/[escript]/trunk/ripley/src/ripleycpp.cpp
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Contents of /trunk/ripley/src/ripleycpp.cpp

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Revision 3991 - (show annotations)
Tue Sep 25 23:52:22 2012 UTC (6 years, 11 months ago) by caltinay
File size: 14798 byte(s)
Updated doxygen cfg file and made a few first changes to doco.

1
2 /*****************************************************************************
3 *
4 * Copyright (c) 2003-2012 by University of Queensland
5 * http://www.uq.edu.au
6 *
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 * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12 * Development since 2012 by School of Earth Sciences
13 *
14 *****************************************************************************/
15
16 #include <ripley/Brick.h>
17 #include <ripley/Rectangle.h>
18 #include <esysUtils/esysExceptionTranslator.h>
19
20 #include <boost/python.hpp>
21 #include <boost/python/module.hpp>
22 #include <boost/python/def.hpp>
23 #include <boost/python/detail/defaults_gen.hpp>
24 #include <boost/version.hpp>
25
26 using namespace boost::python;
27
28 namespace ripley {
29
30 escript::Data readBinaryGrid(std::string filename, escript::FunctionSpace fs,
31 const object& pyFirst, const object& pyNum, const object& pyShape,
32 double fill=0.)
33 {
34 int dim=fs.getDim();
35 std::vector<int> first(dim), numValues(dim), shape;
36
37 if (extract<tuple>(pyFirst).check() || extract<list>(pyFirst).check()) {
38 if (len(pyFirst)==dim) {
39 for (int i=0; i<dim; i++) {
40 first[i]=extract<int>(pyFirst[i]);
41 }
42 } else
43 throw RipleyException("Argument 'first' has wrong length");
44 } else
45 throw RipleyException("Argument 'first' must be a tuple or list");
46
47 if (extract<tuple>(pyNum).check() || extract<list>(pyNum).check()) {
48 if (len(pyNum)==dim) {
49 for (int i=0; i<dim; i++) {
50 numValues[i]=extract<int>(pyNum[i]);
51 }
52 } else
53 throw RipleyException("Argument 'numValues' has wrong length");
54 } else
55 throw RipleyException("Argument 'numValues' must be a tuple or list");
56
57 if (extract<tuple>(pyShape).check() || extract<list>(pyShape).check()) {
58 for (int i=0; i<len(pyShape); i++) {
59 shape.push_back(extract<int>(pyShape[i]));
60 }
61 } else
62 throw RipleyException("Argument 'shape' must be a tuple or list");
63
64 const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
65 if (!dom)
66 throw RipleyException("Function space must be on a ripley domain");
67
68
69 escript::Data res(fill, shape, fs, true);
70
71 dom->readBinaryGrid(res, filename, first, numValues);
72 return res;
73 }
74
75 // These wrappers are required to make the shared pointers work through the
76 // Python wrapper
77
78 // The double for n? is just to keep python happy when people need to deal with
79 // truediv
80 escript::Domain_ptr _brick(double _n0, double _n1, double _n2, const object& l0,
81 const object& l1, const object& l2, int d0, int d1, int d2)
82 {
83 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1), n2=static_cast<int>(_n2);
84 double x0=0., x1=1., y0=0., y1=1., z0=0., z1=1.;
85 if (extract<tuple>(l0).check()) {
86 tuple x=extract<tuple>(l0);
87 if (len(x)==2) {
88 x0=extract<double>(x[0]);
89 x1=extract<double>(x[1]);
90 } else
91 throw RipleyException("Argument l0 must be a float or 2-tuple");
92 } else if (extract<double>(l0).check()) {
93 x1=extract<double>(l0);
94 } else
95 throw RipleyException("Argument l0 must be a float or 2-tuple");
96
97 if (extract<tuple>(l1).check()) {
98 tuple y=extract<tuple>(l1);
99 if (len(y)==2) {
100 y0=extract<double>(y[0]);
101 y1=extract<double>(y[1]);
102 } else
103 throw RipleyException("Argument l1 must be a float or 2-tuple");
104 } else if (extract<double>(l1).check()) {
105 y1=extract<double>(l1);
106 } else
107 throw RipleyException("Argument l1 must be a float or 2-tuple");
108
109 if (extract<tuple>(l2).check()) {
110 tuple z=extract<tuple>(l2);
111 if (len(z)==2) {
112 z0=extract<double>(z[0]);
113 z1=extract<double>(z[1]);
114 } else
115 throw RipleyException("Argument l2 must be a float or 2-tuple");
116 } else if (extract<double>(l2).check()) {
117 z1=extract<double>(l2);
118 } else
119 throw RipleyException("Argument l2 must be a float or 2-tuple");
120
121 return escript::Domain_ptr(new Brick(n0,n1,n2, x0,y0,z0, x1,y1,z1, d0,d1,d2));
122 }
123
124 const int _q[]={0x61686969,0x746c4144,0x79616e43};
125 escript::Domain_ptr _rectangle(double _n0, double _n1, const object& l0,
126 const object& l1, int d0, int d1)
127 {
128 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1);
129 double x0=0., x1=1., y0=0., y1=1.;
130 if (extract<tuple>(l0).check()) {
131 tuple x=extract<tuple>(l0);
132 if (len(x)==2) {
133 x0=extract<double>(x[0]);
134 x1=extract<double>(x[1]);
135 } else
136 throw RipleyException("Argument l0 must be a float or 2-tuple");
137 } else if (extract<double>(l0).check()) {
138 x1=extract<double>(l0);
139 } else
140 throw RipleyException("Argument l0 must be a float or 2-tuple");
141
142 if (extract<tuple>(l1).check()) {
143 tuple y=extract<tuple>(l1);
144 if (len(y)==2) {
145 y0=extract<double>(y[0]);
146 y1=extract<double>(y[1]);
147 } else
148 throw RipleyException("Argument l1 must be a float or 2-tuple");
149 } else if (extract<double>(l1).check()) {
150 y1=extract<double>(l1);
151 } else
152 throw RipleyException("Argument l1 must be a float or 2-tuple");
153
154 return escript::Domain_ptr(new Rectangle(n0,n1, x0,y0, x1,y1, d0,d1));
155 }
156 std::string _who(){int a[]={_q[0]^42,_q[1]^42,_q[2]^42,0};return (char*)&a[0];}
157
158 } // end of namespace
159
160
161 BOOST_PYTHON_MODULE(ripleycpp)
162 {
163 // This feature was added in boost v1.34
164 #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
165 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
166 docstring_options docopt(true, true, false);
167 #endif
168
169 register_exception_translator<ripley::RipleyException>(&(esysUtils::esysExceptionTranslator));
170
171 def("Brick", ripley::_brick, (arg("n0"),arg("n1"),arg("n2"),arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,arg("d0")=-1,arg("d1")=-1,arg("d2")=-1),
172 "Creates a hexagonal mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2].\n\n"
173 ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
174 ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
175 ":param n2: number of elements in direction 2\n:type n2: ``int``\n"
176 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
177 ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
178 ":param l2: length of side 2 or coordinate range of side 2\n:type l2: ``float`` or ``tuple``\n"
179 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
180 ":param d1: number of subdivisions in direction 1\n:type d1: ``int``\n"
181 ":param d2: number of subdivisions in direction 2\n:type d2: ``int``");
182
183 def("Rectangle", ripley::_rectangle, (arg("n0"),arg("n1"),arg("l0")=1.0,arg("l1")=1.0,arg("d0")=-1,arg("d1")=-1),
184 "Creates a rectangular mesh with n0 x n1 elements over the rectangle [0,l0] x [0,l1].\n\n"
185 ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
186 ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
187 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
188 ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
189 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
190 ":param d1: number of subdivisions in direction 1\n:type d1: ``int``");
191 def("_theculprit_", ripley::_who);
192 def("LoadMesh", ripley::RipleyDomain::loadMesh, (arg("filename")),
193 "Loads a ripley domain from a dump file" ":rtype: `Domain`");
194
195 def("ReadMesh", ripley::RipleyDomain::readMesh, (arg("filename")),
196 "Reads a ripley domain from a file created by write().\n\n"
197 ":rtype: `RipleyDomain`\n:param filename:\n:type filename: ``string``\n");
198
199 def("_readBinaryGrid", &ripley::readBinaryGrid, (arg("filename"), arg("functionspace"), arg("first"), arg("numValues"), arg("shape"), arg("fill")=0.));
200
201 class_<ripley::RipleyDomain, bases<escript::AbstractContinuousDomain> >
202 ("RipleyDomain", "", no_init)
203 .def("write", &ripley::RipleyDomain::write, args("filename"),
204 "Writes the current mesh to a file with the given name. It can subsequently be recovered using ReadMesh().")
205 .def("print_mesh_info", &ripley::RipleyDomain::Print_Mesh_Info, (arg("full")=false),
206 "Prints out a summary about the mesh.\n"
207 ":param full: whether to output additional data\n:type full: ``bool``")
208 .def("dump", &ripley::RipleyDomain::dump, args("filename"),
209 "Dumps the mesh to a file with the given name.")
210 .def("getDescription", &ripley::RipleyDomain::getDescription,
211 ":return: a description for this domain\n:rtype: ``string``")
212 .def("getDim", &ripley::RipleyDomain::getDim, ":rtype: ``int``")
213 .def("getDataShape", &ripley::RipleyDomain::getDataShape, args("functionSpaceCode"),
214 ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
215 .def("getNumDataPointsGlobal", &ripley::RipleyDomain::getNumDataPointsGlobal,
216 ":return: the number of data points summed across all MPI processes\n"
217 ":rtype: ``int``")
218 .def("addPDEToSystem",&ripley::RipleyDomain::addPDEToSystem,
219 args("mat", "rhs", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
220 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
221 ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
222 ":param A:\n:type A: `Data`\n"
223 ":param B:\n:type B: `Data`\n"
224 ":param C:\n:type C: `Data`\n"
225 ":param D:\n:type D: `Data`\n"
226 ":param X:\n:type X: `Data`\n"
227 ":param Y:\n:type Y: `Data`\n"
228 ":param d:\n:type d: `Data`\n"
229 ":param d_contact:\n:type d_contact: `Data`\n"
230 ":param y_contact:\n:type y_contact: `Data`"
231 )
232 .def("addPDEToRHS",&ripley::RipleyDomain::addPDEToRHS,
233 args("rhs", "X", "Y", "y", "y_contact"),
234 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
235 ":param rhs:\n:type rhs: `Data`\n"
236 ":param X:\n:type X: `Data`\n"
237 ":param Y:\n:type Y: `Data`\n"
238 ":param y:\n:type y: `Data`\n"
239 ":param y_contact:\n:type y_contact: `Data`"
240 )
241 .def("addPDEToTransportProblem",&ripley::RipleyDomain::addPDEToTransportProblem,
242 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
243 ":param tp:\n:type tp: `TransportProblemAdapter`\n"
244 ":param source:\n:type source: `Data`\n"
245 ":param M:\n:type M: `Data`\n"
246 ":param A:\n:type A: `Data`\n"
247 ":param B:\n:type B: `Data`\n"
248 ":param C:\n:type C: `Data`\n"
249 ":param D:\n:type D: `Data`\n"
250 ":param X:\n:type X: `Data`\n"
251 ":param Y:\n:type Y: `Data`\n"
252 ":param d:\n:type d: `Data`\n"
253 ":param y:\n:type y: `Data`\n"
254 ":param d_contact:\n:type d_contact: `Data`\n"
255 ":param y_contact:\n:type y_contact: `Data`"
256 )
257 .def("newOperator",&ripley::RipleyDomain::newSystemMatrix,
258 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
259 "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
260 ":param row_blocksize:\n:type row_blocksize: ``int``\n"
261 ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
262 ":param column_blocksize:\n:type column_blocksize: ``int``\n"
263 ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
264 ":param type:\n:type type: ``int``"
265 )
266 .def("newTransportProblem",&ripley::RipleyDomain::newTransportProblem,
267 args("theta", "blocksize", "functionspace", "type"),
268 "creates a TransportProblemAdapter\n\n"
269 ":param theta:\n:type theta: ``float``\n"
270 ":param blocksize:\n:type blocksize: ``int``\n"
271 ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
272 ":param type:\n:type type: ``int``"
273 )
274 .def("getSystemMatrixTypeId",&ripley::RipleyDomain::getSystemMatrixTypeId,
275 args("solver", "preconditioner", "package", "symmetry"),
276 ":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"
277 ":rtype: ``int``\n"
278 ":param solver:\n:type solver: ``int``\n"
279 ":param preconditioner:\n:type preconditioner: ``int``\n"
280 ":param package:\n:type package: ``int``\n"
281 ":param symmetry:\n:type symmetry: ``int``"
282 )
283 .def("getTransportTypeId",&ripley::RipleyDomain::getTransportTypeId,
284 args("solver", "preconditioner", "package", "symmetry"),
285 ":return: the identifier of the transport problem type to be used when a particular solver, preconditioner, package and symmetric matrix is used.\n"
286 ":rtype: ``int``\n"
287 ":param solver:\n:type solver: ``int``\n"
288 ":param preconditioner:\n:type preconditioner: ``int``\n"
289 ":param package:\n:type package: ``int``\n"
290 ":param symmetry:\n:type symmetry: ``int``"
291 )
292 .def("getX",&ripley::RipleyDomain::getX, ":return: locations in the FEM nodes\n\n"
293 ":rtype: `Data`")
294 .def("getNormal",&ripley::RipleyDomain::getNormal,
295 ":return: boundary normals at the quadrature point on the face elements\n"
296 ":rtype: `Data`")
297 .def("getSize",&ripley::RipleyDomain::getSize,":return: the element size\n"
298 ":rtype: `Data`")
299 .def("setTagMap",&ripley::RipleyDomain::setTagMap,args("name","tag"),
300 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
301 ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
302 .def("getTag",&ripley::RipleyDomain::getTag,args("name"),":return: tag id for "
303 "``name``\n:rtype: ``string``")
304 .def("isValidTagName",&ripley::RipleyDomain::isValidTagName,args("name"),
305 ":return: True if ``name`` corresponds to a tag, otherwise False\n:rtype: ``bool``")
306 .def("showTagNames",&ripley::RipleyDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
307 .def("getMPISize",&ripley::RipleyDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
308 .def("getMPIRank",&ripley::RipleyDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
309 .def("MPIBarrier",&ripley::RipleyDomain::MPIBarrier,"Wait until all processes have reached this point")
310 .def("onMasterProcessor",&ripley::RipleyDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
311
312 class_<ripley::Brick, bases<ripley::RipleyDomain> >("RipleyBrick", "", no_init);
313 class_<ripley::Rectangle, bases<ripley::RipleyDomain> >("RipleyRectangle", "", no_init);
314 }
315

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