/[escript]/trunk/escript/src/escriptcpp.cpp
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trunk/esys2/escript/src/Data/escriptcpp.cpp revision 147 by jgs, Fri Aug 12 01:45:47 2005 UTC trunk/escript/src/escriptcpp.cpp revision 1796 by jfenwick, Wed Sep 17 01:45:46 2008 UTC
# Line 1  Line 1 
1  //$Id$  
2  /*=============================================================================  /* $Id$ */
3    
4   ******************************************************************************  /*******************************************************
5   *                                                                            *   *
6   *       COPYRIGHT ACcESS 2004 -  All Rights Reserved                         *   *           Copyright 2003-2007 by ACceSS MNRF
7   *                                                                            *   *       Copyright 2007 by University of Queensland
8   * This software is the property of ACcESS.  No part of this code             *   *
9   * may be copied in any form or by any means without the expressed written    *   *                http://esscc.uq.edu.au
10   * consent of ACcESS.  Copying, use or modification of this software          *   *        Primary Business: Queensland, Australia
11   * by any unauthorised person is illegal unless that                          *   *  Licensed under the Open Software License version 3.0
12   * person has a software license agreement with ACcESS.                       *   *     http://www.opensource.org/licenses/osl-3.0.php
13   *                                                                            *   *
14   ******************************************************************************   *******************************************************/
15    
16  ******************************************************************************/  #include "Data.h"
17    #include "FunctionSpace.h"
18  #include "escript/Data/Data.h"  #include "FunctionSpaceFactory.h"
19  #include "escript/Data/DataVariable.h"  #include "DataFactory.h"
20  #include "escript/Data/FunctionSpace.h"  #include "AbstractContinuousDomain.h"
21  #include "escript/Data/FunctionSpaceFactory.h"  #include "AbstractDomain.h"
22  #include "escript/Data/DataFactory.h"  #include "Utils.h"
23  #include "escript/Data/AbstractContinuousDomain.h"  #include "AbstractSystemMatrix.h"
24  #include "escript/Data/AbstractDomain.h"  #include "AbstractTransportProblem.h"
25    #include "DataVector.h"
26    
27    extern "C" {
28    #include "escript/blocktimer.h"
29    }
30    
31  #include "esysUtils/esysExceptionTranslator.h"  #include "esysUtils/esysExceptionTranslator.h"
32    
33  #include <boost/python.hpp>  #include <boost/python.hpp>
# Line 29  Line 35 
35  #include <boost/python/def.hpp>  #include <boost/python/def.hpp>
36  #include <boost/python/object.hpp>  #include <boost/python/object.hpp>
37  #include <boost/python/tuple.hpp>  #include <boost/python/tuple.hpp>
38                                                                                                                                              #include <boost/python/numeric.hpp>
39    
40  using namespace boost::python;  using namespace boost::python;
41    
42  /*! \mainpage Esys Documentation  /*! \mainpage Esys Documentation
# Line 42  using namespace boost::python; Line 49  using namespace boost::python;
49   *   *
50   * - \ref finley   * - \ref finley
51   *   *
52   * - <a href=http://www.esscc.uq.edu.au/~cochrane/esys_python_doc/html/index.html>Python module documentation (doxygen generated)</a>   * - <a href=http://iservo.edu.au/esys/epydoc/index.html>Python module documentation (epydoc generated)</a>
  *  
  * - <a href=http://www.esscc.uq.edu.au/~cochrane/esys_python_doc/index.html>Python module documentation (epydoc generated)</a>  
53   *   *
54   */   */
55    
# Line 70  using namespace boost::python; Line 75  using namespace boost::python;
75    
76  BOOST_PYTHON_MODULE(escriptcpp)  BOOST_PYTHON_MODULE(escriptcpp)
77  {  {
78      def("setNumberOfThreads",escript::setNumberOfThreads);
79      def("getNumberOfThreads",escript::getNumberOfThreads);
80      def("releaseUnusedMemory",escript::releaseUnusedMemory);
81      def("blocktimer_initialize",blocktimer_initialize);
82      def("blocktimer_reportSortByName",blocktimer_reportSortByName);
83      def("blocktimer_reportSortByTime",blocktimer_reportSortByTime);
84      def("blocktimer_increment",blocktimer_increment);
85      def("blocktimer_time",blocktimer_time);
86      def("getVersion",escript::getSvnVersion);
87      def("printParallelThreadCounts",escript::printParallelThreadCnt);
88    
89    
90    //    //
91    // Interface for AbstractDomain    // Interface for AbstractDomain
92    //    //
93    class_<escript::AbstractDomain>("Domain",no_init)    class_<escript::AbstractDomain>("Domain",no_init)
94         .def("setTagMap",&escript::AbstractDomain::setTagMap)
95         .def("getTag",&escript::AbstractDomain::getTag)
96         .def("isValidTagName",&escript::AbstractDomain::isValidTagName)
97         .def("showTagNames",&escript::AbstractDomain::showTagNames)
98       .def("getX",&escript::AbstractDomain::getX)       .def("getX",&escript::AbstractDomain::getX)
99       .def("getNormal",&escript::AbstractDomain::getNormal)       .def("getNormal",&escript::AbstractDomain::getNormal)
100       .def("getSize",&escript::AbstractDomain::getSize)       .def("getSize",&escript::AbstractDomain::getSize)
101         .def("saveVTK",&escript::AbstractDomain::saveVTK)
102         .def("saveDX",&escript::AbstractDomain::saveDX)
103         .def("getMPISize",&escript::AbstractDomain::getMPISize)
104         .def("getMPIRank",&escript::AbstractDomain::getMPIRank)
105    
106       .def(self == self)       .def(self == self)
107       .def(self != self);       .def(self != self);
108    
# Line 90  BOOST_PYTHON_MODULE(escriptcpp) Line 115  BOOST_PYTHON_MODULE(escriptcpp)
115    //    //
116    // Interface for FunctionSpace    // Interface for FunctionSpace
117    //    //
118    class_<escript::FunctionSpace>("FunctionSpace",init<>())    class_<escript::FunctionSpace> fs_definer("FunctionSpace",init<>());
119       .def("getDim",&escript::FunctionSpace::getDim)    fs_definer.def("getDim",&escript::FunctionSpace::getDim);
120       .def("getX",&escript::FunctionSpace::getX)    fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
121       .def("getNormal",&escript::FunctionSpace::getNormal)                   return_internal_reference<>());
122       .def("getSize",&escript::FunctionSpace::getSize)    fs_definer.def("getX",&escript::FunctionSpace::getX);
123       .def("__str__",&escript::FunctionSpace::toString)    fs_definer.def("getNormal",&escript::FunctionSpace::getNormal);
124       .def(self == self)    fs_definer.def("getSize",&escript::FunctionSpace::getSize);
125       .def(self != self);    fs_definer.def("setTags",&escript::FunctionSpace::setTags);
126      fs_definer.def("getTagFromDataPointNo",
127    //                   &escript::FunctionSpace::getTagFromDataPointNo);
128    // Interface for DataVariable    fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo);
129    //    fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags);
130    class_<escript::DataVariable>("DataVariable",init<>())    fs_definer.def("__str__", &escript::FunctionSpace::toString);
131      .def(init<escript::Data*>())    fs_definer.def(self == self);
132      .def("evaluate",&escript::DataVariable::evaluate)    fs_definer.def(self != self);
     .def("sum",&escript::DataVariable::sum)  
     .def("diff",&escript::DataVariable::diff);  
   
133    //    //
134    // Interface for Data    // Interface for Data
135    //    //
136    class_<escript::Data>("Data",init<>())    class_<escript::Data>("Data","TEST DOCUMENTATION",init<>())
137      // various constructors for Data objects      // various constructors for Data objects
138      .def(init<const numeric::array&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))      .def(init<const numeric::array&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
139      .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))      .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
# Line 120  BOOST_PYTHON_MODULE(escriptcpp) Line 142  BOOST_PYTHON_MODULE(escriptcpp)
142      .def(init<const escript::Data&>())      .def(init<const escript::Data&>())
143      // Note for Lutz, Need to specify the call policy in order to return a      // Note for Lutz, Need to specify the call policy in order to return a
144      // reference. In this case return_internal_reference.      // reference. In this case return_internal_reference.
145      .def("toString",&escript::Data::toString)      .def("__str__",&escript::Data::toString)
146      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())
147      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())
148      .def("isEmpty",&escript::Data::isEmpty)      .def("isEmpty",&escript::Data::isEmpty)
149        .def("isProtected",&escript::Data::isProtected)
150        .def("setProtection",&escript::Data::setProtection)
151      .def("getShape",&escript::Data::getShapeTuple)      .def("getShape",&escript::Data::getShapeTuple)
152      .def("getRank",&escript::Data::getDataPointRank)      .def("getRank",&escript::Data::getDataPointRank)
153        .def("dump",&escript::Data::dump)
154      .def("copyWithMask",&escript::Data::copyWithMask)      .def("copyWithMask",&escript::Data::copyWithMask)
155      .def("setTaggedValue",&escript::Data::setTaggedValue)      .def("setTaggedValue",&escript::Data::setTaggedValue)
156      .def("setRefValue",&escript::Data::setRefValue)      .def("setTaggedValue",&escript::Data::setTaggedValueByName)
157      .def("getRefValue",&escript::Data::getRefValue)      .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints)
158        .def("isExpanded",&escript::Data::isExpanded)
159        .def("isTagged",&escript::Data::isTagged)
160      .def("expand",&escript::Data::expand)      .def("expand",&escript::Data::expand)
161      .def("tag",&escript::Data::tag)      .def("tag",&escript::Data::tag)
162      .def("copy",&escript::Data::copy)      .def("copy",&escript::Data::copy)
163        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject)
164        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
165        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint)
166        .def("getValueOfDataPoint",&escript::Data::getValueOfDataPoint)
167        .def("getValueOfGlobalDataPoint",&escript::Data::getValueOfGlobalDataPoint)
168        .def("setToZero",&escript::Data::setToZero)
169        .def("interpolate",&escript::Data::interpolate)
170        .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
171      .def("saveDX",&escript::Data::saveDX)      .def("saveDX",&escript::Data::saveDX)
172      .def("saveVTK",&escript::Data::saveVTK)      .def("saveVTK",&escript::Data::saveVTK)
173      .def("wherePositive",&escript::Data::wherePositive)      .def("getTagNumber",&escript::Data::getTagNumber)
     .def("whereNegative",&escript::Data::whereNegative)  
     .def("whereNonNegative",&escript::Data::whereNonNegative)  
     .def("whereNonPositive",&escript::Data::whereNonPositive)  
     .def("whereZero",&escript::Data::whereZero)  
     .def("whereNonZero",&escript::Data::whereNonZero)  
174      // Unary functions for Data      // Unary functions for Data
175      .def("interpolate",&escript::Data::interpolate)      .def("_interpolate",&escript::Data::interpolate)
176      .def("grad",&escript::Data::gradOn)      .def("_grad",&escript::Data::gradOn)
177      .def("grad",&escript::Data::grad)      .def("_grad",&escript::Data::grad)
178      .def("convertToNumArray",&escript::Data::convertToNumArray)      .def("_transpose",&escript::Data::transpose)
179      .def("convertToNumArrayFromSampleNo",&escript::Data::convertToNumArrayFromSampleNo)      .def("_trace",&escript::Data::trace)
180      .def("convertToNumArrayFromDPNo",&escript::Data::convertToNumArrayFromDPNo)      .def("_maxval",&escript::Data::maxval)
181      .def("fillFromNumArray",&escript::Data::fillFromNumArray)      .def("_minval",&escript::Data::minval)
182      .def("archiveData",&escript::Data::archiveData)      .def("_wherePositive",&escript::Data::wherePositive)
183      .def("extractData",&escript::Data::extractData)      .def("_whereNegative",&escript::Data::whereNegative)
184      .def("integrate",&escript::Data::integrate)      .def("_whereNonNegative",&escript::Data::whereNonNegative)
185      .def("transpose",&escript::Data::transpose)      .def("_whereNonPositive",&escript::Data::whereNonPositive)
186      .def("trace",&escript::Data::trace)      .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
187      .def("sin",&escript::Data::sin)      .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
188      .def("cos",&escript::Data::cos)      .def("_erf",&escript::Data::erf)
189      .def("tan",&escript::Data::tan)      .def("_sin",&escript::Data::sin)
190      .def("log",&escript::Data::log)      .def("_cos",&escript::Data::cos)
191      .def("ln",&escript::Data::ln)      .def("_tan",&escript::Data::tan)
192      .def("Lsup",&escript::Data::Lsup)      .def("_asin",&escript::Data::asin)
193      .def("Linf",&escript::Data::Lsup)      .def("_acos",&escript::Data::acos)
194      .def("sup",&escript::Data::sup)      .def("_atan",&escript::Data::atan)
195      .def("inf",&escript::Data::inf)      .def("_sinh",&escript::Data::sinh)
196        .def("_cosh",&escript::Data::cosh)
197        .def("_tanh",&escript::Data::tanh)
198        .def("_asinh",&escript::Data::asinh)
199        .def("_acosh",&escript::Data::acosh)
200        .def("_atanh",&escript::Data::atanh)
201        .def("_exp",&escript::Data::exp)
202        .def("_sqrt",&escript::Data::sqrt)
203        .def("_log10",&escript::Data::log10)
204        .def("_log",&escript::Data::log)
205        .def("_sign",&escript::Data::sign)
206        .def("_symmetric",&escript::Data::symmetric)
207        .def("_nonsymmetric",&escript::Data::nonsymmetric)
208        .def("_trace",&escript::Data::trace)
209        .def("_swap_axes",&escript::Data::swapaxes)
210        .def("_eigenvalues",&escript::Data::eigenvalues)
211        .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
212        // functions returning a single real number:
213        .def("_Lsup",&escript::Data::Lsup)
214        .def("_sup",&escript::Data::sup)
215        .def("_inf",&escript::Data::inf)
216        .def("_integrate",&escript::Data::integrate)
217    
218        // following implements the python abs operator
219      .def("__abs__",&escript::Data::abs)      .def("__abs__",&escript::Data::abs)
     .def("abs",&escript::Data::abs)  
     .def("exp",&escript::Data::exp)  
     .def("sqrt",&escript::Data::sqrt)  
     .def("maxval",&escript::Data::maxval)  
     .def("minval",&escript::Data::minval)  
     .def("mindp",&escript::Data::mindp)  
     .def("length",&escript::Data::length)  
     .def("sign",&escript::Data::sign)  
220      // following implements the python "-" negation operator      // following implements the python "-" negation operator
221      .def("__neg__",&escript::Data::neg)      .def("__neg__",&escript::Data::neg)
     .def("neg",&escript::Data::neg)  
222      // following implements the python "+" identity operator      // following implements the python "+" identity operator
223      .def("__pos__",&escript::Data::pos)      .def("__pos__",&escript::Data::pos)
     .def("pos",&escript::Data::pos)  
224      // following two functions implement the python [] operator      // following two functions implement the python [] operator
225      .def("__getitem__",&escript::Data::getItem)      .def("__getitem__",&escript::Data::getItem)
226      .def("__setitem__",&escript::Data::setItemO)      .def("__setitem__",&escript::Data::setItemO)
# Line 186  BOOST_PYTHON_MODULE(escriptcpp) Line 228  BOOST_PYTHON_MODULE(escriptcpp)
228      // following two functions implement the python ** operator      // following two functions implement the python ** operator
229      .def("__pow__",&escript::Data::powO)      .def("__pow__",&escript::Data::powO)
230      .def("__pow__",&escript::Data::powD)      .def("__pow__",&escript::Data::powD)
231        .def("__rpow__",&escript::Data::rpowO)
232      // NOTE:: The order of these declarations is important. Anything      // NOTE:: The order of these declarations is important. Anything
233      // declared before the generic declaration isn't found so the generic      // declared before the generic declaration isn't found so the generic
234      // version will be called.      // version will be called.
     .def(self += other<object>())  
     .def(self += self)  
235      .def(self + other<object>())      .def(self + other<object>())
236      .def(other<object>() + self)      .def(other<object>() + self)
237      .def(self + self)      .def(self + self)
238      .def(self -= other<object>())      .def(self += other<object>())
239      .def(self -= self)      .def(self += self)
240    
241      .def(self - other<object>())      .def(self - other<object>())
242      .def(other<object>() - self)      .def(other<object>() - self)
243      .def(self - self)      .def(self - self)
244      .def(self *= other<object>())      .def(self -= other<object>())
245      .def(self *= self)      .def(self -= self)
246    
247      .def(self * other<object>())      .def(self * other<object>())
248      .def(other<object>() * self)      .def(other<object>() * self)
249      .def(self * self)      .def(self * self)
250      .def(self /= other<object>())      .def(self *= other<object>())
251      .def(self /= self)      .def(self *= self)
252    
253      .def(self / other<object>())      .def(self / other<object>())
254      .def(other<object>() / self)      .def(other<object>() / self)
255      .def(self / self)      .def(self / self)
256        .def(self /= other<object>())
257        .def(self /= self)
258      // Need scope resolution due to a bug either in the compiler or      // Need scope resolution due to a bug either in the compiler or
259      // the boost code. This calls operator << for Data.      // the boost code. This calls operator << for Data.
260      .def(self_ns::str(self));      .def(self_ns::str(self));
# Line 217  BOOST_PYTHON_MODULE(escriptcpp) Line 263  BOOST_PYTHON_MODULE(escriptcpp)
263    // Factory methods for function space    // Factory methods for function space
264    //    //
265    def("ContinuousFunction",escript::continuousFunction);    def("ContinuousFunction",escript::continuousFunction);
266      def("ReducedContinuousFunction",escript::reducedContinuousFunction);
267    def("Function",escript::function);    def("Function",escript::function);
268      def("ReducedFunction",escript::reducedFunction);
269    def("FunctionOnBoundary",escript::functionOnBoundary);    def("FunctionOnBoundary",escript::functionOnBoundary);
270      def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary);
271    def("FunctionOnContactZero",escript::functionOnContactZero);    def("FunctionOnContactZero",escript::functionOnContactZero);
272      def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero);
273    def("FunctionOnContactOne",escript::functionOnContactOne);    def("FunctionOnContactOne",escript::functionOnContactOne);
274      def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne);
275    def("Solution",escript::solution);    def("Solution",escript::solution);
276    def("ReducedSolution",escript::reducedSolution);    def("ReducedSolution",escript::reducedSolution);
277    def("DiracDeltaFunction",escript::diracDeltaFunction);    def("DiracDeltaFunction",escript::diracDeltaFunction);
# Line 228  BOOST_PYTHON_MODULE(escriptcpp) Line 279  BOOST_PYTHON_MODULE(escriptcpp)
279    //    //
280    // Factory methods for Data    // Factory methods for Data
281    //    //
282      def("load",escript::load);
283      def("loadIsConfigured",escript::loadConfigured);
284    def("Scalar",escript::Scalar,    def("Scalar",escript::Scalar,
285        (arg("value")=0.0,        (arg("value")=0.0,
286         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
# Line 250  BOOST_PYTHON_MODULE(escriptcpp) Line 303  BOOST_PYTHON_MODULE(escriptcpp)
303         arg("expanded")=false));         arg("expanded")=false));
304    
305    //    //
306      // Binary operators
307      //
308      def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
309          (arg("arg0")=escript::Data(),
310           arg("arg1")=escript::Data(),
311           arg("axis_offset")=0,
312           arg("transpose")=0));
313    
314      //
315    // Interface for AbstractSystemMatrix    // Interface for AbstractSystemMatrix
316    //    //
317    class_<escript::AbstractSystemMatrix>("Operator",init<>())    class_<escript::AbstractSystemMatrix>("Operator",init<>())
# Line 258  BOOST_PYTHON_MODULE(escriptcpp) Line 320  BOOST_PYTHON_MODULE(escriptcpp)
320       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)
321       .def("saveMM",&escript::AbstractSystemMatrix::saveMM)       .def("saveMM",&escript::AbstractSystemMatrix::saveMM)
322       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)
323       .def("setValue",&escript::AbstractSystemMatrix::setValue)       .def("resetValues",&escript::AbstractSystemMatrix::resetValues)
      .def("resetSolver",&escript::AbstractSystemMatrix::resetSolver)  
324       .def(self*other<escript::Data>());       .def(self*other<escript::Data>());
325      //
326      // Interface for AbstractTransportProblem
327      //
328      class_<escript::AbstractTransportProblem>("TransportProblem",init<>())
329         .def("isEmpty",&escript::AbstractTransportProblem::isEmpty)
330         .def("solve",&escript::AbstractTransportProblem::solve)
331         .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue)
332         .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint)
333         .def("reset",&escript::AbstractTransportProblem::resetTransport)
334         .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize);
335    
336    //    //
337    // Register esysExceptionTranslator    // Register esysExceptionTranslator

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