/[escript]/branches/diaplayground/dudley/src/CPPAdapter/dudleycpp.cpp
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Revision 3086 - (hide annotations)
Thu Aug 5 05:07:58 2010 UTC (8 years, 7 months ago) by jfenwick
Original Path: branches/domexper/dudley/src/CPPAdapter/dudleycpp.cpp
File size: 15888 byte(s)
Another pass at removing finley

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 ksteube 817 #ifdef PASO_MPI
16     #include <mpi.h>
17 ksteube 1800 #include "paso/Paso_MPI.h"
18 ksteube 817 #endif
19 jgs 102 extern "C" {
20 jfenwick 3082 #include "../Dudley.h"
21 jgs 102 }
22 jgs 472
23 jgs 203 #include "MeshAdapter.h"
24     #include "MeshAdapterFactory.h"
25     #include "SystemMatrixAdapter.h"
26 gross 1364 #include "TransportProblemAdapter.h"
27 jgs 102
28 jfenwick 3086 #include "DudleyAdapterException.h"
29 gross 727 // #include "esysUtils/EsysException.h"
30 robwdcock 682 #include "esysUtils/esysExceptionTranslator.h"
31 jgs 102
32 robwdcock 682 #include "escript/AbstractContinuousDomain.h"
33 jgs 102
34     #include <boost/python.hpp>
35     #include <boost/python/module.hpp>
36     #include <boost/python/def.hpp>
37     #include <boost/python/detail/defaults_gen.hpp>
38 jfenwick 2064 #include <boost/version.hpp>
39 jgs 102
40     using namespace boost::python;
41    
42     /**
43 jfenwick 3082 \page dudley Dudley
44 jfenwick 3086 Dudley is the python module name that contains the interfaces
45 jfenwick 3082 to the C++ wrapper to dudley.
46 jgs 102
47 jgs 121 \version 1.0.0
48 jgs 102
49 jgs 121 \section class_desc Class Description:
50 jgs 102 Data
51    
52 jgs 121 \section class_limits Class Limitations:
53 jgs 102 None
54    
55 jgs 121 \section class_conds Class Conditions of Use:
56 jgs 102 None
57    
58 jgs 121 \section throws Throws:
59 jgs 102 None
60    
61     */
62    
63 jfenwick 3082 BOOST_PYTHON_MODULE(dudleycpp)
64 jgs 102 {
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     //
72     // NOTE: The return_value_policy is necessary for functions that
73     // return pointers.
74 gross 1382 //
75 jfenwick 3086 register_exception_translator<dudley::DudleyAdapterException>(&(esysUtils::esysExceptionTranslator));
76 jgs 102
77 jfenwick 3082 def("LoadMesh",dudley::loadMesh,
78 jfenwick 2625 (arg("fileName")="file.nc"),":rtype: `Domain`"
79 jfenwick 1872 /* ,return_value_policy<manage_new_object>());*/
80     );
81    
82 jfenwick 3082 def("ReadMesh",dudley::readMesh,
83 jfenwick 1872 (arg("fileName")="file.fly",arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)
84     /* ,return_value_policy<manage_new_object>());*/
85 jfenwick 2625 ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
86     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
87     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
88     ":type integrationOrder: ``int``\n"
89     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
90     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
91 jgs 102
92 jfenwick 3082 def("ReadGmsh",dudley::readGmsh,
93 gross 2722 (arg("fileName")="file.msh",
94     arg("numDim"),
95     arg("integrationOrder")=-1,
96     arg("reducedIntegrationOrder")=-1,
97     arg("optimize")=true,
98     arg("useMacroElements")=false)
99 jfenwick 1872 // ,return_value_policy<manage_new_object>());
100 jfenwick 2625 ,"Read a gmsh mesh file\n\n"
101     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
102     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
103     ":type integrationOrder: ``int``\n"
104     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
105 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``\n"
106     ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
107     );
108 gross 934
109 jfenwick 3082 def ("Brick",dudley::brick,
110 jgs 102 (arg("n0")=1,arg("n1")=1,arg("n2")=1,
111     arg("order")=1,
112     arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,
113     arg("periodic0")=false,arg("periodic1")=false,arg("periodic2")=false,
114 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
115 ksteube 1312 arg("useElementsOnFace")=false,
116     arg("useFullElementOrder")=false,
117 jfenwick 1872 arg("optimize")=false)
118 gross 2722
119 jfenwick 1872 // ,return_value_policy<manage_new_object>());
120 jfenwick 2625 ,"Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2]."
121     "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
122 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
123 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n:param l2:\n"
124     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
125     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
126     ":param useElementsOnFace: whether or not to use elements on face\n"
127     ":type useElementsOnFace: ``int``"
128     ":param periodic0: whether or not boundary conditions are periodic\n"
129     ":param periodic1:\n:param periodic2:\n"
130     ":param useFullElementOrder:\n:param optimize:\n"
131 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
132 jfenwick 2625 );
133 jgs 102
134 jfenwick 3082 def ("Rectangle",dudley::rectangle,
135 jgs 102 (arg("n0")=1,arg("n1")=1,arg("order")=1,
136     arg("l0")=1.0,arg("l1")=1.0,
137     arg("periodic0")=false,arg("periodic1")=false,
138 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
139 ksteube 1312 arg("useElementsOnFace")=false,
140     arg("useFullElementOrder")=false,
141 jfenwick 1872 arg("optimize")=false)
142     // ,return_value_policy<manage_new_object>());
143 jfenwick 2625 ,"Creates a rectangular mesh with n0 x n1 elements over the brick [0,l0] x [0,l1]."
144     "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
145 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
146 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n"
147     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
148     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
149     ":param useElementsOnFace: whether or not to use elements on face\n"
150     ":type useElementsOnFace: ``int``"
151     ":param periodic0: whether or not boundary conditions are periodic\n"
152     ":param periodic1:\n"
153 gross 2722 ":param useFullElementOrder:\n:param optimize:\n"
154     ":param useMacroElements: Enable the usage of first order macro elements.\n:type useMacroElements: ``bool``\n"
155     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
156     );
157 jgs 102
158 jfenwick 3082 def("Merge",dudley::meshMerge,args("meshList")
159 jfenwick 1872 // ,return_value_policy<manage_new_object>());
160 jfenwick 2625 ,"Merges a list of meshes into one mesh.\n\n:rtype: `Domain`"
161 jfenwick 1872 );
162 jgs 110
163 jfenwick 3082 def("GlueFaces",dudley::glueFaces,
164 jfenwick 2625 (arg("meshList"),arg("safetyFactor")=0.2,
165 gross 1062 arg("tolerance")=1.e-8,
166 jfenwick 1872 arg("optimize")=true)
167     // ,return_value_policy<manage_new_object>());
168 jfenwick 2625 ,"Detects matching faces in the mesh, removes them from the mesh and joins the elements touched by the face elements."
169 jfenwick 1872 );
170 jgs 102
171 jfenwick 3082 def("JoinFaces",dudley::joinFaces,
172 jfenwick 2625 (arg("meshList"), arg("safetyFactor")=0.2,
173 gross 1062 arg("tolerance")=1.e-8,
174 jfenwick 1872 arg("optimize")=true)
175     // ,return_value_policy<manage_new_object>());
176 jfenwick 2625 ,"Detects matching faces in the mesh and replaces them by joint elements."
177 jfenwick 1872 );
178 jgs 102
179    
180 jfenwick 3082 class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
181 jfenwick 3086 ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())
182 jfenwick 3082 .def(init<const dudley::MeshAdapter&>())
183     .def("write",&dudley::MeshAdapter::write,args("filename"),
184 jfenwick 2625 "Write the current mesh to a file with the given name.")
185 jfenwick 3082 .def("print_mesh_info",&dudley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
186 jfenwick 2625 ":param full:\n:type full: ``bool``")
187 jfenwick 3082 .def("dump",&dudley::MeshAdapter::dump,args("fileName")
188 jfenwick 2625 ,"dumps the mesh to a file with the given name.")
189 jfenwick 3082 .def("getDescription",&dudley::MeshAdapter::getDescription,
190 jfenwick 2625 ":return: a description for this domain\n:rtype: ``string``")
191 jfenwick 3082 .def("getDim",&dudley::MeshAdapter::getDim,":rtype: ``int``")
192     .def("getDataShape",&dudley::MeshAdapter::getDataShape, args("functionSpaceCode"),
193 jfenwick 2625 ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
194 jfenwick 3082 .def("getNumDataPointsGlobal",&dudley::MeshAdapter::getNumDataPointsGlobal,
195 jfenwick 2625 ":return: the number of data points summed across all MPI processes\n"
196     ":rtype: ``int``")
197 jfenwick 3082 .def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
198 jfenwick 2625 args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
199     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
200     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
201     ":param A:\n:type A: `Data`\n"
202     ":param B:\n:type B: `Data`\n"
203     ":param C:\n:type C: `Data`\n"
204     ":param D:\n:type D: `Data`\n"
205     ":param X:\n:type X: `Data`\n"
206     ":param Y:\n:type Y: `Data`\n"
207     ":param d:\n:type d: `Data`\n"
208     ":param d_contact:\n:type d_contact: `Data`\n"
209     ":param y_contact:\n:type y_contact: `Data`\n"
210     )
211 jfenwick 3082 .def("addPDEToLumpedSystem",&dudley::MeshAdapter::addPDEToLumpedSystem,
212 jfenwick 2625 args("mat", "D", "d"),
213     "adds a PDE onto the lumped stiffness matrix\n\n"
214     ":param mat:\n:type mat: `Data`\n"
215     ":param D:\n:type D: `Data`\n"
216     ":param d:\n:type d: `Data`\n")
217 jfenwick 3082 .def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,
218 jfenwick 2625 args("rhs", "X", "Y", "y", "y_contact"),
219     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
220     ":param rhs:\n:type rhs: `Data`\n"
221     ":param X:\n:type X: `Data`\n"
222     ":param Y:\n:type Y: `Data`\n"
223     ":param y:\n:type y: `Data`\n"
224     ":param y_contact:\n:type y_contact: `Data`"
225     )
226 jfenwick 3082 .def("addPDEToTransportProblem",&dudley::MeshAdapter::addPDEToTransportProblem,
227 jfenwick 2625 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
228     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
229     ":param source:\n:type source: `Data`\n"
230     ":param M:\n:type M: `Data`\n"
231     ":param A:\n:type A: `Data`\n"
232     ":param B:\n:type B: `Data`\n"
233     ":param C:\n:type C: `Data`\n"
234     ":param D:\n:type D: `Data`\n"
235     ":param X:\n:type X: `Data`\n"
236     ":param Y:\n:type Y: `Data`\n"
237     ":param d:\n:type d: `Data`\n"
238     ":param y:\n:type y: `Data`\n"
239     ":param d_contact:\n:type d_contact: `Data`\n"
240     ":param y_contact:\n:type y_contact: `Data`\n"
241     )
242 jfenwick 3082 .def("newOperator",&dudley::MeshAdapter::newSystemMatrix,
243 jfenwick 2625 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
244     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
245     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
246     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
247     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
248     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
249     ":param type:\n:type type: ``int``\n"
250     )
251 jfenwick 3082 .def("newTransportProblem",&dudley::MeshAdapter::newTransportProblem,
252 jfenwick 2625 args("theta", "blocksize", "functionspace", "type"),
253     "creates a TransportProblemAdapter\n\n"
254     ":param theta:\n:type theta: ``float``\n"
255     ":param blocksize:\n:type blocksize: ``int``\n"
256     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
257     ":param type:\n:type type: ``int``\n"
258     )
259 jfenwick 3082 .def("getSystemMatrixTypeId",&dudley::MeshAdapter::getSystemMatrixTypeId,
260 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
261     ":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"
262     ":rtype: ``int``\n"
263     ":param solver:\n:type solver: ``int``\n"
264     ":param preconditioner:\n:type preconditioner: ``int``\n"
265     ":param package:\n:type package: ``int``\n"
266     ":param symmetry:\n:type symmetry: ``int``\n"
267     )
268 jfenwick 3082 .def("getTransportTypeId",&dudley::MeshAdapter::getTransportTypeId,
269 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
270     ":return: the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.\n"
271     ":rtype: ``int``\n"
272     ":param solver:\n:type solver: ``int``\n"
273     ":param preconditioner:\n:type preconditioner: ``int``\n"
274     ":param package:\n:type package: ``int``\n"
275     ":param symmetry:\n:type symmetry: ``int``\n"
276     )
277 jfenwick 3082 .def("setX",&dudley::MeshAdapter::setNewX,
278 jfenwick 2625 args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
279 jfenwick 3082 .def("getX",&dudley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
280 jfenwick 2625 ":rtype: `Data`")
281 jfenwick 3082 .def("getNormal",&dudley::MeshAdapter::getNormal,
282 jfenwick 2625 ":return: boundary normals at the quadrature point on the face elements\n"
283     ":rtype: `Data`")
284 jfenwick 3082 .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
285 jfenwick 2625 ":rtype: `Data`")
286 jfenwick 3082 .def("saveDX",&dudley::MeshAdapter::saveDX,args("filename" ,"arg"),
287 jfenwick 2625 "Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier"
288     "\n\n:param filename: \n:type filename: ``string``\n"
289     "\n:param arg: \n:type arg: ``dict``\n")
290 jfenwick 3082 .def("saveVTK",&dudley::MeshAdapter::saveVTK,
291 jfenwick 2625 args("filename" ,"arg", "metadata", "metadata_schema"),
292     "Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier"
293     "\n\n:param filename:\n:type filename: ``string``\n"
294     ":param arg:\n:type arg: ``dict``\n"
295     ":param metadata:\n:type metadata: ``string``\n"
296     ":param metadata_schema:\n:type metadata_schema: ``string``\n"
297     )
298 jfenwick 3082 .def("setTagMap",&dudley::MeshAdapter::setTagMap,args("name","tag"),
299 jfenwick 2625 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
300     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
301 jfenwick 3082 .def("getTag",&dudley::MeshAdapter::getTag,args("name"),":return: tag id for "
302 jfenwick 2625 "``name``\n:rtype: ``string``")
303 jfenwick 3082 .def("isValidTagName",&dudley::MeshAdapter::isValidTagName,args("name"),
304 jfenwick 2625 ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
305 jfenwick 3082 .def("showTagNames",&dudley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
306     .def("getMPISize",&dudley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
307     .def("getMPIRank",&dudley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
308     .def("MPIBarrier",&dudley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
309     .def("onMasterProcessor",&dudley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
310 jgs 102
311 jfenwick 3082 class_<dudley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >
312 jfenwick 2061 ("OperatorAdapter","A concrete class representing an operator. For more details, please see the c++ documentation.", no_init)
313 jfenwick 3082 .def("print_matrix_info",&dudley::SystemMatrixAdapter::Print_Matrix_Info,(arg("full")=false),"prints information about a system matrix")
314     .def("nullifyRowsAndCols",&dudley::SystemMatrixAdapter::nullifyRowsAndCols)
315     .def("resetValues",&dudley::SystemMatrixAdapter::resetValues, "resets the matrix entries")
316     .def("saveMM",&dudley::SystemMatrixAdapter::saveMM,args("fileName"),
317 jfenwick 2625 "writes the matrix to a file using the Matrix Market file format")
318 jfenwick 3082 .def("saveHB",&dudley::SystemMatrixAdapter::saveHB, args("filename"),
319 jfenwick 2625 "writes the matrix to a file using the Harwell-Boeing file format");
320 jgs 102
321 jfenwick 3082 class_<dudley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >
322 jfenwick 2061 ("TransportProblemAdapter","",no_init)
323 jfenwick 3082 .def("getSafeTimeStepSize",&dudley::TransportProblemAdapter::getSafeTimeStepSize)
324     .def("getUnlimitedTimeStepSize",&dudley::TransportProblemAdapter::getUnlimitedTimeStepSize)
325     .def("resetTransport",&dudley::TransportProblemAdapter::resetTransport,
326 jfenwick 2625 "resets the transport operator typically as they have been updated");
327 jgs 102 }

Properties

Name Value
svn:eol-style native
svn:keywords Author Date Id Revision
svn:mergeinfo /branches/lapack2681/finley/src/CPPAdapter/finleycpp.cpp:2682-2741 /branches/restext/finley/src/CPPAdapter/finleycpp.cpp:2610-2624 /branches/stage3.0/finley/src/CPPAdapter/finleycpp.cpp:2569-2590 /release/3.0/finley/src/CPPAdapter/finleycpp.cpp:2591-2601

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