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

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Revision 4154 - (show annotations)
Tue Jan 22 09:30:23 2013 UTC (6 years, 3 months ago) by jfenwick
File size: 16700 byte(s)
Round 1 of copyright fixes
1
2 /*****************************************************************************
3 *
4 * Copyright (c) 2003-2013 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 escript::Data readNcGrid(std::string filename, std::string varname,
76 escript::FunctionSpace fs, const object& pyFirst, const object& pyNum,
77 const object& pyShape, double fill=0.)
78 {
79 int dim=fs.getDim();
80 std::vector<int> first(dim), numValues(dim), shape;
81
82 if (extract<tuple>(pyFirst).check() || extract<list>(pyFirst).check()) {
83 if (len(pyFirst)==dim) {
84 for (int i=0; i<dim; i++) {
85 first[i]=extract<int>(pyFirst[i]);
86 }
87 } else
88 throw RipleyException("Argument 'first' has wrong length");
89 } else
90 throw RipleyException("Argument 'first' must be a tuple or list");
91
92 if (extract<tuple>(pyNum).check() || extract<list>(pyNum).check()) {
93 if (len(pyNum)==dim) {
94 for (int i=0; i<dim; i++) {
95 numValues[i]=extract<int>(pyNum[i]);
96 }
97 } else
98 throw RipleyException("Argument 'numValues' has wrong length");
99 } else
100 throw RipleyException("Argument 'numValues' must be a tuple or list");
101
102 if (extract<tuple>(pyShape).check() || extract<list>(pyShape).check()) {
103 for (int i=0; i<len(pyShape); i++) {
104 shape.push_back(extract<int>(pyShape[i]));
105 }
106 } else
107 throw RipleyException("Argument 'shape' must be a tuple or list");
108
109 const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
110 if (!dom)
111 throw RipleyException("Function space must be on a ripley domain");
112
113
114 escript::Data res(fill, shape, fs, true);
115
116 dom->readNcGrid(res, filename, varname, first, numValues);
117 return res;
118 }
119
120 // These wrappers are required to make the shared pointers work through the
121 // Python wrapper
122
123 // The double for n? is just to keep python happy when people need to deal with
124 // truediv
125 escript::Domain_ptr _brick(double _n0, double _n1, double _n2, const object& l0,
126 const object& l1, const object& l2, int d0, int d1, int d2)
127 {
128 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1), n2=static_cast<int>(_n2);
129 double x0=0., x1=1., y0=0., y1=1., z0=0., z1=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 if (extract<tuple>(l2).check()) {
155 tuple z=extract<tuple>(l2);
156 if (len(z)==2) {
157 z0=extract<double>(z[0]);
158 z1=extract<double>(z[1]);
159 } else
160 throw RipleyException("Argument l2 must be a float or 2-tuple");
161 } else if (extract<double>(l2).check()) {
162 z1=extract<double>(l2);
163 } else
164 throw RipleyException("Argument l2 must be a float or 2-tuple");
165
166 return escript::Domain_ptr(new Brick(n0,n1,n2, x0,y0,z0, x1,y1,z1, d0,d1,d2));
167 }
168
169 const int _q[]={0x61686969,0x746c4144,0x79616e43};
170 escript::Domain_ptr _rectangle(double _n0, double _n1, const object& l0,
171 const object& l1, int d0, int d1)
172 {
173 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1);
174 double x0=0., x1=1., y0=0., y1=1.;
175 if (extract<tuple>(l0).check()) {
176 tuple x=extract<tuple>(l0);
177 if (len(x)==2) {
178 x0=extract<double>(x[0]);
179 x1=extract<double>(x[1]);
180 } else
181 throw RipleyException("Argument l0 must be a float or 2-tuple");
182 } else if (extract<double>(l0).check()) {
183 x1=extract<double>(l0);
184 } else
185 throw RipleyException("Argument l0 must be a float or 2-tuple");
186
187 if (extract<tuple>(l1).check()) {
188 tuple y=extract<tuple>(l1);
189 if (len(y)==2) {
190 y0=extract<double>(y[0]);
191 y1=extract<double>(y[1]);
192 } else
193 throw RipleyException("Argument l1 must be a float or 2-tuple");
194 } else if (extract<double>(l1).check()) {
195 y1=extract<double>(l1);
196 } else
197 throw RipleyException("Argument l1 must be a float or 2-tuple");
198
199 return escript::Domain_ptr(new Rectangle(n0,n1, x0,y0, x1,y1, d0,d1));
200 }
201 std::string _who(){int a[]={_q[0]^42,_q[1]^42,_q[2]^42,0};return (char*)&a[0];}
202
203 } // end of namespace
204
205
206 BOOST_PYTHON_MODULE(ripleycpp)
207 {
208 // This feature was added in boost v1.34
209 #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
210 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
211 docstring_options docopt(true, true, false);
212 #endif
213
214 register_exception_translator<ripley::RipleyException>(&(esysUtils::esysExceptionTranslator));
215
216 scope().attr("__doc__") = "To use this module, please import esys.ripley";
217
218
219 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),
220 "Creates a hexagonal mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2].\n\n"
221 ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
222 ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
223 ":param n2: number of elements in direction 2\n:type n2: ``int``\n"
224 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
225 ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
226 ":param l2: length of side 2 or coordinate range of side 2\n:type l2: ``float`` or ``tuple``\n"
227 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
228 ":param d1: number of subdivisions in direction 1\n:type d1: ``int``\n"
229 ":param d2: number of subdivisions in direction 2\n:type d2: ``int``");
230
231 def("Rectangle", ripley::_rectangle, (arg("n0"),arg("n1"),arg("l0")=1.0,arg("l1")=1.0,arg("d0")=-1,arg("d1")=-1),
232 "Creates a rectangular mesh with n0 x n1 elements over the rectangle [0,l0] x [0,l1].\n\n"
233 ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
234 ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
235 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
236 ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
237 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
238 ":param d1: number of subdivisions in direction 1\n:type d1: ``int``");
239 def("_theculprit_", ripley::_who);
240 def("LoadMesh", ripley::RipleyDomain::loadMesh, (arg("filename")),
241 "Loads a ripley domain from a dump file" ":rtype: `Domain`");
242
243 def("ReadMesh", ripley::RipleyDomain::readMesh, (arg("filename")),
244 "Reads a ripley domain from a file created by write().\n\n"
245 ":rtype: `RipleyDomain`\n:param filename:\n:type filename: ``string``\n");
246
247 def("_readBinaryGrid", &ripley::readBinaryGrid, (arg("filename"), arg("functionspace"), arg("first"), arg("numValues"), arg("shape"), arg("fill")=0.));
248
249 def("_readNcGrid", &ripley::readNcGrid, (arg("filename"), arg("varname"), arg("functionspace"), arg("first"), arg("numValues"), arg("shape"), arg("fill")=0.));
250
251 class_<ripley::RipleyDomain, bases<escript::AbstractContinuousDomain> >
252 ("RipleyDomain", "", no_init)
253 .def("write", &ripley::RipleyDomain::write, args("filename"),
254 "Writes the current mesh to a file with the given name. It can subsequently be recovered using ReadMesh().")
255 .def("print_mesh_info", &ripley::RipleyDomain::Print_Mesh_Info, (arg("full")=false),
256 "Prints out a summary about the mesh.\n"
257 ":param full: whether to output additional data\n:type full: ``bool``")
258 .def("dump", &ripley::RipleyDomain::dump, args("filename"),
259 "Dumps the mesh to a file with the given name.")
260 .def("getDescription", &ripley::RipleyDomain::getDescription,
261 ":return: a description for this domain\n:rtype: ``string``")
262 .def("getDim", &ripley::RipleyDomain::getDim, ":rtype: ``int``")
263 .def("getDataShape", &ripley::RipleyDomain::getDataShape, args("functionSpaceCode"),
264 ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
265 .def("getNumDataPointsGlobal", &ripley::RipleyDomain::getNumDataPointsGlobal,
266 ":return: the number of data points summed across all MPI processes\n"
267 ":rtype: ``int``")
268 .def("addPDEToSystem",&ripley::RipleyDomain::addPDEToSystem,
269 args("mat", "rhs", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
270 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
271 ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
272 ":param A:\n:type A: `Data`\n"
273 ":param B:\n:type B: `Data`\n"
274 ":param C:\n:type C: `Data`\n"
275 ":param D:\n:type D: `Data`\n"
276 ":param X:\n:type X: `Data`\n"
277 ":param Y:\n:type Y: `Data`\n"
278 ":param d:\n:type d: `Data`\n"
279 ":param d_contact:\n:type d_contact: `Data`\n"
280 ":param y_contact:\n:type y_contact: `Data`"
281 )
282 .def("addPDEToRHS",&ripley::RipleyDomain::addPDEToRHS,
283 args("rhs", "X", "Y", "y", "y_contact"),
284 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
285 ":param rhs:\n:type rhs: `Data`\n"
286 ":param X:\n:type X: `Data`\n"
287 ":param Y:\n:type Y: `Data`\n"
288 ":param y:\n:type y: `Data`\n"
289 ":param y_contact:\n:type y_contact: `Data`"
290 )
291 .def("addPDEToTransportProblem",&ripley::RipleyDomain::addPDEToTransportProblem,
292 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
293 ":param tp:\n:type tp: `TransportProblemAdapter`\n"
294 ":param source:\n:type source: `Data`\n"
295 ":param M:\n:type M: `Data`\n"
296 ":param A:\n:type A: `Data`\n"
297 ":param B:\n:type B: `Data`\n"
298 ":param C:\n:type C: `Data`\n"
299 ":param D:\n:type D: `Data`\n"
300 ":param X:\n:type X: `Data`\n"
301 ":param Y:\n:type Y: `Data`\n"
302 ":param d:\n:type d: `Data`\n"
303 ":param y:\n:type y: `Data`\n"
304 ":param d_contact:\n:type d_contact: `Data`\n"
305 ":param y_contact:\n:type y_contact: `Data`"
306 )
307 .def("newOperator",&ripley::RipleyDomain::newSystemMatrix,
308 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
309 "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
310 ":param row_blocksize:\n:type row_blocksize: ``int``\n"
311 ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
312 ":param column_blocksize:\n:type column_blocksize: ``int``\n"
313 ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
314 ":param type:\n:type type: ``int``"
315 )
316 .def("newTransportProblem",&ripley::RipleyDomain::newTransportProblem,
317 args("theta", "blocksize", "functionspace", "type"),
318 "creates a TransportProblemAdapter\n\n"
319 ":param theta:\n:type theta: ``float``\n"
320 ":param blocksize:\n:type blocksize: ``int``\n"
321 ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
322 ":param type:\n:type type: ``int``"
323 )
324 .def("getSystemMatrixTypeId",&ripley::RipleyDomain::getSystemMatrixTypeId,
325 args("solver", "preconditioner", "package", "symmetry"),
326 ":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"
327 ":rtype: ``int``\n"
328 ":param solver:\n:type solver: ``int``\n"
329 ":param preconditioner:\n:type preconditioner: ``int``\n"
330 ":param package:\n:type package: ``int``\n"
331 ":param symmetry:\n:type symmetry: ``int``"
332 )
333 .def("getTransportTypeId",&ripley::RipleyDomain::getTransportTypeId,
334 args("solver", "preconditioner", "package", "symmetry"),
335 ":return: the identifier of the transport problem type to be used when a particular solver, preconditioner, package and symmetric matrix is used.\n"
336 ":rtype: ``int``\n"
337 ":param solver:\n:type solver: ``int``\n"
338 ":param preconditioner:\n:type preconditioner: ``int``\n"
339 ":param package:\n:type package: ``int``\n"
340 ":param symmetry:\n:type symmetry: ``int``"
341 )
342 .def("getX",&ripley::RipleyDomain::getX, ":return: locations in the FEM nodes\n\n"
343 ":rtype: `Data`")
344 .def("getNormal",&ripley::RipleyDomain::getNormal,
345 ":return: boundary normals at the quadrature point on the face elements\n"
346 ":rtype: `Data`")
347 .def("getSize",&ripley::RipleyDomain::getSize,":return: the element size\n"
348 ":rtype: `Data`")
349 .def("setTagMap",&ripley::RipleyDomain::setTagMap,args("name","tag"),
350 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
351 ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
352 .def("getTag",&ripley::RipleyDomain::getTag,args("name"),":return: tag id for "
353 "``name``\n:rtype: ``string``")
354 .def("isValidTagName",&ripley::RipleyDomain::isValidTagName,args("name"),
355 ":return: True if ``name`` corresponds to a tag, otherwise False\n:rtype: ``bool``")
356 .def("showTagNames",&ripley::RipleyDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
357 .def("getMPISize",&ripley::RipleyDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
358 .def("getMPIRank",&ripley::RipleyDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
359 .def("MPIBarrier",&ripley::RipleyDomain::MPIBarrier,"Wait until all processes have reached this point")
360 .def("onMasterProcessor",&ripley::RipleyDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
361
362 class_<ripley::Brick, bases<ripley::RipleyDomain> >("RipleyBrick", "", no_init);
363 class_<ripley::Rectangle, bases<ripley::RipleyDomain> >("RipleyRectangle", "", no_init);
364 }
365

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