/[escript]/branches/diaplayground/dudley/src/CPPAdapter/dudleycpp.cpp
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Revision 3115 - (hide annotations)
Sun Aug 29 23:14:35 2010 UTC (8 years, 6 months ago) by jfenwick
Original Path: branches/domexper/dudley/src/CPPAdapter/dudleycpp.cpp
File size: 15610 byte(s)
Now have cubes facing the correct direction

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 jfenwick 2625 ,"Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2]."
119     "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
120 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
121 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n:param l2:\n"
122     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
123     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
124     ":param useElementsOnFace: whether or not to use elements on face\n"
125     ":type useElementsOnFace: ``int``"
126     ":param periodic0: whether or not boundary conditions are periodic\n"
127     ":param periodic1:\n:param periodic2:\n"
128     ":param useFullElementOrder:\n:param optimize:\n"
129 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
130 jfenwick 2625 );
131 jgs 102
132 jfenwick 3082 def ("Rectangle",dudley::rectangle,
133 jgs 102 (arg("n0")=1,arg("n1")=1,arg("order")=1,
134     arg("l0")=1.0,arg("l1")=1.0,
135     arg("periodic0")=false,arg("periodic1")=false,
136 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
137 ksteube 1312 arg("useElementsOnFace")=false,
138     arg("useFullElementOrder")=false,
139 jfenwick 1872 arg("optimize")=false)
140 jfenwick 2625 ,"Creates a rectangular mesh with n0 x n1 elements over the brick [0,l0] x [0,l1]."
141     "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
142 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
143 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n"
144     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
145     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
146     ":param useElementsOnFace: whether or not to use elements on face\n"
147     ":type useElementsOnFace: ``int``"
148     ":param periodic0: whether or not boundary conditions are periodic\n"
149     ":param periodic1:\n"
150 gross 2722 ":param useFullElementOrder:\n:param optimize:\n"
151     ":param useMacroElements: Enable the usage of first order macro elements.\n:type useMacroElements: ``bool``\n"
152     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
153     );
154 jgs 102
155 jfenwick 3082 def("Merge",dudley::meshMerge,args("meshList")
156 jfenwick 1872 // ,return_value_policy<manage_new_object>());
157 jfenwick 2625 ,"Merges a list of meshes into one mesh.\n\n:rtype: `Domain`"
158 jfenwick 1872 );
159 jgs 110
160 jfenwick 3082 def("GlueFaces",dudley::glueFaces,
161 jfenwick 2625 (arg("meshList"),arg("safetyFactor")=0.2,
162 gross 1062 arg("tolerance")=1.e-8,
163 jfenwick 1872 arg("optimize")=true)
164     // ,return_value_policy<manage_new_object>());
165 jfenwick 2625 ,"Detects matching faces in the mesh, removes them from the mesh and joins the elements touched by the face elements."
166 jfenwick 1872 );
167 jgs 102
168 jfenwick 3082 def("JoinFaces",dudley::joinFaces,
169 jfenwick 2625 (arg("meshList"), arg("safetyFactor")=0.2,
170 gross 1062 arg("tolerance")=1.e-8,
171 jfenwick 1872 arg("optimize")=true)
172     // ,return_value_policy<manage_new_object>());
173 jfenwick 2625 ,"Detects matching faces in the mesh and replaces them by joint elements."
174 jfenwick 1872 );
175 jgs 102
176    
177 jfenwick 3082 class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
178 jfenwick 3086 ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())
179 jfenwick 3082 .def(init<const dudley::MeshAdapter&>())
180     .def("write",&dudley::MeshAdapter::write,args("filename"),
181 jfenwick 2625 "Write the current mesh to a file with the given name.")
182 jfenwick 3082 .def("print_mesh_info",&dudley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
183 jfenwick 2625 ":param full:\n:type full: ``bool``")
184 jfenwick 3082 .def("dump",&dudley::MeshAdapter::dump,args("fileName")
185 jfenwick 2625 ,"dumps the mesh to a file with the given name.")
186 jfenwick 3082 .def("getDescription",&dudley::MeshAdapter::getDescription,
187 jfenwick 2625 ":return: a description for this domain\n:rtype: ``string``")
188 jfenwick 3082 .def("getDim",&dudley::MeshAdapter::getDim,":rtype: ``int``")
189     .def("getDataShape",&dudley::MeshAdapter::getDataShape, args("functionSpaceCode"),
190 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``")
191 jfenwick 3082 .def("getNumDataPointsGlobal",&dudley::MeshAdapter::getNumDataPointsGlobal,
192 jfenwick 2625 ":return: the number of data points summed across all MPI processes\n"
193     ":rtype: ``int``")
194 jfenwick 3082 .def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
195 jfenwick 3114 args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y"),
196 jfenwick 2625 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
197     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
198     ":param A:\n:type A: `Data`\n"
199     ":param B:\n:type B: `Data`\n"
200     ":param C:\n:type C: `Data`\n"
201     ":param D:\n:type D: `Data`\n"
202     ":param X:\n:type X: `Data`\n"
203     ":param Y:\n:type Y: `Data`\n"
204     ":param d:\n:type d: `Data`\n"
205     )
206 jfenwick 3082 .def("addPDEToLumpedSystem",&dudley::MeshAdapter::addPDEToLumpedSystem,
207 jfenwick 2625 args("mat", "D", "d"),
208     "adds a PDE onto the lumped stiffness matrix\n\n"
209     ":param mat:\n:type mat: `Data`\n"
210     ":param D:\n:type D: `Data`\n"
211     ":param d:\n:type d: `Data`\n")
212 jfenwick 3082 .def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,
213 jfenwick 2625 args("rhs", "X", "Y", "y", "y_contact"),
214     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
215     ":param rhs:\n:type rhs: `Data`\n"
216     ":param X:\n:type X: `Data`\n"
217     ":param Y:\n:type Y: `Data`\n"
218     ":param y:\n:type y: `Data`\n"
219     )
220 jfenwick 3082 .def("addPDEToTransportProblem",&dudley::MeshAdapter::addPDEToTransportProblem,
221 jfenwick 2625 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
222     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
223     ":param source:\n:type source: `Data`\n"
224     ":param M:\n:type M: `Data`\n"
225     ":param A:\n:type A: `Data`\n"
226     ":param B:\n:type B: `Data`\n"
227     ":param C:\n:type C: `Data`\n"
228     ":param D:\n:type D: `Data`\n"
229     ":param X:\n:type X: `Data`\n"
230     ":param Y:\n:type Y: `Data`\n"
231     ":param d:\n:type d: `Data`\n"
232     ":param y:\n:type y: `Data`\n"
233     ":param d_contact:\n:type d_contact: `Data`\n"
234     ":param y_contact:\n:type y_contact: `Data`\n"
235     )
236 jfenwick 3082 .def("newOperator",&dudley::MeshAdapter::newSystemMatrix,
237 jfenwick 2625 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
238     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
239     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
240     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
241     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
242     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
243     ":param type:\n:type type: ``int``\n"
244     )
245 jfenwick 3082 .def("newTransportProblem",&dudley::MeshAdapter::newTransportProblem,
246 jfenwick 2625 args("theta", "blocksize", "functionspace", "type"),
247     "creates a TransportProblemAdapter\n\n"
248     ":param theta:\n:type theta: ``float``\n"
249     ":param blocksize:\n:type blocksize: ``int``\n"
250     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
251     ":param type:\n:type type: ``int``\n"
252     )
253 jfenwick 3082 .def("getSystemMatrixTypeId",&dudley::MeshAdapter::getSystemMatrixTypeId,
254 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
255     ":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"
256     ":rtype: ``int``\n"
257     ":param solver:\n:type solver: ``int``\n"
258     ":param preconditioner:\n:type preconditioner: ``int``\n"
259     ":param package:\n:type package: ``int``\n"
260     ":param symmetry:\n:type symmetry: ``int``\n"
261     )
262 jfenwick 3082 .def("getTransportTypeId",&dudley::MeshAdapter::getTransportTypeId,
263 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
264     ":return: the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.\n"
265     ":rtype: ``int``\n"
266     ":param solver:\n:type solver: ``int``\n"
267     ":param preconditioner:\n:type preconditioner: ``int``\n"
268     ":param package:\n:type package: ``int``\n"
269     ":param symmetry:\n:type symmetry: ``int``\n"
270     )
271 jfenwick 3082 .def("setX",&dudley::MeshAdapter::setNewX,
272 jfenwick 2625 args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
273 jfenwick 3082 .def("getX",&dudley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
274 jfenwick 2625 ":rtype: `Data`")
275 jfenwick 3082 .def("getNormal",&dudley::MeshAdapter::getNormal,
276 jfenwick 2625 ":return: boundary normals at the quadrature point on the face elements\n"
277     ":rtype: `Data`")
278 jfenwick 3082 .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
279 jfenwick 2625 ":rtype: `Data`")
280 jfenwick 3082 .def("saveDX",&dudley::MeshAdapter::saveDX,args("filename" ,"arg"),
281 jfenwick 2625 "Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier"
282     "\n\n:param filename: \n:type filename: ``string``\n"
283     "\n:param arg: \n:type arg: ``dict``\n")
284 jfenwick 3082 .def("saveVTK",&dudley::MeshAdapter::saveVTK,
285 jfenwick 2625 args("filename" ,"arg", "metadata", "metadata_schema"),
286     "Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier"
287     "\n\n:param filename:\n:type filename: ``string``\n"
288     ":param arg:\n:type arg: ``dict``\n"
289     ":param metadata:\n:type metadata: ``string``\n"
290     ":param metadata_schema:\n:type metadata_schema: ``string``\n"
291     )
292 jfenwick 3082 .def("setTagMap",&dudley::MeshAdapter::setTagMap,args("name","tag"),
293 jfenwick 2625 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
294     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
295 jfenwick 3082 .def("getTag",&dudley::MeshAdapter::getTag,args("name"),":return: tag id for "
296 jfenwick 2625 "``name``\n:rtype: ``string``")
297 jfenwick 3082 .def("isValidTagName",&dudley::MeshAdapter::isValidTagName,args("name"),
298 jfenwick 2625 ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
299 jfenwick 3082 .def("showTagNames",&dudley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
300     .def("getMPISize",&dudley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
301     .def("getMPIRank",&dudley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
302     .def("MPIBarrier",&dudley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
303     .def("onMasterProcessor",&dudley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
304 jgs 102
305 jfenwick 3082 class_<dudley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >
306 jfenwick 2061 ("OperatorAdapter","A concrete class representing an operator. For more details, please see the c++ documentation.", no_init)
307 jfenwick 3082 .def("print_matrix_info",&dudley::SystemMatrixAdapter::Print_Matrix_Info,(arg("full")=false),"prints information about a system matrix")
308     .def("nullifyRowsAndCols",&dudley::SystemMatrixAdapter::nullifyRowsAndCols)
309     .def("resetValues",&dudley::SystemMatrixAdapter::resetValues, "resets the matrix entries")
310     .def("saveMM",&dudley::SystemMatrixAdapter::saveMM,args("fileName"),
311 jfenwick 2625 "writes the matrix to a file using the Matrix Market file format")
312 jfenwick 3082 .def("saveHB",&dudley::SystemMatrixAdapter::saveHB, args("filename"),
313 jfenwick 2625 "writes the matrix to a file using the Harwell-Boeing file format");
314 jgs 102
315 jfenwick 3082 class_<dudley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >
316 jfenwick 2061 ("TransportProblemAdapter","",no_init)
317 jfenwick 3082 .def("getSafeTimeStepSize",&dudley::TransportProblemAdapter::getSafeTimeStepSize)
318     .def("getUnlimitedTimeStepSize",&dudley::TransportProblemAdapter::getUnlimitedTimeStepSize)
319     .def("resetTransport",&dudley::TransportProblemAdapter::resetTransport,
320 jfenwick 2625 "resets the transport operator typically as they have been updated");
321 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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