/[escript]/branches/dirac/finley/src/CPPAdapter/finleycpp.cpp
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Revision 3554 - (hide annotations)
Tue Aug 23 00:23:53 2011 UTC (7 years, 9 months ago) by jfenwick
File size: 18100 byte(s)
First step towards moving dirac

1 jgs 102
2 ksteube 1312 /*******************************************************
3 ksteube 1811 *
4 jfenwick 2881 * Copyright (c) 2003-2010 by University of Queensland
5 ksteube 1811 * Earth Systems Science Computational Center (ESSCC)
6     * http://www.uq.edu.au/esscc
7     *
8     * Primary Business: Queensland, Australia
9     * Licensed under the Open Software License version 3.0
10     * http://www.opensource.org/licenses/osl-3.0.php
11     *
12     *******************************************************/
13 ksteube 1312
14 ksteube 1811
15 jfenwick 3259 #ifdef ESYS_MPI
16     #include "esysUtils/Esys_MPI.h"
17 ksteube 817 #endif
18 jgs 102 extern "C" {
19 robwdcock 682 #include "../Finley.h"
20 jgs 102 }
21 jgs 472
22 jgs 203 #include "MeshAdapter.h"
23     #include "MeshAdapterFactory.h"
24     #include "SystemMatrixAdapter.h"
25 gross 1364 #include "TransportProblemAdapter.h"
26 jgs 102
27 gross 727 #include "FinleyAdapterException.h"
28     // #include "esysUtils/EsysException.h"
29 robwdcock 682 #include "esysUtils/esysExceptionTranslator.h"
30 jgs 102
31 robwdcock 682 #include "escript/AbstractContinuousDomain.h"
32 jgs 102
33     #include <boost/python.hpp>
34     #include <boost/python/module.hpp>
35     #include <boost/python/def.hpp>
36     #include <boost/python/detail/defaults_gen.hpp>
37 jfenwick 2064 #include <boost/version.hpp>
38 jgs 102
39     using namespace boost::python;
40    
41     /**
42 jgs 121 \page finley Finley
43     Finley is the python module name that contains the interfaces
44 jgs 102 to the C++ wrapper to finley.
45    
46 jgs 121 \version 1.0.0
47 jgs 102
48 jgs 121 \section class_desc Class Description:
49 jgs 102 Data
50    
51 jgs 121 \section class_limits Class Limitations:
52 jgs 102 None
53    
54 jgs 121 \section class_conds Class Conditions of Use:
55 jgs 102 None
56    
57 jgs 121 \section throws Throws:
58 jgs 102 None
59    
60     */
61    
62     //
63     // The BOOST_PYTHON_FUNCTION_OVERLOADS macro generates function overloads for optional
64     // arguments to the respective finley functions.
65     // !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
66     //
67     // NOTE: If the number of arguments to the finley functions change
68     // the magic numbers in the BOOST_PYTHON_FUNCTION_OVERLOADS call
69     // must change.
70     //
71     // !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
72     // BOOST_PYTHON_FUNCTION_OVERLOADS(readMesh_overloads,finley::readMesh,1,2)
73     // BOOST_PYTHON_FUNCTION_OVERLOADS(brick_overloads,finley::brick,0,12)
74     // BOOST_PYTHON_FUNCTION_OVERLOADS(rectangle_overloads,finley::rectangle,0,9)
75     // BOOST_PYTHON_FUNCTION_OVERLOADS(interval_overloads,finley::interval,0,6)
76     // BOOST_PYTHON_FUNCTION_OVERLOADS(glueFaces_overloads,finley::glueFaces,1,3)
77     // BOOST_PYTHON_FUNCTION_OVERLOADS(joinFaces_overloads,finley::joinFaces,1,3)
78    
79     BOOST_PYTHON_MODULE(finleycpp)
80     {
81 jfenwick 2064 // This feature was added in boost v1.34
82 phornby 2076 #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
83 jfenwick 2061 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
84     docstring_options docopt(true, true, false);
85 jfenwick 2064 #endif
86 jgs 102
87     //
88     // NOTE: The return_value_policy is necessary for functions that
89     // return pointers.
90 gross 1382 //
91     register_exception_translator<finley::FinleyAdapterException>(&(esysUtils::esysExceptionTranslator));
92 jgs 102
93 ksteube 1345 def("LoadMesh",finley::loadMesh,
94 jfenwick 2625 (arg("fileName")="file.nc"),":rtype: `Domain`"
95 jfenwick 1872 /* ,return_value_policy<manage_new_object>());*/
96     );
97    
98 jgs 102 def("ReadMesh",finley::readMesh,
99 jfenwick 1872 (arg("fileName")="file.fly",arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)
100     /* ,return_value_policy<manage_new_object>());*/
101 jfenwick 2625 ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\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``");
107 jgs 102
108 gross 934 def("ReadGmsh",finley::readGmsh,
109 gross 2722 (arg("fileName")="file.msh",
110     arg("numDim"),
111     arg("integrationOrder")=-1,
112     arg("reducedIntegrationOrder")=-1,
113     arg("optimize")=true,
114     arg("useMacroElements")=false)
115 jfenwick 1872 // ,return_value_policy<manage_new_object>());
116 jfenwick 2625 ,"Read a gmsh mesh file\n\n"
117     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
118     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
119     ":type integrationOrder: ``int``\n"
120     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
121 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``\n"
122     ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
123     );
124 gross 934
125 jfenwick 3554 def ("__Brick_driver",finley::brick_driver,
126     (arg("params"))
127 jfenwick 2625 ,"Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2]."
128     "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
129 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
130 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n:param l2:\n"
131     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
132     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
133     ":param useElementsOnFace: whether or not to use elements on face\n"
134     ":type useElementsOnFace: ``int``"
135     ":param periodic0: whether or not boundary conditions are periodic\n"
136     ":param periodic1:\n:param periodic2:\n"
137     ":param useFullElementOrder:\n:param optimize:\n"
138 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
139 jfenwick 2625 );
140 jgs 102
141 jfenwick 3554 def ("__Rectangle_driver",finley::rectangle,
142 jgs 102 (arg("n0")=1,arg("n1")=1,arg("order")=1,
143     arg("l0")=1.0,arg("l1")=1.0,
144     arg("periodic0")=false,arg("periodic1")=false,
145 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
146 ksteube 1312 arg("useElementsOnFace")=false,
147     arg("useFullElementOrder")=false,
148 jfenwick 3554 arg("optimize")=false,
149     arg("points")=finley::EmptyPythonList,
150     arg("tags")=finley::EmptyPythonList)
151 jfenwick 1872 // ,return_value_policy<manage_new_object>());
152 jfenwick 2625 ,"Creates a rectangular mesh with n0 x n1 elements over the brick [0,l0] x [0,l1]."
153     "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
154 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
155 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n"
156     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
157     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
158     ":param useElementsOnFace: whether or not to use elements on face\n"
159     ":type useElementsOnFace: ``int``"
160     ":param periodic0: whether or not boundary conditions are periodic\n"
161     ":param periodic1:\n"
162 gross 2722 ":param useFullElementOrder:\n:param optimize:\n"
163     ":param useMacroElements: Enable the usage of first order macro elements.\n:type useMacroElements: ``bool``\n"
164     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
165     );
166 jgs 102
167 jfenwick 2625 def("Merge",finley::meshMerge,args("meshList")
168 jfenwick 1872 // ,return_value_policy<manage_new_object>());
169 jfenwick 2625 ,"Merges a list of meshes into one mesh.\n\n:rtype: `Domain`"
170 jfenwick 1872 );
171 jgs 110
172 jgs 102 def("GlueFaces",finley::glueFaces,
173 jfenwick 2625 (arg("meshList"),arg("safetyFactor")=0.2,
174 gross 1062 arg("tolerance")=1.e-8,
175 jfenwick 1872 arg("optimize")=true)
176     // ,return_value_policy<manage_new_object>());
177 jfenwick 2625 ,"Detects matching faces in the mesh, removes them from the mesh and joins the elements touched by the face elements."
178 jfenwick 1872 );
179 jgs 102
180     def("JoinFaces",finley::joinFaces,
181 jfenwick 2625 (arg("meshList"), arg("safetyFactor")=0.2,
182 gross 1062 arg("tolerance")=1.e-8,
183 jfenwick 1872 arg("optimize")=true)
184     // ,return_value_policy<manage_new_object>());
185 jfenwick 2625 ,"Detects matching faces in the mesh and replaces them by joint elements."
186 jfenwick 1872 );
187 jgs 102
188    
189     class_<finley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
190 jfenwick 2061 ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Finley_Mesh*> >())
191 jgs 102 .def(init<const finley::MeshAdapter&>())
192 jfenwick 2625 .def("write",&finley::MeshAdapter::write,args("filename"),
193     "Write the current mesh to a file with the given name.")
194     .def("print_mesh_info",&finley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
195     ":param full:\n:type full: ``bool``")
196     .def("dump",&finley::MeshAdapter::dump,args("fileName")
197     ,"dumps the mesh to a file with the given name.")
198     .def("getDescription",&finley::MeshAdapter::getDescription,
199     ":return: a description for this domain\n:rtype: ``string``")
200     .def("getDim",&finley::MeshAdapter::getDim,":rtype: ``int``")
201     .def("getDataShape",&finley::MeshAdapter::getDataShape, args("functionSpaceCode"),
202     ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
203     .def("getNumDataPointsGlobal",&finley::MeshAdapter::getNumDataPointsGlobal,
204     ":return: the number of data points summed across all MPI processes\n"
205     ":rtype: ``int``")
206     .def("addPDEToSystem",&finley::MeshAdapter::addPDEToSystem,
207     args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
208     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
209     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
210     ":param A:\n:type A: `Data`\n"
211     ":param B:\n:type B: `Data`\n"
212     ":param C:\n:type C: `Data`\n"
213     ":param D:\n:type D: `Data`\n"
214     ":param X:\n:type X: `Data`\n"
215     ":param Y:\n:type Y: `Data`\n"
216     ":param d:\n:type d: `Data`\n"
217     ":param d_contact:\n:type d_contact: `Data`\n"
218     ":param y_contact:\n:type y_contact: `Data`\n"
219     )
220     .def("addPDEToLumpedSystem",&finley::MeshAdapter::addPDEToLumpedSystem,
221     args("mat", "D", "d"),
222     "adds a PDE onto the lumped stiffness matrix\n\n"
223     ":param mat:\n:type mat: `Data`\n"
224     ":param D:\n:type D: `Data`\n"
225 gross 3379 ":param d:\n:type d: `Data`\n"
226     ":param useHRZ:\n:type useHRZ: bool\n")
227 jfenwick 2625 .def("addPDEToRHS",&finley::MeshAdapter::addPDEToRHS,
228     args("rhs", "X", "Y", "y", "y_contact"),
229     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
230     ":param rhs:\n:type rhs: `Data`\n"
231     ":param X:\n:type X: `Data`\n"
232     ":param Y:\n:type Y: `Data`\n"
233     ":param y:\n:type y: `Data`\n"
234     ":param y_contact:\n:type y_contact: `Data`"
235     )
236     .def("addPDEToTransportProblem",&finley::MeshAdapter::addPDEToTransportProblem,
237     args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
238     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
239     ":param source:\n:type source: `Data`\n"
240     ":param M:\n:type M: `Data`\n"
241     ":param A:\n:type A: `Data`\n"
242     ":param B:\n:type B: `Data`\n"
243     ":param C:\n:type C: `Data`\n"
244     ":param D:\n:type D: `Data`\n"
245     ":param X:\n:type X: `Data`\n"
246     ":param Y:\n:type Y: `Data`\n"
247     ":param d:\n:type d: `Data`\n"
248     ":param y:\n:type y: `Data`\n"
249     ":param d_contact:\n:type d_contact: `Data`\n"
250     ":param y_contact:\n:type y_contact: `Data`\n"
251     )
252     .def("newOperator",&finley::MeshAdapter::newSystemMatrix,
253     args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
254     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
255     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
256     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
257     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
258     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
259     ":param type:\n:type type: ``int``\n"
260     )
261     .def("newTransportProblem",&finley::MeshAdapter::newTransportProblem,
262     args("theta", "blocksize", "functionspace", "type"),
263     "creates a TransportProblemAdapter\n\n"
264     ":param theta:\n:type theta: ``float``\n"
265     ":param blocksize:\n:type blocksize: ``int``\n"
266     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
267     ":param type:\n:type type: ``int``\n"
268     )
269     .def("getSystemMatrixTypeId",&finley::MeshAdapter::getSystemMatrixTypeId,
270     args("solver", "preconditioner", "package", "symmetry"),
271     ":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"
272     ":rtype: ``int``\n"
273     ":param solver:\n:type solver: ``int``\n"
274     ":param preconditioner:\n:type preconditioner: ``int``\n"
275     ":param package:\n:type package: ``int``\n"
276     ":param symmetry:\n:type symmetry: ``int``\n"
277     )
278     .def("getTransportTypeId",&finley::MeshAdapter::getTransportTypeId,
279     args("solver", "preconditioner", "package", "symmetry"),
280     ":return: the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.\n"
281     ":rtype: ``int``\n"
282     ":param solver:\n:type solver: ``int``\n"
283     ":param preconditioner:\n:type preconditioner: ``int``\n"
284     ":param package:\n:type package: ``int``\n"
285     ":param symmetry:\n:type symmetry: ``int``\n"
286     )
287     .def("setX",&finley::MeshAdapter::setNewX,
288     args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
289     .def("getX",&finley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
290     ":rtype: `Data`")
291     .def("getNormal",&finley::MeshAdapter::getNormal,
292     ":return: boundary normals at the quadrature point on the face elements\n"
293     ":rtype: `Data`")
294     .def("getSize",&finley::MeshAdapter::getSize,":return: the element size\n"
295     ":rtype: `Data`")
296     .def("saveDX",&finley::MeshAdapter::saveDX,args("filename" ,"arg"),
297     "Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier"
298     "\n\n:param filename: \n:type filename: ``string``\n"
299     "\n:param arg: \n:type arg: ``dict``\n")
300     .def("saveVTK",&finley::MeshAdapter::saveVTK,
301     args("filename" ,"arg", "metadata", "metadata_schema"),
302     "Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier"
303     "\n\n:param filename:\n:type filename: ``string``\n"
304     ":param arg:\n:type arg: ``dict``\n"
305     ":param metadata:\n:type metadata: ``string``\n"
306     ":param metadata_schema:\n:type metadata_schema: ``string``\n"
307     )
308     .def("setTagMap",&finley::MeshAdapter::setTagMap,args("name","tag"),
309     "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
310     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
311     .def("getTag",&finley::MeshAdapter::getTag,args("name"),":return: tag id for "
312     "``name``\n:rtype: ``string``")
313     .def("isValidTagName",&finley::MeshAdapter::isValidTagName,args("name"),
314     ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
315     .def("showTagNames",&finley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
316     .def("getMPISize",&finley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
317     .def("getMPIRank",&finley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
318     .def("MPIBarrier",&finley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
319 gross 3515 .def("onMasterProcessor",&finley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")
320 jfenwick 3554 // .def("addDiracPoints", &finley::MeshAdapter::addDiracPoints,(arg("points"), arg("tags")=finley::EmptyPythonList),
321     // "adds points to support more Dirac delta function.\n\n"
322     // ":param points: list of points where Dirac delta function are to be defined. The location will be adjusted to\n"
323     // " to match the nearest node of the finite element mesh.\n:type points: ``list`` of ``list``s of ``floats``\n"
324     // ":param tags: list of tags to be assigned to the points.\n:type tags: ``list`` of ``int``s or ``strings``\n"
325     // )
326     // .def("addDiracPoint", &finley::MeshAdapter::addDiracPoint,(arg("point"), arg("tag")=-1),
327     // "adds a point to support more Dirac delta function.\n\n"
328     // ":param point: point where Dirac delta function are to be defined. The location will be adjusted to\n"
329     // " to match the nearest node of the finite element mesh.\n:type point: ``list`` of ``floats``\n"
330     // ":param tags: tag to be assigned to the point.\n:type tag: ``int``s or ``strings``\n"
331     // )
332     // .def("addDiracPoint", &finley::MeshAdapter::addDiracPointWithTagName,(arg("point"), arg("tag")),
333     // "adds a point to support more Dirac delta function.\n\n"
334     // ":param point: point where Dirac delta function are to be defined. The location will be adjusted to\n"
335     // " to match the nearest node of the finite element mesh.\n:type point: ``list`` of ``floats``\n"
336     // ":param tags: tag to be assigned to the point.\n:type tag: ``int``s or ``strings``\n"
337     // )
338 gross 3515 ;
339 jgs 102
340     class_<finley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >
341 jfenwick 2061 ("OperatorAdapter","A concrete class representing an operator. For more details, please see the c++ documentation.", no_init)
342 jfenwick 2625 .def("print_matrix_info",&finley::SystemMatrixAdapter::Print_Matrix_Info,(arg("full")=false),"prints information about a system matrix")
343 jgs 102 .def("nullifyRowsAndCols",&finley::SystemMatrixAdapter::nullifyRowsAndCols)
344 jfenwick 2625 .def("resetValues",&finley::SystemMatrixAdapter::resetValues, "resets the matrix entries")
345     .def("saveMM",&finley::SystemMatrixAdapter::saveMM,args("fileName"),
346     "writes the matrix to a file using the Matrix Market file format")
347     .def("saveHB",&finley::SystemMatrixAdapter::saveHB, args("filename"),
348     "writes the matrix to a file using the Harwell-Boeing file format");
349 jgs 102
350 gross 1364 class_<finley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >
351 jfenwick 2061 ("TransportProblemAdapter","",no_init)
352 gross 1407 .def("getSafeTimeStepSize",&finley::TransportProblemAdapter::getSafeTimeStepSize)
353 gross 1859 .def("getUnlimitedTimeStepSize",&finley::TransportProblemAdapter::getUnlimitedTimeStepSize)
354 jfenwick 2625 .def("resetTransport",&finley::TransportProblemAdapter::resetTransport,
355     "resets the transport operator typically as they have been updated");
356 jgs 102 }

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