/[escript]/branches/diaplayground/dudley/src/CPPAdapter/dudleycpp.cpp
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Revision 4657 - (hide annotations)
Thu Feb 6 06:12:20 2014 UTC (5 years, 1 month ago) by jfenwick
Original Path: trunk/dudley/src/CPPAdapter/dudleycpp.cpp
File size: 13269 byte(s)
I changed some files.
Updated copyright notices, added GeoComp.



1 jgs 102
2 jfenwick 3981 /*****************************************************************************
3 ksteube 1811 *
4 jfenwick 4657 * Copyright (c) 2003-2014 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 jfenwick 4657 * Development 2012-2013 by School of Earth Sciences
13     * Development from 2014 by Centre for Geoscience Computing (GeoComp)
14 jfenwick 3981 *
15     *****************************************************************************/
16 ksteube 1312
17 ksteube 1811
18 jfenwick 3231 #ifdef ESYS_MPI
19     #include "esysUtils/Esys_MPI.h"
20 ksteube 817 #endif
21 jfenwick 3082 #include "../Dudley.h"
22 jgs 472
23 jfenwick 3675 #include <pasowrap/SystemMatrixAdapter.h>
24     #include <pasowrap/TransportProblemAdapter.h>
25    
26 jgs 203 #include "MeshAdapter.h"
27     #include "MeshAdapterFactory.h"
28 jgs 102
29 jfenwick 3086 #include "DudleyAdapterException.h"
30 gross 727 // #include "esysUtils/EsysException.h"
31 robwdcock 682 #include "esysUtils/esysExceptionTranslator.h"
32 jgs 102
33 robwdcock 682 #include "escript/AbstractContinuousDomain.h"
34 jgs 102
35     #include <boost/python.hpp>
36     #include <boost/python/module.hpp>
37     #include <boost/python/def.hpp>
38     #include <boost/python/detail/defaults_gen.hpp>
39 jfenwick 2064 #include <boost/version.hpp>
40 jgs 102
41     using namespace boost::python;
42    
43 jfenwick 3082 BOOST_PYTHON_MODULE(dudleycpp)
44 jgs 102 {
45 jfenwick 2064 // This feature was added in boost v1.34
46 phornby 2076 #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
47 jfenwick 2061 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
48     docstring_options docopt(true, true, false);
49 jfenwick 2064 #endif
50 jgs 102
51 jfenwick 3994 scope().attr("__doc__") = "To use this module, please import esys.dudley";
52    
53    
54 jgs 102 //
55     // NOTE: The return_value_policy is necessary for functions that
56     // return pointers.
57 gross 1382 //
58 jfenwick 3086 register_exception_translator<dudley::DudleyAdapterException>(&(esysUtils::esysExceptionTranslator));
59 jgs 102
60 jfenwick 3082 def("LoadMesh",dudley::loadMesh,
61 jfenwick 2625 (arg("fileName")="file.nc"),":rtype: `Domain`"
62 jfenwick 1872 /* ,return_value_policy<manage_new_object>());*/
63     );
64    
65 jfenwick 3082 def("ReadMesh",dudley::readMesh,
66 jfenwick 1872 (arg("fileName")="file.fly",arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)
67     /* ,return_value_policy<manage_new_object>());*/
68 jfenwick 2625 ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
69     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
70     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
71     ":type integrationOrder: ``int``\n"
72     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
73     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
74 jgs 102
75 jfenwick 3082 def("ReadGmsh",dudley::readGmsh,
76 gross 2722 (arg("fileName")="file.msh",
77     arg("numDim"),
78     arg("integrationOrder")=-1,
79     arg("reducedIntegrationOrder")=-1,
80     arg("optimize")=true,
81     arg("useMacroElements")=false)
82 jfenwick 1872 // ,return_value_policy<manage_new_object>());
83 jfenwick 2625 ,"Read a gmsh mesh file\n\n"
84     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
85     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
86     ":type integrationOrder: ``int``\n"
87     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
88 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``\n"
89     ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
90     );
91 gross 934
92 jfenwick 3082 def ("Brick",dudley::brick,
93 jgs 102 (arg("n0")=1,arg("n1")=1,arg("n2")=1,
94     arg("order")=1,
95     arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,
96     arg("periodic0")=false,arg("periodic1")=false,arg("periodic2")=false,
97 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
98 ksteube 1312 arg("useElementsOnFace")=false,
99     arg("useFullElementOrder")=false,
100 jfenwick 1872 arg("optimize")=false)
101 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]."
102 jfenwick 3892 "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
103 jfenwick 2625 "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
104 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
105 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n:param l2:\n"
106     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
107     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
108     ":param useElementsOnFace: whether or not to use elements on face\n"
109     ":type useElementsOnFace: ``int``"
110     ":param periodic0: whether or not boundary conditions are periodic\n"
111     ":param periodic1:\n:param periodic2:\n"
112     ":param useFullElementOrder:\n:param optimize:\n"
113 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
114 jfenwick 2625 );
115 jgs 102
116 jfenwick 3082 def ("Rectangle",dudley::rectangle,
117 jgs 102 (arg("n0")=1,arg("n1")=1,arg("order")=1,
118     arg("l0")=1.0,arg("l1")=1.0,
119     arg("periodic0")=false,arg("periodic1")=false,
120 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
121 ksteube 1312 arg("useElementsOnFace")=false,
122     arg("useFullElementOrder")=false,
123 jfenwick 1872 arg("optimize")=false)
124 jfenwick 3469 ,"Creates a triangular mesh by subdividing n0 x n1 rectangular elements over the brick [0,l0] x [0,l1]."
125 jfenwick 3892 "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
126 jfenwick 2625 "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
127 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
128 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n"
129     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
130     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
131     ":param useElementsOnFace: whether or not to use elements on face\n"
132     ":type useElementsOnFace: ``int``"
133     ":param periodic0: whether or not boundary conditions are periodic\n"
134     ":param periodic1:\n"
135 gross 2722 ":param useFullElementOrder:\n:param optimize:\n"
136     ":param useMacroElements: Enable the usage of first order macro elements.\n:type useMacroElements: ``bool``\n"
137     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
138     );
139 jgs 102
140 jfenwick 3082 class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
141 jfenwick 3086 ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())
142 jfenwick 3082 .def(init<const dudley::MeshAdapter&>())
143     .def("write",&dudley::MeshAdapter::write,args("filename"),
144 jfenwick 2625 "Write the current mesh to a file with the given name.")
145 jfenwick 3082 .def("print_mesh_info",&dudley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
146 jfenwick 2625 ":param full:\n:type full: ``bool``")
147 jfenwick 3082 .def("dump",&dudley::MeshAdapter::dump,args("fileName")
148 jfenwick 2625 ,"dumps the mesh to a file with the given name.")
149 jfenwick 3082 .def("getDescription",&dudley::MeshAdapter::getDescription,
150 jfenwick 2625 ":return: a description for this domain\n:rtype: ``string``")
151 jfenwick 3082 .def("getDim",&dudley::MeshAdapter::getDim,":rtype: ``int``")
152     .def("getDataShape",&dudley::MeshAdapter::getDataShape, args("functionSpaceCode"),
153 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``")
154 jfenwick 3082 .def("getNumDataPointsGlobal",&dudley::MeshAdapter::getNumDataPointsGlobal,
155 jfenwick 2625 ":return: the number of data points summed across all MPI processes\n"
156     ":rtype: ``int``")
157 jfenwick 3082 .def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
158 jfenwick 3269 args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
159 jfenwick 2625 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
160     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
161     ":param A:\n:type A: `Data`\n"
162     ":param B:\n:type B: `Data`\n"
163     ":param C:\n:type C: `Data`\n"
164     ":param D:\n:type D: `Data`\n"
165     ":param X:\n:type X: `Data`\n"
166     ":param Y:\n:type Y: `Data`\n"
167     ":param d:\n:type d: `Data`\n"
168 jfenwick 3269 ":param d_contact:\n:type d_contact: `Data`\n"
169     ":param y_contact:\n:type y_contact: `Data`\n"
170 jfenwick 2625 )
171 jfenwick 3082 .def("addPDEToLumpedSystem",&dudley::MeshAdapter::addPDEToLumpedSystem,
172 jfenwick 2625 args("mat", "D", "d"),
173     "adds a PDE onto the lumped stiffness matrix\n\n"
174     ":param mat:\n:type mat: `Data`\n"
175     ":param D:\n:type D: `Data`\n"
176 gross 3379 ":param d:\n:type d: `Data`\n"
177     ":param useHRZ:\n:type useHRZ: bool\n"
178     )
179 jfenwick 3082 .def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,
180 jfenwick 2625 args("rhs", "X", "Y", "y", "y_contact"),
181     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
182     ":param rhs:\n:type rhs: `Data`\n"
183     ":param X:\n:type X: `Data`\n"
184     ":param Y:\n:type Y: `Data`\n"
185     ":param y:\n:type y: `Data`\n"
186 jfenwick 3269 ":param y_contact:\n:type y_contact: `Data`"
187 jfenwick 2625 )
188 jfenwick 3082 .def("addPDEToTransportProblem",&dudley::MeshAdapter::addPDEToTransportProblem,
189 jfenwick 2625 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
190     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
191     ":param source:\n:type source: `Data`\n"
192     ":param M:\n:type M: `Data`\n"
193     ":param A:\n:type A: `Data`\n"
194     ":param B:\n:type B: `Data`\n"
195     ":param C:\n:type C: `Data`\n"
196     ":param D:\n:type D: `Data`\n"
197     ":param X:\n:type X: `Data`\n"
198     ":param Y:\n:type Y: `Data`\n"
199     ":param d:\n:type d: `Data`\n"
200     ":param y:\n:type y: `Data`\n"
201     ":param d_contact:\n:type d_contact: `Data`\n"
202     ":param y_contact:\n:type y_contact: `Data`\n"
203     )
204 jfenwick 3082 .def("newOperator",&dudley::MeshAdapter::newSystemMatrix,
205 jfenwick 2625 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
206     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
207     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
208     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
209     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
210     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
211     ":param type:\n:type type: ``int``\n"
212     )
213 jfenwick 3082 .def("newTransportProblem",&dudley::MeshAdapter::newTransportProblem,
214 jfenwick 2625 args("theta", "blocksize", "functionspace", "type"),
215     "creates a TransportProblemAdapter\n\n"
216     ":param theta:\n:type theta: ``float``\n"
217     ":param blocksize:\n:type blocksize: ``int``\n"
218     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
219     ":param type:\n:type type: ``int``\n"
220     )
221 jfenwick 3082 .def("getSystemMatrixTypeId",&dudley::MeshAdapter::getSystemMatrixTypeId,
222 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
223 caltinay 4286 ":return: the identifier of the matrix type to be used for the global stiffness matrix when a particular solver, package, preconditioner, and symmetric matrix is used.\n"
224 jfenwick 2625 ":rtype: ``int``\n"
225     ":param solver:\n:type solver: ``int``\n"
226     ":param preconditioner:\n:type preconditioner: ``int``\n"
227     ":param package:\n:type package: ``int``\n"
228     ":param symmetry:\n:type symmetry: ``int``\n"
229     )
230 jfenwick 3082 .def("getTransportTypeId",&dudley::MeshAdapter::getTransportTypeId,
231 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
232 caltinay 4286 ":return: the identifier of the transport problem type to be used when a particular solver, preconditioner, package and symmetric matrix is used.\n"
233 jfenwick 2625 ":rtype: ``int``\n"
234     ":param solver:\n:type solver: ``int``\n"
235     ":param preconditioner:\n:type preconditioner: ``int``\n"
236     ":param package:\n:type package: ``int``\n"
237     ":param symmetry:\n:type symmetry: ``int``\n"
238     )
239 jfenwick 3082 .def("setX",&dudley::MeshAdapter::setNewX,
240 jfenwick 2625 args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
241 jfenwick 3082 .def("getX",&dudley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
242 jfenwick 2625 ":rtype: `Data`")
243 jfenwick 3082 .def("getNormal",&dudley::MeshAdapter::getNormal,
244 jfenwick 2625 ":return: boundary normals at the quadrature point on the face elements\n"
245     ":rtype: `Data`")
246 jfenwick 3082 .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
247 jfenwick 2625 ":rtype: `Data`")
248 jfenwick 3082 .def("setTagMap",&dudley::MeshAdapter::setTagMap,args("name","tag"),
249 jfenwick 2625 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
250     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
251 jfenwick 3082 .def("getTag",&dudley::MeshAdapter::getTag,args("name"),":return: tag id for "
252 jfenwick 2625 "``name``\n:rtype: ``string``")
253 jfenwick 3082 .def("isValidTagName",&dudley::MeshAdapter::isValidTagName,args("name"),
254 jfenwick 2625 ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
255 jfenwick 3082 .def("showTagNames",&dudley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
256     .def("getMPISize",&dudley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
257     .def("getMPIRank",&dudley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
258     .def("MPIBarrier",&dudley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
259     .def("onMasterProcessor",&dudley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
260 jgs 102
261     }

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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