/[escript]/trunk/escript/src/escriptcpp.cpp
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Contents of /trunk/escript/src/escriptcpp.cpp

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Revision 1800 - (show annotations)
Thu Sep 18 05:28:20 2008 UTC (11 years ago) by ksteube
File size: 13507 byte(s)
Serialized parallel I/O when writing mesh or data to NetCDF file on multiple MPI processors.
Added domain method getMPIComm() to complement getMPISize() and getMPIRank().

1
2 /* $Id$ */
3
4 /*******************************************************
5 *
6 * Copyright 2003-2007 by ACceSS MNRF
7 * Copyright 2007 by University of Queensland
8 *
9 * http://esscc.uq.edu.au
10 * Primary Business: Queensland, Australia
11 * Licensed under the Open Software License version 3.0
12 * http://www.opensource.org/licenses/osl-3.0.php
13 *
14 *******************************************************/
15
16 #include "Data.h"
17 #include "FunctionSpace.h"
18 #include "FunctionSpaceFactory.h"
19 #include "DataFactory.h"
20 #include "AbstractContinuousDomain.h"
21 #include "AbstractDomain.h"
22 #include "Utils.h"
23 #include "AbstractSystemMatrix.h"
24 #include "AbstractTransportProblem.h"
25 #include "DataVector.h"
26 #include "paso/Paso_MPI.h"
27
28 extern "C" {
29 #include "escript/blocktimer.h"
30 }
31
32 #include "esysUtils/esysExceptionTranslator.h"
33
34 #include <boost/python.hpp>
35 #include <boost/python/module.hpp>
36 #include <boost/python/def.hpp>
37 #include <boost/python/object.hpp>
38 #include <boost/python/tuple.hpp>
39 #include <boost/python/numeric.hpp>
40
41 using namespace boost::python;
42
43 /*! \mainpage Esys Documentation
44 *
45 * \version 1.0.0
46 *
47 * - \ref escript
48 *
49 * - \ref esys_exception "Esys Exception"
50 *
51 * - \ref finley
52 *
53 * - <a href=http://iservo.edu.au/esys/epydoc/index.html>Python module documentation (epydoc generated)</a>
54 *
55 */
56
57 /*! \page escript Escript
58 * Escript is the python module that contains the interfaces
59 * to the C++ side of escript.
60 *
61 * \version 1.0.0
62 *
63 * \section class_desc Class Description:
64 * Data
65 *
66 * \section class_limits Class Limitations:
67 * None
68 *
69 * \section class_conds Class Conditions of Use:
70 * None
71 *
72 * \section class_throws Throws:
73 * None
74 *
75 */
76
77 BOOST_PYTHON_MODULE(escriptcpp)
78 {
79 def("setNumberOfThreads",escript::setNumberOfThreads);
80 def("getNumberOfThreads",escript::getNumberOfThreads);
81 def("releaseUnusedMemory",escript::releaseUnusedMemory);
82 def("blocktimer_initialize",blocktimer_initialize);
83 def("blocktimer_reportSortByName",blocktimer_reportSortByName);
84 def("blocktimer_reportSortByTime",blocktimer_reportSortByTime);
85 def("blocktimer_increment",blocktimer_increment);
86 def("blocktimer_time",blocktimer_time);
87 def("getVersion",escript::getSvnVersion);
88 def("printParallelThreadCounts",escript::printParallelThreadCnt);
89
90
91 //
92 // Interface for AbstractDomain
93 //
94 class_<escript::AbstractDomain>("Domain",no_init)
95 .def("setTagMap",&escript::AbstractDomain::setTagMap)
96 .def("getTag",&escript::AbstractDomain::getTag)
97 .def("isValidTagName",&escript::AbstractDomain::isValidTagName)
98 .def("showTagNames",&escript::AbstractDomain::showTagNames)
99 .def("getX",&escript::AbstractDomain::getX)
100 .def("getNormal",&escript::AbstractDomain::getNormal)
101 .def("getSize",&escript::AbstractDomain::getSize)
102 .def("saveVTK",&escript::AbstractDomain::saveVTK)
103 .def("saveDX",&escript::AbstractDomain::saveDX)
104 .def("getMPISize",&escript::AbstractDomain::getMPISize)
105 .def("getMPIRank",&escript::AbstractDomain::getMPIRank)
106 .def("getMPIComm",&escript::AbstractDomain::getMPIComm)
107
108 .def(self == self)
109 .def(self != self);
110
111 //
112 // Interface for AbstractContinuousDomain
113 //
114 class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain",no_init)
115 .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId);
116
117 //
118 // Interface for FunctionSpace
119 //
120 class_<escript::FunctionSpace> fs_definer("FunctionSpace",init<>());
121 fs_definer.def("getDim",&escript::FunctionSpace::getDim);
122 fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
123 return_internal_reference<>());
124 fs_definer.def("getX",&escript::FunctionSpace::getX);
125 fs_definer.def("getNormal",&escript::FunctionSpace::getNormal);
126 fs_definer.def("getSize",&escript::FunctionSpace::getSize);
127 fs_definer.def("setTags",&escript::FunctionSpace::setTags);
128 fs_definer.def("getTagFromDataPointNo",
129 &escript::FunctionSpace::getTagFromDataPointNo);
130 fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo);
131 fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags);
132 fs_definer.def("__str__", &escript::FunctionSpace::toString);
133 fs_definer.def(self == self);
134 fs_definer.def(self != self);
135 //
136 // Interface for Data
137 //
138 class_<escript::Data>("Data","TEST DOCUMENTATION",init<>())
139 // various constructors for Data objects
140 .def(init<const numeric::array&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
141 .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
142 .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))
143 .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))
144 .def(init<const escript::Data&>())
145 // Note for Lutz, Need to specify the call policy in order to return a
146 // reference. In this case return_internal_reference.
147 .def("__str__",&escript::Data::toString)
148 .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())
149 .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())
150 .def("isEmpty",&escript::Data::isEmpty)
151 .def("isProtected",&escript::Data::isProtected)
152 .def("setProtection",&escript::Data::setProtection)
153 .def("getShape",&escript::Data::getShapeTuple)
154 .def("getRank",&escript::Data::getDataPointRank)
155 .def("dump",&escript::Data::dump)
156 .def("copyWithMask",&escript::Data::copyWithMask)
157 .def("setTaggedValue",&escript::Data::setTaggedValue)
158 .def("setTaggedValue",&escript::Data::setTaggedValueByName)
159 .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints)
160 .def("isExpanded",&escript::Data::isExpanded)
161 .def("isTagged",&escript::Data::isTagged)
162 .def("expand",&escript::Data::expand)
163 .def("tag",&escript::Data::tag)
164 .def("copy",&escript::Data::copy)
165 .def("copy",&escript::Data::copySelf,return_value_policy<manage_new_object>())
166 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject)
167 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
168 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint)
169 .def("getValueOfDataPoint",&escript::Data::getValueOfDataPoint)
170 .def("getValueOfGlobalDataPoint",&escript::Data::getValueOfGlobalDataPoint)
171 .def("setToZero",&escript::Data::setToZero)
172 .def("interpolate",&escript::Data::interpolate)
173 .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
174 .def("saveDX",&escript::Data::saveDX)
175 .def("saveVTK",&escript::Data::saveVTK)
176 .def("getTagNumber",&escript::Data::getTagNumber)
177 // Unary functions for Data
178 .def("_interpolate",&escript::Data::interpolate)
179 .def("_grad",&escript::Data::gradOn)
180 .def("_grad",&escript::Data::grad)
181 .def("_transpose",&escript::Data::transpose)
182 .def("_trace",&escript::Data::trace)
183 .def("_maxval",&escript::Data::maxval)
184 .def("_minval",&escript::Data::minval)
185 .def("_wherePositive",&escript::Data::wherePositive)
186 .def("_whereNegative",&escript::Data::whereNegative)
187 .def("_whereNonNegative",&escript::Data::whereNonNegative)
188 .def("_whereNonPositive",&escript::Data::whereNonPositive)
189 .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
190 .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
191 .def("_erf",&escript::Data::erf)
192 .def("_sin",&escript::Data::sin)
193 .def("_cos",&escript::Data::cos)
194 .def("_tan",&escript::Data::tan)
195 .def("_asin",&escript::Data::asin)
196 .def("_acos",&escript::Data::acos)
197 .def("_atan",&escript::Data::atan)
198 .def("_sinh",&escript::Data::sinh)
199 .def("_cosh",&escript::Data::cosh)
200 .def("_tanh",&escript::Data::tanh)
201 .def("_asinh",&escript::Data::asinh)
202 .def("_acosh",&escript::Data::acosh)
203 .def("_atanh",&escript::Data::atanh)
204 .def("_exp",&escript::Data::exp)
205 .def("_sqrt",&escript::Data::sqrt)
206 .def("_log10",&escript::Data::log10)
207 .def("_log",&escript::Data::log)
208 .def("_sign",&escript::Data::sign)
209 .def("_symmetric",&escript::Data::symmetric)
210 .def("_nonsymmetric",&escript::Data::nonsymmetric)
211 .def("_trace",&escript::Data::trace)
212 .def("_swap_axes",&escript::Data::swapaxes)
213 .def("_eigenvalues",&escript::Data::eigenvalues)
214 .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
215 // functions returning a single real number:
216 .def("_Lsup",&escript::Data::Lsup)
217 .def("_sup",&escript::Data::sup)
218 .def("_inf",&escript::Data::inf)
219 .def("_integrate",&escript::Data::integrate)
220
221 // following implements the python abs operator
222 .def("__abs__",&escript::Data::abs)
223 // following implements the python "-" negation operator
224 .def("__neg__",&escript::Data::neg)
225 // following implements the python "+" identity operator
226 .def("__pos__",&escript::Data::pos)
227 // following two functions implement the python [] operator
228 .def("__getitem__",&escript::Data::getItem)
229 .def("__setitem__",&escript::Data::setItemO)
230 .def("__setitem__",&escript::Data::setItemD)
231 // following two functions implement the python ** operator
232 .def("__pow__",&escript::Data::powO)
233 .def("__pow__",&escript::Data::powD)
234 .def("__rpow__",&escript::Data::rpowO)
235 // NOTE:: The order of these declarations is important. Anything
236 // declared before the generic declaration isn't found so the generic
237 // version will be called.
238 .def(self + other<object>())
239 .def(other<object>() + self)
240 .def(self + self)
241 .def(self += other<object>())
242 .def(self += self)
243
244 .def(self - other<object>())
245 .def(other<object>() - self)
246 .def(self - self)
247 .def(self -= other<object>())
248 .def(self -= self)
249
250 .def(self * other<object>())
251 .def(other<object>() * self)
252 .def(self * self)
253 .def(self *= other<object>())
254 .def(self *= self)
255
256 .def(self / other<object>())
257 .def(other<object>() / self)
258 .def(self / self)
259 .def(self /= other<object>())
260 .def(self /= self)
261 // Need scope resolution due to a bug either in the compiler or
262 // the boost code. This calls operator << for Data.
263 .def(self_ns::str(self));
264
265 //
266 // Factory methods for function space
267 //
268 def("ContinuousFunction",escript::continuousFunction);
269 def("ReducedContinuousFunction",escript::reducedContinuousFunction);
270 def("Function",escript::function);
271 def("ReducedFunction",escript::reducedFunction);
272 def("FunctionOnBoundary",escript::functionOnBoundary);
273 def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary);
274 def("FunctionOnContactZero",escript::functionOnContactZero);
275 def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero);
276 def("FunctionOnContactOne",escript::functionOnContactOne);
277 def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne);
278 def("Solution",escript::solution);
279 def("ReducedSolution",escript::reducedSolution);
280 def("DiracDeltaFunction",escript::diracDeltaFunction);
281
282 //
283 // Factory methods for Data
284 //
285 def("load",escript::load);
286 def("loadIsConfigured",escript::loadConfigured);
287 def("Scalar",escript::Scalar,
288 (arg("value")=0.0,
289 arg("what")=escript::FunctionSpace(),
290 arg("expanded")=false));
291 def("Vector",escript::Vector,
292 (arg("value")=0.0,
293 arg("what")=escript::FunctionSpace(),
294 arg("expanded")=false));
295 def("Tensor",escript::Tensor,
296 (arg("value")=0.0,
297 arg("what")=escript::FunctionSpace(),
298 arg("expanded")=false));
299 def("Tensor3",escript::Tensor3,
300 (arg("value")=0.0,
301 arg("what")=escript::FunctionSpace(),
302 arg("expanded")=false));
303 def("Tensor4",escript::Tensor4,
304 (arg("value")=0.0,
305 arg("what")=escript::FunctionSpace(),
306 arg("expanded")=false));
307
308 //
309 // Binary operators
310 //
311 def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
312 (arg("arg0")=escript::Data(),
313 arg("arg1")=escript::Data(),
314 arg("axis_offset")=0,
315 arg("transpose")=0));
316
317 //
318 // Interface for AbstractSystemMatrix
319 //
320 class_<escript::AbstractSystemMatrix>("Operator",init<>())
321 .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty)
322 .def("solve",&escript::AbstractSystemMatrix::solve)
323 .def("of",&escript::AbstractSystemMatrix::vectorMultiply)
324 .def("saveMM",&escript::AbstractSystemMatrix::saveMM)
325 .def("saveHB",&escript::AbstractSystemMatrix::saveHB)
326 .def("resetValues",&escript::AbstractSystemMatrix::resetValues)
327 .def(self*other<escript::Data>());
328 //
329 // Interface for AbstractTransportProblem
330 //
331 class_<escript::AbstractTransportProblem>("TransportProblem",init<>())
332 .def("isEmpty",&escript::AbstractTransportProblem::isEmpty)
333 .def("solve",&escript::AbstractTransportProblem::solve)
334 .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue)
335 .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint)
336 .def("reset",&escript::AbstractTransportProblem::resetTransport)
337 .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize);
338
339 //
340 // Register esysExceptionTranslator
341 //
342 register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);
343
344 }

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