/[escript]/branches/diaplayground/dudley/src/CPPAdapter/dudleycpp.cpp
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Revision 3981 - (hide annotations)
Fri Sep 21 02:47:54 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk/dudley/src/CPPAdapter/dudleycpp.cpp
File size: 14156 byte(s)
First pass of updating copyright notices
1 jgs 102
2 jfenwick 3981 /*****************************************************************************
3 ksteube 1811 *
4 jfenwick 3911 * Copyright (c) 2003-2012 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     * Development since 2012 by School of Earth Sciences
13     *
14     *****************************************************************************/
15 ksteube 1312
16 ksteube 1811
17 jfenwick 3231 #ifdef ESYS_MPI
18     #include "esysUtils/Esys_MPI.h"
19 ksteube 817 #endif
20 jgs 102 extern "C" {
21 jfenwick 3082 #include "../Dudley.h"
22 jgs 102 }
23 jgs 472
24 jfenwick 3675 #include <pasowrap/SystemMatrixAdapter.h>
25     #include <pasowrap/TransportProblemAdapter.h>
26    
27 jgs 203 #include "MeshAdapter.h"
28     #include "MeshAdapterFactory.h"
29 jgs 102
30 jfenwick 3086 #include "DudleyAdapterException.h"
31 gross 727 // #include "esysUtils/EsysException.h"
32 robwdcock 682 #include "esysUtils/esysExceptionTranslator.h"
33 jgs 102
34 robwdcock 682 #include "escript/AbstractContinuousDomain.h"
35 jgs 102
36     #include <boost/python.hpp>
37     #include <boost/python/module.hpp>
38     #include <boost/python/def.hpp>
39     #include <boost/python/detail/defaults_gen.hpp>
40 jfenwick 2064 #include <boost/version.hpp>
41 jgs 102
42     using namespace boost::python;
43    
44     /**
45 jfenwick 3082 \page dudley Dudley
46 jfenwick 3086 Dudley is the python module name that contains the interfaces
47 jfenwick 3082 to the C++ wrapper to dudley.
48 jgs 102
49 jgs 121 \version 1.0.0
50 jgs 102
51 jgs 121 \section class_desc Class Description:
52 jgs 102 Data
53    
54 jgs 121 \section class_limits Class Limitations:
55 jgs 102 None
56    
57 jgs 121 \section class_conds Class Conditions of Use:
58 jgs 102 None
59    
60 jgs 121 \section throws Throws:
61 jgs 102 None
62    
63     */
64    
65 jfenwick 3082 BOOST_PYTHON_MODULE(dudleycpp)
66 jgs 102 {
67 jfenwick 2064 // This feature was added in boost v1.34
68 phornby 2076 #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
69 jfenwick 2061 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
70     docstring_options docopt(true, true, false);
71 jfenwick 2064 #endif
72 jgs 102
73     //
74     // NOTE: The return_value_policy is necessary for functions that
75     // return pointers.
76 gross 1382 //
77 jfenwick 3086 register_exception_translator<dudley::DudleyAdapterException>(&(esysUtils::esysExceptionTranslator));
78 jgs 102
79 jfenwick 3082 def("LoadMesh",dudley::loadMesh,
80 jfenwick 2625 (arg("fileName")="file.nc"),":rtype: `Domain`"
81 jfenwick 1872 /* ,return_value_policy<manage_new_object>());*/
82     );
83    
84 jfenwick 3082 def("ReadMesh",dudley::readMesh,
85 jfenwick 1872 (arg("fileName")="file.fly",arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)
86     /* ,return_value_policy<manage_new_object>());*/
87 jfenwick 2625 ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
88     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
89     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
90     ":type integrationOrder: ``int``\n"
91     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
92     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
93 jgs 102
94 jfenwick 3082 def("ReadGmsh",dudley::readGmsh,
95 gross 2722 (arg("fileName")="file.msh",
96     arg("numDim"),
97     arg("integrationOrder")=-1,
98     arg("reducedIntegrationOrder")=-1,
99     arg("optimize")=true,
100     arg("useMacroElements")=false)
101 jfenwick 1872 // ,return_value_policy<manage_new_object>());
102 jfenwick 2625 ,"Read a gmsh mesh file\n\n"
103     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
104     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
105     ":type integrationOrder: ``int``\n"
106     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
107 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``\n"
108     ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
109     );
110 gross 934
111 jfenwick 3082 def ("Brick",dudley::brick,
112 jgs 102 (arg("n0")=1,arg("n1")=1,arg("n2")=1,
113     arg("order")=1,
114     arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,
115     arg("periodic0")=false,arg("periodic1")=false,arg("periodic2")=false,
116 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
117 ksteube 1312 arg("useElementsOnFace")=false,
118     arg("useFullElementOrder")=false,
119 jfenwick 1872 arg("optimize")=false)
120 jfenwick 3469 ,"Creates a tetrahedral mesh by subdividing n0 x n1 x n2 rectangular elements over the brick [0,l0] x [0,l1] x [0,l2]."
121 jfenwick 3892 "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
122 jfenwick 2625 "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
123 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
124 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n:param l2:\n"
125     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
126     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
127     ":param useElementsOnFace: whether or not to use elements on face\n"
128     ":type useElementsOnFace: ``int``"
129     ":param periodic0: whether or not boundary conditions are periodic\n"
130     ":param periodic1:\n:param periodic2:\n"
131     ":param useFullElementOrder:\n:param optimize:\n"
132 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
133 jfenwick 2625 );
134 jgs 102
135 jfenwick 3082 def ("Rectangle",dudley::rectangle,
136 jgs 102 (arg("n0")=1,arg("n1")=1,arg("order")=1,
137     arg("l0")=1.0,arg("l1")=1.0,
138     arg("periodic0")=false,arg("periodic1")=false,
139 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
140 ksteube 1312 arg("useElementsOnFace")=false,
141     arg("useFullElementOrder")=false,
142 jfenwick 1872 arg("optimize")=false)
143 jfenwick 3469 ,"Creates a triangular mesh by subdividing n0 x n1 rectangular elements over the brick [0,l0] x [0,l1]."
144 jfenwick 3892 "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
145 jfenwick 2625 "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
146 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
147 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n"
148     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
149     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
150     ":param useElementsOnFace: whether or not to use elements on face\n"
151     ":type useElementsOnFace: ``int``"
152     ":param periodic0: whether or not boundary conditions are periodic\n"
153     ":param periodic1:\n"
154 gross 2722 ":param useFullElementOrder:\n:param optimize:\n"
155     ":param useMacroElements: Enable the usage of first order macro elements.\n:type useMacroElements: ``bool``\n"
156     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
157     );
158 jgs 102
159 jfenwick 3082 class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
160 jfenwick 3086 ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())
161 jfenwick 3082 .def(init<const dudley::MeshAdapter&>())
162     .def("write",&dudley::MeshAdapter::write,args("filename"),
163 jfenwick 2625 "Write the current mesh to a file with the given name.")
164 jfenwick 3082 .def("print_mesh_info",&dudley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
165 jfenwick 2625 ":param full:\n:type full: ``bool``")
166 jfenwick 3082 .def("dump",&dudley::MeshAdapter::dump,args("fileName")
167 jfenwick 2625 ,"dumps the mesh to a file with the given name.")
168 jfenwick 3082 .def("getDescription",&dudley::MeshAdapter::getDescription,
169 jfenwick 2625 ":return: a description for this domain\n:rtype: ``string``")
170 jfenwick 3082 .def("getDim",&dudley::MeshAdapter::getDim,":rtype: ``int``")
171     .def("getDataShape",&dudley::MeshAdapter::getDataShape, args("functionSpaceCode"),
172 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``")
173 jfenwick 3082 .def("getNumDataPointsGlobal",&dudley::MeshAdapter::getNumDataPointsGlobal,
174 jfenwick 2625 ":return: the number of data points summed across all MPI processes\n"
175     ":rtype: ``int``")
176 jfenwick 3082 .def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
177 jfenwick 3269 args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
178 jfenwick 2625 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
179     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
180     ":param A:\n:type A: `Data`\n"
181     ":param B:\n:type B: `Data`\n"
182     ":param C:\n:type C: `Data`\n"
183     ":param D:\n:type D: `Data`\n"
184     ":param X:\n:type X: `Data`\n"
185     ":param Y:\n:type Y: `Data`\n"
186     ":param d:\n:type d: `Data`\n"
187 jfenwick 3269 ":param d_contact:\n:type d_contact: `Data`\n"
188     ":param y_contact:\n:type y_contact: `Data`\n"
189 jfenwick 2625 )
190 jfenwick 3082 .def("addPDEToLumpedSystem",&dudley::MeshAdapter::addPDEToLumpedSystem,
191 jfenwick 2625 args("mat", "D", "d"),
192     "adds a PDE onto the lumped stiffness matrix\n\n"
193     ":param mat:\n:type mat: `Data`\n"
194     ":param D:\n:type D: `Data`\n"
195 gross 3379 ":param d:\n:type d: `Data`\n"
196     ":param useHRZ:\n:type useHRZ: bool\n"
197     )
198 jfenwick 3082 .def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,
199 jfenwick 2625 args("rhs", "X", "Y", "y", "y_contact"),
200     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
201     ":param rhs:\n:type rhs: `Data`\n"
202     ":param X:\n:type X: `Data`\n"
203     ":param Y:\n:type Y: `Data`\n"
204     ":param y:\n:type y: `Data`\n"
205 jfenwick 3269 ":param y_contact:\n:type y_contact: `Data`"
206 jfenwick 2625 )
207 jfenwick 3082 .def("addPDEToTransportProblem",&dudley::MeshAdapter::addPDEToTransportProblem,
208 jfenwick 2625 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
209     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
210     ":param source:\n:type source: `Data`\n"
211     ":param M:\n:type M: `Data`\n"
212     ":param A:\n:type A: `Data`\n"
213     ":param B:\n:type B: `Data`\n"
214     ":param C:\n:type C: `Data`\n"
215     ":param D:\n:type D: `Data`\n"
216     ":param X:\n:type X: `Data`\n"
217     ":param Y:\n:type Y: `Data`\n"
218     ":param d:\n:type d: `Data`\n"
219     ":param y:\n:type y: `Data`\n"
220     ":param d_contact:\n:type d_contact: `Data`\n"
221     ":param y_contact:\n:type y_contact: `Data`\n"
222     )
223 jfenwick 3082 .def("newOperator",&dudley::MeshAdapter::newSystemMatrix,
224 jfenwick 2625 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
225     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
226     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
227     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
228     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
229     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
230     ":param type:\n:type type: ``int``\n"
231     )
232 jfenwick 3082 .def("newTransportProblem",&dudley::MeshAdapter::newTransportProblem,
233 jfenwick 2625 args("theta", "blocksize", "functionspace", "type"),
234     "creates a TransportProblemAdapter\n\n"
235     ":param theta:\n:type theta: ``float``\n"
236     ":param blocksize:\n:type blocksize: ``int``\n"
237     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
238     ":param type:\n:type type: ``int``\n"
239     )
240 jfenwick 3082 .def("getSystemMatrixTypeId",&dudley::MeshAdapter::getSystemMatrixTypeId,
241 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
242     ":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"
243     ":rtype: ``int``\n"
244     ":param solver:\n:type solver: ``int``\n"
245     ":param preconditioner:\n:type preconditioner: ``int``\n"
246     ":param package:\n:type package: ``int``\n"
247     ":param symmetry:\n:type symmetry: ``int``\n"
248     )
249 jfenwick 3082 .def("getTransportTypeId",&dudley::MeshAdapter::getTransportTypeId,
250 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
251     ":return: the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.\n"
252     ":rtype: ``int``\n"
253     ":param solver:\n:type solver: ``int``\n"
254     ":param preconditioner:\n:type preconditioner: ``int``\n"
255     ":param package:\n:type package: ``int``\n"
256     ":param symmetry:\n:type symmetry: ``int``\n"
257     )
258 jfenwick 3082 .def("setX",&dudley::MeshAdapter::setNewX,
259 jfenwick 2625 args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
260 jfenwick 3082 .def("getX",&dudley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
261 jfenwick 2625 ":rtype: `Data`")
262 jfenwick 3082 .def("getNormal",&dudley::MeshAdapter::getNormal,
263 jfenwick 2625 ":return: boundary normals at the quadrature point on the face elements\n"
264     ":rtype: `Data`")
265 jfenwick 3082 .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
266 jfenwick 2625 ":rtype: `Data`")
267 jfenwick 3082 .def("saveDX",&dudley::MeshAdapter::saveDX,args("filename" ,"arg"),
268 jfenwick 2625 "Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier"
269     "\n\n:param filename: \n:type filename: ``string``\n"
270     "\n:param arg: \n:type arg: ``dict``\n")
271 jfenwick 3082 .def("saveVTK",&dudley::MeshAdapter::saveVTK,
272 jfenwick 2625 args("filename" ,"arg", "metadata", "metadata_schema"),
273     "Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier"
274     "\n\n:param filename:\n:type filename: ``string``\n"
275     ":param arg:\n:type arg: ``dict``\n"
276     ":param metadata:\n:type metadata: ``string``\n"
277     ":param metadata_schema:\n:type metadata_schema: ``string``\n"
278     )
279 jfenwick 3082 .def("setTagMap",&dudley::MeshAdapter::setTagMap,args("name","tag"),
280 jfenwick 2625 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
281     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
282 jfenwick 3082 .def("getTag",&dudley::MeshAdapter::getTag,args("name"),":return: tag id for "
283 jfenwick 2625 "``name``\n:rtype: ``string``")
284 jfenwick 3082 .def("isValidTagName",&dudley::MeshAdapter::isValidTagName,args("name"),
285 jfenwick 2625 ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
286 jfenwick 3082 .def("showTagNames",&dudley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
287     .def("getMPISize",&dudley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
288     .def("getMPIRank",&dudley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
289     .def("MPIBarrier",&dudley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
290     .def("onMasterProcessor",&dudley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
291 jgs 102
292     }

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/pasowrap/dudley/src/CPPAdapter/dudleycpp.cpp:3661-3674 /branches/py3_attempt2/dudley/src/CPPAdapter/dudleycpp.cpp:3871-3891 /branches/restext/finley/src/CPPAdapter/finleycpp.cpp:2610-2624 /branches/ripleygmg_from_3668/dudley/src/CPPAdapter/dudleycpp.cpp:3669-3791 /branches/stage3.0/finley/src/CPPAdapter/finleycpp.cpp:2569-2590 /branches/symbolic_from_3470/dudley/src/CPPAdapter/dudleycpp.cpp:3471-3974 /branches/symbolic_from_3470/ripley/test/python/dudley/src/CPPAdapter/dudleycpp.cpp:3517-3974 /release/3.0/finley/src/CPPAdapter/finleycpp.cpp:2591-2601 /trunk/ripley/test/python/dudley/src/CPPAdapter/dudleycpp.cpp:3480-3515

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