/[escript]/trunk/finley/src/CPPAdapter/finleycpp.cpp
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Contents of /trunk/finley/src/CPPAdapter/finleycpp.cpp

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Revision 3991 - (show annotations)
Tue Sep 25 23:52:22 2012 UTC (7 years ago) by caltinay
File size: 17530 byte(s)
Updated doxygen cfg file and made a few first changes to doco.

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" {
21 #include "../Finley.h"
22 }
23
24 #include <pasowrap/SystemMatrixAdapter.h>
25 #include <pasowrap/TransportProblemAdapter.h>
26
27
28 #include "MeshAdapter.h"
29 #include "MeshAdapterFactory.h"
30 // #include "SystemMatrixAdapter.h"
31 // #include "TransportProblemAdapter.h"
32
33 #include "FinleyAdapterException.h"
34 // #include "esysUtils/EsysException.h"
35 #include "esysUtils/esysExceptionTranslator.h"
36
37 #include "escript/AbstractContinuousDomain.h"
38
39 #include <boost/python.hpp>
40 #include <boost/python/module.hpp>
41 #include <boost/python/def.hpp>
42 #include <boost/python/detail/defaults_gen.hpp>
43 #include <boost/version.hpp>
44
45 using namespace boost::python;
46
47 //
48 // The BOOST_PYTHON_FUNCTION_OVERLOADS macro generates function overloads for optional
49 // arguments to the respective finley functions.
50 // !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
51 //
52 // NOTE: If the number of arguments to the finley functions change
53 // the magic numbers in the BOOST_PYTHON_FUNCTION_OVERLOADS call
54 // must change.
55 //
56 // !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
57 // BOOST_PYTHON_FUNCTION_OVERLOADS(readMesh_overloads,finley::readMesh,1,2)
58 // BOOST_PYTHON_FUNCTION_OVERLOADS(brick_overloads,finley::brick,0,12)
59 // BOOST_PYTHON_FUNCTION_OVERLOADS(rectangle_overloads,finley::rectangle,0,9)
60 // BOOST_PYTHON_FUNCTION_OVERLOADS(interval_overloads,finley::interval,0,6)
61 // BOOST_PYTHON_FUNCTION_OVERLOADS(glueFaces_overloads,finley::glueFaces,1,3)
62 // BOOST_PYTHON_FUNCTION_OVERLOADS(joinFaces_overloads,finley::joinFaces,1,3)
63
64 BOOST_PYTHON_MODULE(finleycpp)
65 {
66 // This feature was added in boost v1.34
67 #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
68 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
69 docstring_options docopt(true, true, false);
70 #endif
71
72 //
73 // NOTE: The return_value_policy is necessary for functions that
74 // return pointers.
75 //
76 register_exception_translator<finley::FinleyAdapterException>(&(esysUtils::esysExceptionTranslator));
77
78 def("LoadMesh",finley::loadMesh,
79 (arg("fileName")="file.nc"),":rtype: `Domain`"
80 /* ,return_value_policy<manage_new_object>());*/
81 );
82
83 def("ReadMesh",finley::readMesh,
84 (arg("fileName")="file.fly",arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)
85 /* ,return_value_policy<manage_new_object>());*/
86 ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
87 ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
88 ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
89 ":type integrationOrder: ``int``\n"
90 ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
91 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
92
93 def("ReadGmsh",finley::readGmsh,
94 (arg("fileName")="file.msh",
95 arg("numDim"),
96 arg("integrationOrder")=-1,
97 arg("reducedIntegrationOrder")=-1,
98 arg("optimize")=true,
99 arg("useMacroElements")=false)
100 // ,return_value_policy<manage_new_object>());
101 ,"Read a gmsh mesh file\n\n"
102 ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
103 ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
104 ":type integrationOrder: ``int``\n"
105 ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
106 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``\n"
107 ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
108 );
109
110 def ("__Brick_driver",finley::brick_driver,
111 (arg("params"))
112 ,"Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2]."
113 "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
114 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
115 ":param l0: length of side 0\n:param l1:\n:param l2:\n"
116 ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
117 ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
118 ":param useElementsOnFace: whether or not to use elements on face\n"
119 ":type useElementsOnFace: ``int``"
120 ":param periodic0: whether or not boundary conditions are periodic\n"
121 ":param periodic1:\n:param periodic2:\n"
122 ":param useFullElementOrder:\n:param optimize:\n"
123 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
124 );
125
126 def ("__Rectangle_driver",finley::rectangle_driver,
127 (arg("args"))
128 // ,return_value_policy<manage_new_object>());
129 ,"Creates a rectangular mesh with n0 x n1 elements over the brick [0,l0] x [0,l1]."
130 "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
131 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
132 ":param l0: length of side 0\n:param l1:\n"
133 ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
134 ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
135 ":param useElementsOnFace: whether or not to use elements on face\n"
136 ":type useElementsOnFace: ``int``"
137 ":param periodic0: whether or not boundary conditions are periodic\n"
138 ":param periodic1:\n"
139 ":param useFullElementOrder:\n:param optimize:\n"
140 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
141 );
142
143 def("Merge",finley::meshMerge,args("meshList")
144 // ,return_value_policy<manage_new_object>());
145 ,"Merges a list of meshes into one mesh.\n\n:rtype: `Domain`"
146 );
147
148 def("GlueFaces",finley::glueFaces,
149 (arg("meshList"),arg("safetyFactor")=0.2,
150 arg("tolerance")=1.e-8,
151 arg("optimize")=true)
152 // ,return_value_policy<manage_new_object>());
153 ,"Detects matching faces in the mesh, removes them from the mesh and joins the elements touched by the face elements."
154 );
155
156 def("JoinFaces",finley::joinFaces,
157 (arg("meshList"), arg("safetyFactor")=0.2,
158 arg("tolerance")=1.e-8,
159 arg("optimize")=true)
160 // ,return_value_policy<manage_new_object>());
161 ,"Detects matching faces in the mesh and replaces them by joint elements."
162 );
163
164
165 class_<finley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
166 ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Finley_Mesh*> >())
167 .def(init<const finley::MeshAdapter&>())
168 .def("write",&finley::MeshAdapter::write,args("filename"),
169 "Write the current mesh to a file with the given name.")
170 .def("print_mesh_info",&finley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
171 ":param full:\n:type full: ``bool``")
172 .def("dump",&finley::MeshAdapter::dump,args("fileName")
173 ,"dumps the mesh to a file with the given name.")
174 .def("getDescription",&finley::MeshAdapter::getDescription,
175 ":return: a description for this domain\n:rtype: ``string``")
176 .def("getDim",&finley::MeshAdapter::getDim,":rtype: ``int``")
177 .def("getDataShape",&finley::MeshAdapter::getDataShape, args("functionSpaceCode"),
178 ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
179 .def("getNumDataPointsGlobal",&finley::MeshAdapter::getNumDataPointsGlobal,
180 ":return: the number of data points summed across all MPI processes\n"
181 ":rtype: ``int``")
182 .def("addPDEToSystem",&finley::MeshAdapter::addPDEToSystem,
183 args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
184 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
185 ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
186 ":param A:\n:type A: `Data`\n"
187 ":param B:\n:type B: `Data`\n"
188 ":param C:\n:type C: `Data`\n"
189 ":param D:\n:type D: `Data`\n"
190 ":param X:\n:type X: `Data`\n"
191 ":param Y:\n:type Y: `Data`\n"
192 ":param d:\n:type d: `Data`\n"
193 ":param d_contact:\n:type d_contact: `Data`\n"
194 ":param y_contact:\n:type y_contact: `Data`\n"
195 )
196 .def("addPDEToLumpedSystem",&finley::MeshAdapter::addPDEToLumpedSystem,
197 args("mat", "D", "d"),
198 "adds a PDE onto the lumped stiffness matrix\n\n"
199 ":param mat:\n:type mat: `Data`\n"
200 ":param D:\n:type D: `Data`\n"
201 ":param d:\n:type d: `Data`\n"
202 ":param useHRZ:\n:type useHRZ: bool\n")
203 .def("addPDEToRHS",&finley::MeshAdapter::addPDEToRHS,
204 args("rhs", "X", "Y", "y", "y_contact"),
205 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
206 ":param rhs:\n:type rhs: `Data`\n"
207 ":param X:\n:type X: `Data`\n"
208 ":param Y:\n:type Y: `Data`\n"
209 ":param y:\n:type y: `Data`\n"
210 ":param y_contact:\n:type y_contact: `Data`"
211 )
212 .def("addPDEToTransportProblem",&finley::MeshAdapter::addPDEToTransportProblem,
213 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
214 ":param tp:\n:type tp: `TransportProblemAdapter`\n"
215 ":param source:\n:type source: `Data`\n"
216 ":param M:\n:type M: `Data`\n"
217 ":param A:\n:type A: `Data`\n"
218 ":param B:\n:type B: `Data`\n"
219 ":param C:\n:type C: `Data`\n"
220 ":param D:\n:type D: `Data`\n"
221 ":param X:\n:type X: `Data`\n"
222 ":param Y:\n:type Y: `Data`\n"
223 ":param d:\n:type d: `Data`\n"
224 ":param y:\n:type y: `Data`\n"
225 ":param d_contact:\n:type d_contact: `Data`\n"
226 ":param y_contact:\n:type y_contact: `Data`\n"
227 )
228 .def("newOperator",&finley::MeshAdapter::newSystemMatrix,
229 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
230 "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
231 ":param row_blocksize:\n:type row_blocksize: ``int``\n"
232 ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
233 ":param column_blocksize:\n:type column_blocksize: ``int``\n"
234 ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
235 ":param type:\n:type type: ``int``\n"
236 )
237 .def("newTransportProblem",&finley::MeshAdapter::newTransportProblem,
238 args("theta", "blocksize", "functionspace", "type"),
239 "creates a TransportProblemAdapter\n\n"
240 ":param theta:\n:type theta: ``float``\n"
241 ":param blocksize:\n:type blocksize: ``int``\n"
242 ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
243 ":param type:\n:type type: ``int``\n"
244 )
245 .def("getSystemMatrixTypeId",&finley::MeshAdapter::getSystemMatrixTypeId,
246 args("solver", "preconditioner", "package", "symmetry"),
247 ":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"
248 ":rtype: ``int``\n"
249 ":param solver:\n:type solver: ``int``\n"
250 ":param preconditioner:\n:type preconditioner: ``int``\n"
251 ":param package:\n:type package: ``int``\n"
252 ":param symmetry:\n:type symmetry: ``int``\n"
253 )
254 .def("getTransportTypeId",&finley::MeshAdapter::getTransportTypeId,
255 args("solver", "preconditioner", "package", "symmetry"),
256 ":return: the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.\n"
257 ":rtype: ``int``\n"
258 ":param solver:\n:type solver: ``int``\n"
259 ":param preconditioner:\n:type preconditioner: ``int``\n"
260 ":param package:\n:type package: ``int``\n"
261 ":param symmetry:\n:type symmetry: ``int``\n"
262 )
263 .def("setX",&finley::MeshAdapter::setNewX,
264 args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
265 .def("getX",&finley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
266 ":rtype: `Data`")
267 .def("getNormal",&finley::MeshAdapter::getNormal,
268 ":return: boundary normals at the quadrature point on the face elements\n"
269 ":rtype: `Data`")
270 .def("getSize",&finley::MeshAdapter::getSize,":return: the element size\n"
271 ":rtype: `Data`")
272 .def("saveDX",&finley::MeshAdapter::saveDX,args("filename" ,"arg"),
273 "Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier"
274 "\n\n:param filename: \n:type filename: ``string``\n"
275 "\n:param arg: \n:type arg: ``dict``\n")
276 .def("saveVTK",&finley::MeshAdapter::saveVTK,
277 args("filename" ,"arg", "metadata", "metadata_schema"),
278 "Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier"
279 "\n\n:param filename:\n:type filename: ``string``\n"
280 ":param arg:\n:type arg: ``dict``\n"
281 ":param metadata:\n:type metadata: ``string``\n"
282 ":param metadata_schema:\n:type metadata_schema: ``string``\n"
283 )
284 .def("setTagMap",&finley::MeshAdapter::setTagMap,args("name","tag"),
285 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
286 ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
287 .def("getTag",&finley::MeshAdapter::getTag,args("name"),":return: tag id for "
288 "``name``\n:rtype: ``string``")
289 .def("isValidTagName",&finley::MeshAdapter::isValidTagName,args("name"),
290 ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
291 .def("showTagNames",&finley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
292 .def("getMPISize",&finley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
293 .def("getMPIRank",&finley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
294 .def("MPIBarrier",&finley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
295 .def("onMasterProcessor",&finley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")
296 // .def("addDiracPoints", &finley::MeshAdapter::addDiracPoints,(arg("points"), arg("tags")=finley::EmptyPythonList),
297 // "adds points to support more Dirac delta function.\n\n"
298 // ":param points: list of points where Dirac delta function are to be defined. The location will be adjusted to\n"
299 // " to match the nearest node of the finite element mesh.\n:type points: ``list`` of ``list``s of ``floats``\n"
300 // ":param tags: list of tags to be assigned to the points.\n:type tags: ``list`` of ``int``s or ``strings``\n"
301 // )
302 // .def("addDiracPoint", &finley::MeshAdapter::addDiracPoint,(arg("point"), arg("tag")=-1),
303 // "adds a point to support more Dirac delta function.\n\n"
304 // ":param point: point where Dirac delta function are to be defined. The location will be adjusted to\n"
305 // " to match the nearest node of the finite element mesh.\n:type point: ``list`` of ``floats``\n"
306 // ":param tags: tag to be assigned to the point.\n:type tag: ``int``s or ``strings``\n"
307 // )
308 // .def("addDiracPoint", &finley::MeshAdapter::addDiracPointWithTagName,(arg("point"), arg("tag")),
309 // "adds a point to support more Dirac delta function.\n\n"
310 // ":param point: point where Dirac delta function are to be defined. The location will be adjusted to\n"
311 // " to match the nearest node of the finite element mesh.\n:type point: ``list`` of ``floats``\n"
312 // ":param tags: tag to be assigned to the point.\n:type tag: ``int``s or ``strings``\n"
313 // )
314 ;
315
316 // class_<finley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >
317 // ("OperatorAdapter","A concrete class representing an operator. For more details, please see the c++ documentation.", no_init)
318 // .def("print_matrix_info",&finley::SystemMatrixAdapter::Print_Matrix_Info,(arg("full")=false),"prints information about a system matrix")
319 // .def("nullifyRowsAndCols",&finley::SystemMatrixAdapter::nullifyRowsAndCols)
320 // .def("resetValues",&finley::SystemMatrixAdapter::resetValues, "resets the matrix entries")
321 // .def("saveMM",&finley::SystemMatrixAdapter::saveMM,args("fileName"),
322 // "writes the matrix to a file using the Matrix Market file format")
323 // .def("saveHB",&finley::SystemMatrixAdapter::saveHB, args("filename"),
324 // "writes the matrix to a file using the Harwell-Boeing file format");
325 //
326 // class_<finley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >
327 // ("TransportProblemAdapter","",no_init)
328 // .def("getSafeTimeStepSize",&finley::TransportProblemAdapter::getSafeTimeStepSize)
329 // .def("getUnlimitedTimeStepSize",&finley::TransportProblemAdapter::getUnlimitedTimeStepSize)
330 // .def("resetTransport",&finley::TransportProblemAdapter::resetTransport,
331 // "resets the transport operator typically as they have been updated");
332 }

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