/[escript]/branches/diaplayground/dudley/src/CPPAdapter/dudleycpp.cpp
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Revision 4346 - (hide annotations)
Tue Apr 2 04:46:45 2013 UTC (6 years ago) by jfenwick
Original Path: trunk/dudley/src/CPPAdapter/dudleycpp.cpp
File size: 13201 byte(s)
Bringing the changes from doubleplusgood branch.
Can't merge directly because svn doesn't transfer changes to renamed files (mutter grumble).
1 jgs 102
2 jfenwick 3981 /*****************************************************************************
3 ksteube 1811 *
4 jfenwick 4154 * Copyright (c) 2003-2013 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 jfenwick 3082 #include "../Dudley.h"
21 jgs 472
22 jfenwick 3675 #include <pasowrap/SystemMatrixAdapter.h>
23     #include <pasowrap/TransportProblemAdapter.h>
24    
25 jgs 203 #include "MeshAdapter.h"
26     #include "MeshAdapterFactory.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 jfenwick 3082 BOOST_PYTHON_MODULE(dudleycpp)
43 jgs 102 {
44 jfenwick 2064 // This feature was added in boost v1.34
45 phornby 2076 #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
46 jfenwick 2061 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
47     docstring_options docopt(true, true, false);
48 jfenwick 2064 #endif
49 jgs 102
50 jfenwick 3994 scope().attr("__doc__") = "To use this module, please import esys.dudley";
51    
52    
53 jgs 102 //
54     // NOTE: The return_value_policy is necessary for functions that
55     // return pointers.
56 gross 1382 //
57 jfenwick 3086 register_exception_translator<dudley::DudleyAdapterException>(&(esysUtils::esysExceptionTranslator));
58 jgs 102
59 jfenwick 3082 def("LoadMesh",dudley::loadMesh,
60 jfenwick 2625 (arg("fileName")="file.nc"),":rtype: `Domain`"
61 jfenwick 1872 /* ,return_value_policy<manage_new_object>());*/
62     );
63    
64 jfenwick 3082 def("ReadMesh",dudley::readMesh,
65 jfenwick 1872 (arg("fileName")="file.fly",arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)
66     /* ,return_value_policy<manage_new_object>());*/
67 jfenwick 2625 ,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
68     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
69     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
70     ":type integrationOrder: ``int``\n"
71     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
72     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
73 jgs 102
74 jfenwick 3082 def("ReadGmsh",dudley::readGmsh,
75 gross 2722 (arg("fileName")="file.msh",
76     arg("numDim"),
77     arg("integrationOrder")=-1,
78     arg("reducedIntegrationOrder")=-1,
79     arg("optimize")=true,
80     arg("useMacroElements")=false)
81 jfenwick 1872 // ,return_value_policy<manage_new_object>());
82 jfenwick 2625 ,"Read a gmsh mesh file\n\n"
83     ":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
84     ":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
85     ":type integrationOrder: ``int``\n"
86     ":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
87 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``\n"
88     ":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
89     );
90 gross 934
91 jfenwick 3082 def ("Brick",dudley::brick,
92 jgs 102 (arg("n0")=1,arg("n1")=1,arg("n2")=1,
93     arg("order")=1,
94     arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,
95     arg("periodic0")=false,arg("periodic1")=false,arg("periodic2")=false,
96 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
97 ksteube 1312 arg("useElementsOnFace")=false,
98     arg("useFullElementOrder")=false,
99 jfenwick 1872 arg("optimize")=false)
100 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]."
101 jfenwick 3892 "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
102 jfenwick 2625 "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
103 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
104 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n:param l2:\n"
105     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
106     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
107     ":param useElementsOnFace: whether or not to use elements on face\n"
108     ":type useElementsOnFace: ``int``"
109     ":param periodic0: whether or not boundary conditions are periodic\n"
110     ":param periodic1:\n:param periodic2:\n"
111     ":param useFullElementOrder:\n:param optimize:\n"
112 gross 2722 ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
113 jfenwick 2625 );
114 jgs 102
115 jfenwick 3082 def ("Rectangle",dudley::rectangle,
116 jgs 102 (arg("n0")=1,arg("n1")=1,arg("order")=1,
117     arg("l0")=1.0,arg("l1")=1.0,
118     arg("periodic0")=false,arg("periodic1")=false,
119 gross 1059 arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
120 ksteube 1312 arg("useElementsOnFace")=false,
121     arg("useFullElementOrder")=false,
122 jfenwick 1872 arg("optimize")=false)
123 jfenwick 3469 ,"Creates a triangular mesh by subdividing n0 x n1 rectangular elements over the brick [0,l0] x [0,l1]."
124 jfenwick 3892 "We accept floating point values for n0, n1 only to ease transition of scripts to python3 when the time comes."
125 jfenwick 2625 "\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
126 gross 2722 ":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
127 jfenwick 2625 ":param l0: length of side 0\n:param l1:\n"
128     ":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
129     ":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
130     ":param useElementsOnFace: whether or not to use elements on face\n"
131     ":type useElementsOnFace: ``int``"
132     ":param periodic0: whether or not boundary conditions are periodic\n"
133     ":param periodic1:\n"
134 gross 2722 ":param useFullElementOrder:\n:param optimize:\n"
135     ":param useMacroElements: Enable the usage of first order macro elements.\n:type useMacroElements: ``bool``\n"
136     ":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
137     );
138 jgs 102
139 jfenwick 3082 class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
140 jfenwick 3086 ("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())
141 jfenwick 3082 .def(init<const dudley::MeshAdapter&>())
142     .def("write",&dudley::MeshAdapter::write,args("filename"),
143 jfenwick 2625 "Write the current mesh to a file with the given name.")
144 jfenwick 3082 .def("print_mesh_info",&dudley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
145 jfenwick 2625 ":param full:\n:type full: ``bool``")
146 jfenwick 3082 .def("dump",&dudley::MeshAdapter::dump,args("fileName")
147 jfenwick 2625 ,"dumps the mesh to a file with the given name.")
148 jfenwick 3082 .def("getDescription",&dudley::MeshAdapter::getDescription,
149 jfenwick 2625 ":return: a description for this domain\n:rtype: ``string``")
150 jfenwick 3082 .def("getDim",&dudley::MeshAdapter::getDim,":rtype: ``int``")
151     .def("getDataShape",&dudley::MeshAdapter::getDataShape, args("functionSpaceCode"),
152 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``")
153 jfenwick 3082 .def("getNumDataPointsGlobal",&dudley::MeshAdapter::getNumDataPointsGlobal,
154 jfenwick 2625 ":return: the number of data points summed across all MPI processes\n"
155     ":rtype: ``int``")
156 jfenwick 3082 .def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
157 jfenwick 3269 args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
158 jfenwick 2625 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
159     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
160     ":param A:\n:type A: `Data`\n"
161     ":param B:\n:type B: `Data`\n"
162     ":param C:\n:type C: `Data`\n"
163     ":param D:\n:type D: `Data`\n"
164     ":param X:\n:type X: `Data`\n"
165     ":param Y:\n:type Y: `Data`\n"
166     ":param d:\n:type d: `Data`\n"
167 jfenwick 3269 ":param d_contact:\n:type d_contact: `Data`\n"
168     ":param y_contact:\n:type y_contact: `Data`\n"
169 jfenwick 2625 )
170 jfenwick 3082 .def("addPDEToLumpedSystem",&dudley::MeshAdapter::addPDEToLumpedSystem,
171 jfenwick 2625 args("mat", "D", "d"),
172     "adds a PDE onto the lumped stiffness matrix\n\n"
173     ":param mat:\n:type mat: `Data`\n"
174     ":param D:\n:type D: `Data`\n"
175 gross 3379 ":param d:\n:type d: `Data`\n"
176     ":param useHRZ:\n:type useHRZ: bool\n"
177     )
178 jfenwick 3082 .def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,
179 jfenwick 2625 args("rhs", "X", "Y", "y", "y_contact"),
180     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
181     ":param rhs:\n:type rhs: `Data`\n"
182     ":param X:\n:type X: `Data`\n"
183     ":param Y:\n:type Y: `Data`\n"
184     ":param y:\n:type y: `Data`\n"
185 jfenwick 3269 ":param y_contact:\n:type y_contact: `Data`"
186 jfenwick 2625 )
187 jfenwick 3082 .def("addPDEToTransportProblem",&dudley::MeshAdapter::addPDEToTransportProblem,
188 jfenwick 2625 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
189     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
190     ":param source:\n:type source: `Data`\n"
191     ":param M:\n:type M: `Data`\n"
192     ":param A:\n:type A: `Data`\n"
193     ":param B:\n:type B: `Data`\n"
194     ":param C:\n:type C: `Data`\n"
195     ":param D:\n:type D: `Data`\n"
196     ":param X:\n:type X: `Data`\n"
197     ":param Y:\n:type Y: `Data`\n"
198     ":param d:\n:type d: `Data`\n"
199     ":param y:\n:type y: `Data`\n"
200     ":param d_contact:\n:type d_contact: `Data`\n"
201     ":param y_contact:\n:type y_contact: `Data`\n"
202     )
203 jfenwick 3082 .def("newOperator",&dudley::MeshAdapter::newSystemMatrix,
204 jfenwick 2625 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
205     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
206     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
207     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
208     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
209     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
210     ":param type:\n:type type: ``int``\n"
211     )
212 jfenwick 3082 .def("newTransportProblem",&dudley::MeshAdapter::newTransportProblem,
213 jfenwick 2625 args("theta", "blocksize", "functionspace", "type"),
214     "creates a TransportProblemAdapter\n\n"
215     ":param theta:\n:type theta: ``float``\n"
216     ":param blocksize:\n:type blocksize: ``int``\n"
217     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
218     ":param type:\n:type type: ``int``\n"
219     )
220 jfenwick 3082 .def("getSystemMatrixTypeId",&dudley::MeshAdapter::getSystemMatrixTypeId,
221 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
222 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"
223 jfenwick 2625 ":rtype: ``int``\n"
224     ":param solver:\n:type solver: ``int``\n"
225     ":param preconditioner:\n:type preconditioner: ``int``\n"
226     ":param package:\n:type package: ``int``\n"
227     ":param symmetry:\n:type symmetry: ``int``\n"
228     )
229 jfenwick 3082 .def("getTransportTypeId",&dudley::MeshAdapter::getTransportTypeId,
230 jfenwick 2625 args("solver", "preconditioner", "package", "symmetry"),
231 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"
232 jfenwick 2625 ":rtype: ``int``\n"
233     ":param solver:\n:type solver: ``int``\n"
234     ":param preconditioner:\n:type preconditioner: ``int``\n"
235     ":param package:\n:type package: ``int``\n"
236     ":param symmetry:\n:type symmetry: ``int``\n"
237     )
238 jfenwick 3082 .def("setX",&dudley::MeshAdapter::setNewX,
239 jfenwick 2625 args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
240 jfenwick 3082 .def("getX",&dudley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
241 jfenwick 2625 ":rtype: `Data`")
242 jfenwick 3082 .def("getNormal",&dudley::MeshAdapter::getNormal,
243 jfenwick 2625 ":return: boundary normals at the quadrature point on the face elements\n"
244     ":rtype: `Data`")
245 jfenwick 3082 .def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
246 jfenwick 2625 ":rtype: `Data`")
247 jfenwick 3082 .def("setTagMap",&dudley::MeshAdapter::setTagMap,args("name","tag"),
248 jfenwick 2625 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
249     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
250 jfenwick 3082 .def("getTag",&dudley::MeshAdapter::getTag,args("name"),":return: tag id for "
251 jfenwick 2625 "``name``\n:rtype: ``string``")
252 jfenwick 3082 .def("isValidTagName",&dudley::MeshAdapter::isValidTagName,args("name"),
253 jfenwick 2625 ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
254 jfenwick 3082 .def("showTagNames",&dudley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
255     .def("getMPISize",&dudley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
256     .def("getMPIRank",&dudley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
257     .def("MPIBarrier",&dudley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
258     .def("onMasterProcessor",&dudley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
259 jgs 102
260     }

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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