/[escript]/trunk/escript/src/escriptcpp.cpp
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Revision 2482 - (hide annotations)
Fri Jun 19 05:56:20 2009 UTC (10 years, 4 months ago) by jfenwick
File size: 16004 byte(s)
Added run_data_access.py to unit tests - tests things like toListOfTuples.
Corrected some doco comments.
Added TestDomain class to escript.
This should allow more testing without resorting to finley.
1 jgs 102
2 ksteube 1312 /*******************************************************
3 ksteube 1811 *
4     * Copyright (c) 2003-2008 by University of Queensland
5     * Earth Systems Science Computational Center (ESSCC)
6     * http://www.uq.edu.au/esscc
7     *
8     * Primary Business: Queensland, Australia
9     * Licensed under the Open Software License version 3.0
10     * http://www.opensource.org/licenses/osl-3.0.php
11     *
12     *******************************************************/
13 ksteube 1312
14 ksteube 1811
15 jgs 474 #include "Data.h"
16     #include "FunctionSpace.h"
17     #include "FunctionSpaceFactory.h"
18     #include "DataFactory.h"
19     #include "AbstractContinuousDomain.h"
20     #include "AbstractDomain.h"
21     #include "Utils.h"
22 jgs 480 #include "AbstractSystemMatrix.h"
23 gross 1364 #include "AbstractTransportProblem.h"
24 gross 797 #include "DataVector.h"
25 ksteube 1800 #include "paso/Paso_MPI.h"
26 jfenwick 1897 #include "EscriptParams.h"
27 jfenwick 2482 #include "TestDomain.h"
28 jgs 474
29 jfenwick 1872
30 ksteube 1312 extern "C" {
31 phornby 2078 #include "esysUtils/blocktimer.h"
32 ksteube 1312 }
33    
34 robwdcock 682 #include "esysUtils/esysExceptionTranslator.h"
35 jgs 102
36 gross 2100 #include <boost/version.hpp>
37 jgs 102 #include <boost/python.hpp>
38     #include <boost/python/module.hpp>
39     #include <boost/python/def.hpp>
40     #include <boost/python/object.hpp>
41     #include <boost/python/tuple.hpp>
42 gross 285 #include <boost/python/numeric.hpp>
43 jfenwick 1872 #include <boost/smart_ptr.hpp>
44 jfenwick 2064 #include <boost/version.hpp>
45 gross 285
46 jgs 102 using namespace boost::python;
47    
48 jgs 121 /*! \mainpage Esys Documentation
49     *
50 jfenwick 2459 * \version 2.9.0
51 jgs 121 *
52     * - \ref escript
53     *
54     * - \ref esys_exception "Esys Exception"
55     *
56     * - \ref finley
57     *
58 jfenwick 2283 * - <a href="../../epydoc/index.html">Python module documentation (epydoc generated)</a>
59 jgs 122 *
60 jgs 121 */
61 jgs 102
62 jgs 121 /*! \page escript Escript
63     * Escript is the python module that contains the interfaces
64     * to the C++ side of escript.
65     *
66 jfenwick 2459 *
67 jgs 121 *
68     * \section class_desc Class Description:
69     * Data
70     *
71     * \section class_limits Class Limitations:
72     * None
73     *
74     * \section class_conds Class Conditions of Use:
75     * None
76     *
77     * \section class_throws Throws:
78     * None
79     *
80     */
81 jgs 102
82     BOOST_PYTHON_MODULE(escriptcpp)
83     {
84 jfenwick 2064 // This feature was added in boost v1.34
85 phornby 2076 #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
86     //#if ((BOOST_VERSION/100)%1000) > 34
87 jfenwick 2061 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
88 gross 2100 #if BOOST_VERSION > 103399
89 jfenwick 2061 docstring_options docopt(true, true, false);
90 gross 2100 #endif
91 jfenwick 2064 #endif
92 jfenwick 2061
93 gross 391 def("setNumberOfThreads",escript::setNumberOfThreads);
94     def("getNumberOfThreads",escript::getNumberOfThreads);
95 gross 797 def("releaseUnusedMemory",escript::releaseUnusedMemory);
96 ksteube 1312 def("blocktimer_initialize",blocktimer_initialize);
97     def("blocktimer_reportSortByName",blocktimer_reportSortByName);
98     def("blocktimer_reportSortByTime",blocktimer_reportSortByTime);
99     def("blocktimer_increment",blocktimer_increment);
100     def("blocktimer_time",blocktimer_time);
101 ksteube 1247 def("getVersion",escript::getSvnVersion);
102 ksteube 1561 def("printParallelThreadCounts",escript::printParallelThreadCnt);
103 ksteube 1805 def("getMPISizeWorld",escript::getMPISizeWorld);
104     def("getMPIRankWorld",escript::getMPIRankWorld);
105 gross 2313 def("MPIBarrierWorld",escript::MPIBarrierWorld);
106 gross 2308 def("getMPIWorldMax",escript::getMPIWorldMax);
107 gross 2100 def("getMachinePrecision",escript::getMachinePrecision);
108     def("getMaxFloat",escript::getMaxFloat);
109 jgs 102 //
110     // Interface for AbstractDomain
111     //
112 jfenwick 2061 class_<escript::AbstractDomain, escript::Domain_ptr>("Domain","Base class for all domains.",no_init)
113 gross 1044 .def("setTagMap",&escript::AbstractDomain::setTagMap)
114     .def("getTag",&escript::AbstractDomain::getTag)
115     .def("isValidTagName",&escript::AbstractDomain::isValidTagName)
116     .def("showTagNames",&escript::AbstractDomain::showTagNames)
117 jgs 102 .def("getX",&escript::AbstractDomain::getX)
118 jfenwick 1803 .def("getDim",&escript::AbstractDomain::getDim)
119 jgs 102 .def("getNormal",&escript::AbstractDomain::getNormal)
120     .def("getSize",&escript::AbstractDomain::getSize)
121 jgs 153 .def("saveVTK",&escript::AbstractDomain::saveVTK)
122 gross 2417 .def("dump",&escript::AbstractDomain::dump)
123 jgs 153 .def("saveDX",&escript::AbstractDomain::saveDX)
124 ksteube 1312 .def("getMPISize",&escript::AbstractDomain::getMPISize)
125     .def("getMPIRank",&escript::AbstractDomain::getMPIRank)
126 ksteube 1877 .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier)
127     .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor)
128 ksteube 1312
129 jgs 102 .def(self == self)
130     .def(self != self);
131    
132     //
133     // Interface for AbstractContinuousDomain
134     //
135 jfenwick 2061 class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain","Class representing continuous domains",no_init)
136 gross 1859 .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId)
137     .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId);
138 jgs 102
139 jfenwick 2482
140 jgs 102 //
141 jfenwick 2482 // Interface for TestDomain
142     //
143     class_ <escript::TestDomain, bases<escript::AbstractDomain> >("TestDomain", "Test Class for domains with no structure. May be removed from future releases without notice.", init<int,int>());
144    
145     // This is the only python visible way to get a TestDomain
146     def("getTestDomainFunctionSpace",&escript::getTestDomainFunctionSpace, "For testing only. May be removed without notice.");
147    
148     //
149 jgs 102 // Interface for FunctionSpace
150     //
151 jfenwick 2061 class_<escript::FunctionSpace> fs_definer("FunctionSpace","",init<>()); // Doco goes in the empty string param
152 trankine 1426 fs_definer.def("getDim",&escript::FunctionSpace::getDim);
153 jfenwick 1872 // fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
154     // return_internal_reference<>());
155     fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython);
156 trankine 1426 fs_definer.def("getX",&escript::FunctionSpace::getX);
157     fs_definer.def("getNormal",&escript::FunctionSpace::getNormal);
158     fs_definer.def("getSize",&escript::FunctionSpace::getSize);
159     fs_definer.def("setTags",&escript::FunctionSpace::setTags);
160     fs_definer.def("getTagFromDataPointNo",
161     &escript::FunctionSpace::getTagFromDataPointNo);
162 gross 1718 fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo);
163 gross 1716 fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags);
164 phornby 1628 fs_definer.def("__str__", &escript::FunctionSpace::toString);
165 trankine 1426 fs_definer.def(self == self);
166     fs_definer.def(self != self);
167 jgs 102 //
168     // Interface for Data
169     //
170 jfenwick 2061 class_<escript::Data>("Data","Represents a collection of datapoints. It is used to store the values of a function. For more details please consult the c++ class documentation.",init<>() )
171 jgs 102 // various constructors for Data objects
172     .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
173     .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))
174     .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))
175     .def(init<const escript::Data&>())
176     // Note for Lutz, Need to specify the call policy in order to return a
177     // reference. In this case return_internal_reference.
178 ksteube 1312 .def("__str__",&escript::Data::toString)
179 jfenwick 1872 .def("getDomain",&escript::Data::getDomainPython)
180     .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>())
181 jgs 102 .def("isEmpty",&escript::Data::isEmpty)
182 gross 783 .def("isProtected",&escript::Data::isProtected)
183     .def("setProtection",&escript::Data::setProtection)
184 jgs 102 .def("getShape",&escript::Data::getShapeTuple)
185     .def("getRank",&escript::Data::getDataPointRank)
186 gross 950 .def("dump",&escript::Data::dump)
187 jfenwick 2482 .def("toListOfTuples",&escript::Data::toListOfTuples, (arg("scalarastuple")=true))
188 jgs 102 .def("copyWithMask",&escript::Data::copyWithMask)
189     .def("setTaggedValue",&escript::Data::setTaggedValue)
190 gross 1044 .def("setTaggedValue",&escript::Data::setTaggedValueByName)
191 gross 921 .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints)
192 gross 1141 .def("isExpanded",&escript::Data::isExpanded)
193     .def("isTagged",&escript::Data::isTagged)
194 jfenwick 2005 .def("isConstant",&escript::Data::isConstant)
195     .def("isLazy",&escript::Data::isLazy)
196     .def("isReady",&escript::Data::isReady)
197 jgs 119 .def("expand",&escript::Data::expand)
198     .def("tag",&escript::Data::tag)
199 jfenwick 2005 .def("resolve",&escript::Data::resolve)
200 jgs 126 .def("copy",&escript::Data::copy)
201 jfenwick 2105 .def("copy",&escript::Data::copySelf)
202 jfenwick 2005 .def("delay",&escript::Data::delay)
203 gross 1034 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject)
204     .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
205 gross 921 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint)
206 jfenwick 2271 .def("getTupleForDataPoint",&escript::Data::getValueOfDataPointAsTuple)
207     .def("getTupleForGlobalDataPoint",&escript::Data::getValueOfGlobalDataPointAsTuple)
208 gross 1118 .def("setToZero",&escript::Data::setToZero)
209 gross 285 .def("interpolate",&escript::Data::interpolate)
210 gross 921 .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
211 jfenwick 2476 .def("maxGlobalDataPoint",&escript::Data::maxGlobalDataPoint)
212 gross 285 .def("saveDX",&escript::Data::saveDX)
213     .def("saveVTK",&escript::Data::saveVTK)
214 jgs 149 .def("getTagNumber",&escript::Data::getTagNumber)
215 gross 285 // Unary functions for Data
216     .def("_interpolate",&escript::Data::interpolate)
217     .def("_grad",&escript::Data::gradOn)
218     .def("_grad",&escript::Data::grad)
219     .def("_transpose",&escript::Data::transpose)
220     .def("_trace",&escript::Data::trace)
221     .def("_maxval",&escript::Data::maxval)
222     .def("_minval",&escript::Data::minval)
223 gross 698 .def("_wherePositive",&escript::Data::wherePositive)
224     .def("_whereNegative",&escript::Data::whereNegative)
225     .def("_whereNonNegative",&escript::Data::whereNonNegative)
226     .def("_whereNonPositive",&escript::Data::whereNonPositive)
227 jgs 571 .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
228     .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
229 ksteube 876 .def("_erf",&escript::Data::erf)
230 gross 285 .def("_sin",&escript::Data::sin)
231     .def("_cos",&escript::Data::cos)
232     .def("_tan",&escript::Data::tan)
233     .def("_asin",&escript::Data::asin)
234     .def("_acos",&escript::Data::acos)
235     .def("_atan",&escript::Data::atan)
236     .def("_sinh",&escript::Data::sinh)
237     .def("_cosh",&escript::Data::cosh)
238     .def("_tanh",&escript::Data::tanh)
239     .def("_asinh",&escript::Data::asinh)
240     .def("_acosh",&escript::Data::acosh)
241     .def("_atanh",&escript::Data::atanh)
242     .def("_exp",&escript::Data::exp)
243     .def("_sqrt",&escript::Data::sqrt)
244     .def("_log10",&escript::Data::log10)
245     .def("_log",&escript::Data::log)
246     .def("_sign",&escript::Data::sign)
247 ksteube 775 .def("_symmetric",&escript::Data::symmetric)
248     .def("_nonsymmetric",&escript::Data::nonsymmetric)
249 gross 800 .def("_trace",&escript::Data::trace)
250 gross 804 .def("_swap_axes",&escript::Data::swapaxes)
251 gross 576 .def("_eigenvalues",&escript::Data::eigenvalues)
252     .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
253 gross 285 // functions returning a single real number:
254     .def("_Lsup",&escript::Data::Lsup)
255     .def("_sup",&escript::Data::sup)
256     .def("_inf",&escript::Data::inf)
257 jfenwick 2271 .def("_integrateToTuple",&escript::Data::integrateToTuple)
258 gross 285
259     // following implements the python abs operator
260 jgs 108 .def("__abs__",&escript::Data::abs)
261 jgs 102 // following implements the python "-" negation operator
262     .def("__neg__",&escript::Data::neg)
263     // following implements the python "+" identity operator
264     .def("__pos__",&escript::Data::pos)
265     // following two functions implement the python [] operator
266     .def("__getitem__",&escript::Data::getItem)
267     .def("__setitem__",&escript::Data::setItemO)
268     .def("__setitem__",&escript::Data::setItemD)
269     // following two functions implement the python ** operator
270     .def("__pow__",&escript::Data::powO)
271     .def("__pow__",&escript::Data::powD)
272 gross 699 .def("__rpow__",&escript::Data::rpowO)
273 jgs 102 // NOTE:: The order of these declarations is important. Anything
274     // declared before the generic declaration isn't found so the generic
275     // version will be called.
276     .def(self + other<object>())
277     .def(other<object>() + self)
278     .def(self + self)
279 gross 285 .def(self += other<object>())
280     .def(self += self)
281    
282 jgs 102 .def(self - other<object>())
283     .def(other<object>() - self)
284     .def(self - self)
285 gross 285 .def(self -= other<object>())
286     .def(self -= self)
287    
288 jgs 102 .def(self * other<object>())
289     .def(other<object>() * self)
290     .def(self * self)
291 gross 285 .def(self *= other<object>())
292     .def(self *= self)
293    
294 jgs 102 .def(self / other<object>())
295     .def(other<object>() / self)
296     .def(self / self)
297 gross 285 .def(self /= other<object>())
298     .def(self /= self)
299 jgs 102 // Need scope resolution due to a bug either in the compiler or
300     // the boost code. This calls operator << for Data.
301     .def(self_ns::str(self));
302    
303     //
304     // Factory methods for function space
305     //
306     def("ContinuousFunction",escript::continuousFunction);
307 gross 1062 def("ReducedContinuousFunction",escript::reducedContinuousFunction);
308 jgs 102 def("Function",escript::function);
309 gross 1062 def("ReducedFunction",escript::reducedFunction);
310 jgs 102 def("FunctionOnBoundary",escript::functionOnBoundary);
311 gross 1062 def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary);
312 jgs 102 def("FunctionOnContactZero",escript::functionOnContactZero);
313 gross 1062 def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero);
314 jgs 102 def("FunctionOnContactOne",escript::functionOnContactOne);
315 gross 1062 def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne);
316 jgs 102 def("Solution",escript::solution);
317     def("ReducedSolution",escript::reducedSolution);
318     def("DiracDeltaFunction",escript::diracDeltaFunction);
319    
320     //
321     // Factory methods for Data
322     //
323 gross 950 def("load",escript::load);
324 gross 1023 def("loadIsConfigured",escript::loadConfigured);
325 jgs 102 def("Scalar",escript::Scalar,
326     (arg("value")=0.0,
327     arg("what")=escript::FunctionSpace(),
328     arg("expanded")=false));
329     def("Vector",escript::Vector,
330     (arg("value")=0.0,
331     arg("what")=escript::FunctionSpace(),
332     arg("expanded")=false));
333     def("Tensor",escript::Tensor,
334     (arg("value")=0.0,
335     arg("what")=escript::FunctionSpace(),
336     arg("expanded")=false));
337     def("Tensor3",escript::Tensor3,
338     (arg("value")=0.0,
339     arg("what")=escript::FunctionSpace(),
340     arg("expanded")=false));
341     def("Tensor4",escript::Tensor4,
342     (arg("value")=0.0,
343     arg("what")=escript::FunctionSpace(),
344     arg("expanded")=false));
345    
346     //
347 ksteube 813 // Binary operators
348     //
349     def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
350     (arg("arg0")=escript::Data(),
351     arg("arg1")=escript::Data(),
352     arg("axis_offset")=0,
353     arg("transpose")=0));
354    
355     //
356 jgs 102 // Interface for AbstractSystemMatrix
357     //
358 jfenwick 2061 class_<escript::AbstractSystemMatrix>("Operator","",init<>()) // Doco goes in the empty string param
359 jgs 102 .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty)
360     .def("solve",&escript::AbstractSystemMatrix::solve)
361     .def("of",&escript::AbstractSystemMatrix::vectorMultiply)
362     .def("saveMM",&escript::AbstractSystemMatrix::saveMM)
363 jgs 123 .def("saveHB",&escript::AbstractSystemMatrix::saveHB)
364 jgs 149 .def("resetValues",&escript::AbstractSystemMatrix::resetValues)
365 jgs 102 .def(self*other<escript::Data>());
366 gross 1364 //
367     // Interface for AbstractTransportProblem
368     //
369 jfenwick 2061 class_<escript::AbstractTransportProblem>("TransportProblem","",init<>()) // Doco goes in the empty string param
370 gross 1364 .def("isEmpty",&escript::AbstractTransportProblem::isEmpty)
371     .def("solve",&escript::AbstractTransportProblem::solve)
372 gross 1370 .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue)
373 gross 1417 .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint)
374     .def("reset",&escript::AbstractTransportProblem::resetTransport)
375 gross 1841 .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
376 gross 1859 .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize)
377     .def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize);
378 jgs 102
379 jfenwick 1897 // Functions to modify global parameters
380     def("setEscriptParamInt",escript::setEscriptParamInt,
381     (arg("value")=0));
382     def("getEscriptParamInt",escript::getEscriptParamInt,
383     (arg("sentinel")=0));
384 jfenwick 2142 def("listEscriptParams",escript::listEscriptParams);
385 jfenwick 1897
386 jgs 102 //
387     // Register esysExceptionTranslator
388     //
389     register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);
390     }

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