("fileName")="file.msh",
101     // arg("numDim"),
102     // arg("integrationOrder")=-1,
103     // arg("reducedIntegrationOrder")=-1,
104     // arg("optimize")=true,
105     // arg("useMacroElements")=false)
106 jfenwick 2625 ,"Read a gmsh mesh file\n\n"
107     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
108     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
109     ":type integrationOrder: ``int``\n"
110     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
111 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``\n"
112     ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
113     );
114 gross 934
115 jfenwick 3558 def ("__Brick_driver",finley::brick_driver,
116     (arg("params"))
117 jfenwick 2625 ,"Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2]."
118     "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
119 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
120 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n:param l2:\n"
121     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
122     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
123     ":param useElementsOnFace: whether or not to use elements on face\n"
124     ":type useElementsOnFace: ``int``"
125     ":param periodic0: whether or not boundary conditions are periodic\n"
126     ":param periodic1:\n:param periodic2:\n"
127     ":param useFullElementOrder:\n:param optimize:\n"
128 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
129 jfenwick 2625 );
130 jgs 102
131 jfenwick 3558 def ("__Rectangle_driver",finley::rectangle_driver,
132     (arg("args"))
133 jfenwick 1872 // ,return_value_policy<manage_new_object>());
134 jfenwick 2625 ,"Creates a rectangular mesh with n0 x n1 elements over the brick [0,l0] x [0,l1]."
135     "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
136 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
137 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n"
138     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
139     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
140     ":param useElementsOnFace: whether or not to use elements on face\n"
141     ":type useElementsOnFace: ``int``"
142     ":param periodic0: whether or not boundary conditions are periodic\n"
143     ":param periodic1:\n"
144 gross 2722 ":param useFullElementOrder:\n:param optimize:\n"
145     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
146     );
147 jgs 102
148 jfenwick 2625 def("Merge",finley::meshMerge,args("meshList")
149 jfenwick 1872 // ,return_value_policy<manage_new_object>());
150 jfenwick 2625 ,"Merges a list of meshes into one mesh.\n\n:rtype: `Domain`"
151 jfenwick 1872 );
152 jgs 110
153 jgs 102 def("GlueFaces",finley::glueFaces,
154 jfenwick 2625 (arg("meshList"),arg("safetyFactor")=0.2,
155 gross 1062 arg("tolerance")=1.e-8,
156 jfenwick 1872 arg("optimize")=true)
157     // ,return_value_policy<manage_new_object>());
158 jfenwick 2625 ,"Detects matching faces in the mesh, removes them from the mesh and joins the elements touched by the face elements."
159 jfenwick 1872 );
160 jgs 102
161     def("JoinFaces",finley::joinFaces,
162 jfenwick 2625 (arg("meshList"), arg("safetyFactor")=0.2,
163 gross 1062 arg("tolerance")=1.e-8,
164 jfenwick 1872 arg("optimize")=true)
165     // ,return_value_policy<manage_new_object>());
166 jfenwick 2625 ,"Detects matching faces in the mesh and replaces them by joint elements."
167 jfenwick 1872 );
168 jgs 102
169    
170     class_<finley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
171 caltinay 4496 ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <finley::Mesh*> >())
172 jgs 102 .def(init<const finley::MeshAdapter&>())
173 jfenwick 2625 .def("write",&finley::MeshAdapter::write,args("filename"),
174     "Write the current mesh to a file with the given name.")
175     .def("print_mesh_info",&finley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
176     ":param full:\n:type full: ``bool``")
177     .def("dump",&finley::MeshAdapter::dump,args("fileName")
178     ,"dumps the mesh to a file with the given name.")
179     .def("getDescription",&finley::MeshAdapter::getDescription,
180     ":return: a description for this domain\n:rtype: ``string``")
181     .def("getDim",&finley::MeshAdapter::getDim,":rtype: ``int``")
182     .def("getDataShape",&finley::MeshAdapter::getDataShape, args("functionSpaceCode"),
183     ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
184     .def("getNumDataPointsGlobal",&finley::MeshAdapter::getNumDataPointsGlobal,
185     ":return: the number of data points summed across all MPI processes\n"
186     ":rtype: ``int``")
187     .def("addPDEToSystem",&finley::MeshAdapter::addPDEToSystem,
188     args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
189     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
190     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
191     ":param A:\n:type A: `Data`\n"
192     ":param B:\n:type B: `Data`\n"
193     ":param C:\n:type C: `Data`\n"
194     ":param D:\n:type D: `Data`\n"
195     ":param X:\n:type X: `Data`\n"
196     ":param Y:\n:type Y: `Data`\n"
197     ":param d:\n:type d: `Data`\n"
198     ":param d_contact:\n:type d_contact: `Data`\n"
199     ":param y_contact:\n:type y_contact: `Data`\n"
200     )
201     .def("addPDEToLumpedSystem",&finley::MeshAdapter::addPDEToLumpedSystem,
202     args("mat", "D", "d"),
203     "adds a PDE onto the lumped stiffness matrix\n\n"
204     ":param mat:\n:type mat: `Data`\n"
205     ":param D:\n:type D: `Data`\n"
206 gross 3379 ":param d:\n:type d: `Data`\n"
207     ":param useHRZ:\n:type useHRZ: bool\n")
208 jfenwick 2625 .def("addPDEToRHS",&finley::MeshAdapter::addPDEToRHS,
209     args("rhs", "X", "Y", "y", "y_contact"),
210     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
211     ":param rhs:\n:type rhs: `Data`\n"
212     ":param X:\n:type X: `Data`\n"
213     ":param Y:\n:type Y: `Data`\n"
214     ":param y:\n:type y: `Data`\n"
215     ":param y_contact:\n:type y_contact: `Data`"
216     )
217     .def("addPDEToTransportProblem",&finley::MeshAdapter::addPDEToTransportProblem,
218     args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
219     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
220     ":param source:\n:type source: `Data`\n"
221     ":param M:\n:type M: `Data`\n"
222     ":param A:\n:type A: `Data`\n"
223     ":param B:\n:type B: `Data`\n"
224     ":param C:\n:type C: `Data`\n"
225     ":param D:\n:type D: `Data`\n"
226     ":param X:\n:type X: `Data`\n"
227     ":param Y:\n:type Y: `Data`\n"
228     ":param d:\n:type d: `Data`\n"
229     ":param y:\n:type y: `Data`\n"
230     ":param d_contact:\n:type d_contact: `Data`\n"
231     ":param y_contact:\n:type y_contact: `Data`\n"
232     )
233     .def("newOperator",&finley::MeshAdapter::newSystemMatrix,
234     args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
235     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
236     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
237     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
238     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
239     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
240     ":param type:\n:type type: ``int``\n"
241     )
242     .def("newTransportProblem",&finley::MeshAdapter::newTransportProblem,
243     args("theta", "blocksize", "functionspace", "type"),
244     "creates a TransportProblemAdapter\n\n"
245     ":param theta:\n:type theta: ``float``\n"
246     ":param blocksize:\n:type blocksize: ``int``\n"
247     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
248     ":param type:\n:type type: ``int``\n"
249     )
250     .def("getSystemMatrixTypeId",&finley::MeshAdapter::getSystemMatrixTypeId,
251 caltinay 5136 args("options"),
252     ":return: the identifier of the matrix type to be used for the global stiffness matrix when particular solver options are used.\n"
253 jfenwick 2625 ":rtype: ``int``\n"
254 caltinay 5136 ":param options:\n:type options: `SolverBuddy`\n"
255 jfenwick 2625 )
256     .def("getTransportTypeId",&finley::MeshAdapter::getTransportTypeId,
257     args("solver", "preconditioner", "package", "symmetry"),
258 caltinay 4286 ":return: the identifier of the transport problem type to be used when a particular solver, preconditioner, package and symmetric matrix is used.\n"
259 jfenwick 2625 ":rtype: ``int``\n"
260     ":param solver:\n:type solver: ``int``\n"
261     ":param preconditioner:\n:type preconditioner: ``int``\n"
262     ":param package:\n:type package: ``int``\n"
263     ":param symmetry:\n:type symmetry: ``int``\n"
264     )
265     .def("setX",&finley::MeshAdapter::setNewX,
266     args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
267     .def("getX",&finley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
268     ":rtype: `Data`")
269     .def("getNormal",&finley::MeshAdapter::getNormal,
270     ":return: boundary normals at the quadrature point on the face elements\n"
271     ":rtype: `Data`")
272     .def("getSize",&finley::MeshAdapter::getSize,":return: the element size\n"
273     ":rtype: `Data`")
274     .def("setTagMap",&finley::MeshAdapter::setTagMap,args("name","tag"),
275     "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
276     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
277     .def("getTag",&finley::MeshAdapter::getTag,args("name"),":return: tag id for "
278     "``name``\n:rtype: ``string``")
279     .def("isValidTagName",&finley::MeshAdapter::isValidTagName,args("name"),
280     ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
281     .def("showTagNames",&finley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
282     .def("getMPISize",&finley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
283     .def("getMPIRank",&finley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
284     .def("MPIBarrier",&finley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
285 gross 3515 .def("onMasterProcessor",&finley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")
286 jfenwick 3558 // .def("addDiracPoints", &finley::MeshAdapter::addDiracPoints,(arg("points"), arg("tags")=finley::EmptyPythonList),
287     // "adds points to support more Dirac delta function.\n\n"
288     // ":param points: list of points where Dirac delta function are to be defined. The location will be adjusted to\n"
289     // " to match the nearest node of the finite element mesh.\n:type points: ``list`` of ``list``s of ``floats``\n"
290     // ":param tags: list of tags to be assigned to the points.\n:type tags: ``list`` of ``int``s or ``strings``\n"
291     // )
292     // .def("addDiracPoint", &finley::MeshAdapter::addDiracPoint,(arg("point"), arg("tag")=-1),
293     // "adds a point to support more Dirac delta function.\n\n"
294     // ":param point: point where Dirac delta function are to be defined. The location will be adjusted to\n"
295     // " to match the nearest node of the finite element mesh.\n:type point: ``list`` of ``floats``\n"
296     // ":param tags: tag to be assigned to the point.\n:type tag: ``int``s or ``strings``\n"
297     // )
298     // .def("addDiracPoint", &finley::MeshAdapter::addDiracPointWithTagName,(arg("point"), arg("tag")),
299     // "adds a point to support more Dirac delta function.\n\n"
300     // ":param point: point where Dirac delta function are to be defined. The location will be adjusted to\n"
301     // " to match the nearest node of the finite element mesh.\n:type point: ``list`` of ``floats``\n"
302     // ":param tags: tag to be assigned to the point.\n:type tag: ``int``s or ``strings``\n"
303     // )
304 gross 3515 ;
305 jgs 102
306 jfenwick 3675 // class_<finley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >
307     // ("OperatorAdapter","A concrete class representing an operator. For more details, please see the c++ documentation.", no_init)
308     // .def("print_matrix_info",&finley::SystemMatrixAdapter::Print_Matrix_Info,(arg("full")=false),"prints information about a system matrix")
309     // .def("nullifyRowsAndCols",&finley::SystemMatrixAdapter::nullifyRowsAndCols)
310     // .def("resetValues",&finley::SystemMatrixAdapter::resetValues, "resets the matrix entries")
311     // .def("saveMM",&finley::SystemMatrixAdapter::saveMM,args("fileName"),
312     // "writes the matrix to a file using the Matrix Market file format")
313     // .def("saveHB",&finley::SystemMatrixAdapter::saveHB, args("filename"),
314     // "writes the matrix to a file using the Harwell-Boeing file format");
315     //
316     // class_<finley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >
317     // ("TransportProblemAdapter","",no_init)
318     // .def("getSafeTimeStepSize",&finley::TransportProblemAdapter::getSafeTimeStepSize)
319     // .def("getUnlimitedTimeStepSize",&finley::TransportProblemAdapter::getUnlimitedTimeStepSize)
320     // .def("resetTransport",&finley::TransportProblemAdapter::resetTransport,
321     // "resets the transport operator typically as they have been updated");
322 jgs 102 }

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