/[escript]/trunk/escript/src/escriptcpp.cpp
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trunk/esys2/escript/src/Data/escriptcpp.cpp revision 119 by jgs, Tue Apr 12 04:45:05 2005 UTC temp/escript/src/escriptcpp.cpp revision 1387 by trankine, Fri Jan 11 07:45:26 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/FunctionSpace.h"  #include "DataFactory.h"
20  #include "escript/Data/FunctionSpaceFactory.h"  #include "AbstractContinuousDomain.h"
21  #include "escript/Data/DataFactory.h"  #include "AbstractDomain.h"
22  #include "escript/Data/AbstractContinuousDomain.h"  #include "Utils.h"
23  #include "escript/Data/AbstractDomain.h"  #include "AbstractSystemMatrix.h"
24    #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 28  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>
 using namespace boost::python;  
   
 /**  
    @memo  
    escript is the python module that contains the interfaces  
    to the C++ side of escript.  
   
    @version 1.0.0  
39    
40     @doc  using namespace boost::python;
   
    Class Description:  
    Data  
   
    Class Limitations:  
    None  
   
    Class Conditions of Use:  
    None  
   
    Throws:  
    None  
41    
42  */  /*! \mainpage Esys Documentation
43     *
44     * \version 1.0.0
45     *
46     * - \ref escript
47     *
48     * - \ref esys_exception "Esys Exception"
49     *
50     * - \ref finley
51     *
52     * - <a href=http://iservo.edu.au/esys/epydoc/index.html>Python module documentation (epydoc generated)</a>
53     *
54     */
55    
56    /*! \page escript Escript
57     * Escript is the python module that contains the interfaces
58     * to the C++ side of escript.
59     *
60     * \version 1.0.0
61     *
62     * \section class_desc Class Description:
63     * Data
64     *
65     * \section class_limits Class Limitations:
66     * None
67     *
68     * \section class_conds Class Conditions of Use:
69     * None
70     *
71     * \section class_throws Throws:
72     * None
73     *
74     */
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    
88    
89    //    //
90    // Interface for AbstractDomain    // Interface for AbstractDomain
91    //    //
92    class_<escript::AbstractDomain>("Domain",no_init)    class_<escript::AbstractDomain>("Domain",no_init)
93         .def("setTagMap",&escript::AbstractDomain::setTagMap)
94         .def("getTag",&escript::AbstractDomain::getTag)
95         .def("isValidTagName",&escript::AbstractDomain::isValidTagName)
96         .def("showTagNames",&escript::AbstractDomain::showTagNames)
97       .def("getX",&escript::AbstractDomain::getX)       .def("getX",&escript::AbstractDomain::getX)
98       .def("getNormal",&escript::AbstractDomain::getNormal)       .def("getNormal",&escript::AbstractDomain::getNormal)
99       .def("getSize",&escript::AbstractDomain::getSize)       .def("getSize",&escript::AbstractDomain::getSize)
100         .def("saveVTK",&escript::AbstractDomain::saveVTK)
101         .def("saveDX",&escript::AbstractDomain::saveDX)
102         .def("getMPISize",&escript::AbstractDomain::getMPISize)
103         .def("getMPIRank",&escript::AbstractDomain::getMPIRank)
104    
105       .def(self == self)       .def(self == self)
106       .def(self != self);       .def(self != self);
107    
# Line 78  BOOST_PYTHON_MODULE(escriptcpp) Line 116  BOOST_PYTHON_MODULE(escriptcpp)
116    //    //
117    class_<escript::FunctionSpace>("FunctionSpace",init<>())    class_<escript::FunctionSpace>("FunctionSpace",init<>())
118       .def("getDim",&escript::FunctionSpace::getDim)       .def("getDim",&escript::FunctionSpace::getDim)
119         .def("getDomain",&escript::FunctionSpace::getDomain,return_internal_reference<>())
120       .def("getX",&escript::FunctionSpace::getX)       .def("getX",&escript::FunctionSpace::getX)
121       .def("getNormal",&escript::FunctionSpace::getNormal)       .def("getNormal",&escript::FunctionSpace::getNormal)
122       .def("getSize",&escript::FunctionSpace::getSize)       .def("getSize",&escript::FunctionSpace::getSize)
123       .def("toString",&escript::FunctionSpace::toString)       .def("setTags",&escript::FunctionSpace::setTags)
124         .def("getTagFromDataPointNo",&escript::FunctionSpace::getTagFromDataPointNo)
125         .def("__str__",&escript::FunctionSpace::toString)
126       .def(self == self)       .def(self == self)
127       .def(self != self);       .def(self != self);
   
128    //    //
129    // Interface for Data    // Interface for Data
130    //    //
131    class_<escript::Data>("Data",init<>())    class_<escript::Data>("Data","TEST DOCUMENTATION",init<>())
132      // various constructors for Data objects      // various constructors for Data objects
133      .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")))
134      .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 97  BOOST_PYTHON_MODULE(escriptcpp) Line 137  BOOST_PYTHON_MODULE(escriptcpp)
137      .def(init<const escript::Data&>())      .def(init<const escript::Data&>())
138      // 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
139      // reference. In this case return_internal_reference.      // reference. In this case return_internal_reference.
140      .def("toString",&escript::Data::toString)      .def("__str__",&escript::Data::toString)
141      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())
142      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())
143      .def("isEmpty",&escript::Data::isEmpty)      .def("isEmpty",&escript::Data::isEmpty)
144        .def("isProtected",&escript::Data::isProtected)
145        .def("setProtection",&escript::Data::setProtection)
146      .def("getShape",&escript::Data::getShapeTuple)      .def("getShape",&escript::Data::getShapeTuple)
147      .def("getRank",&escript::Data::getDataPointRank)      .def("getRank",&escript::Data::getDataPointRank)
148        .def("dump",&escript::Data::dump)
149      .def("copyWithMask",&escript::Data::copyWithMask)      .def("copyWithMask",&escript::Data::copyWithMask)
150      .def("setTaggedValue",&escript::Data::setTaggedValue)      .def("setTaggedValue",&escript::Data::setTaggedValue)
151      .def("setRefValue",&escript::Data::setRefValue)      .def("setTaggedValue",&escript::Data::setTaggedValueByName)
152      .def("getRefValue",&escript::Data::getRefValue)      .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints)
153        .def("isExpanded",&escript::Data::isExpanded)
154        .def("isTagged",&escript::Data::isTagged)
155      .def("expand",&escript::Data::expand)      .def("expand",&escript::Data::expand)
156      .def("tag",&escript::Data::tag)      .def("tag",&escript::Data::tag)
157        .def("copy",&escript::Data::copy)
158        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject)
159        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
160        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint)
161        .def("getValueOfDataPoint",&escript::Data::getValueOfDataPoint)
162        .def("getValueOfGlobalDataPoint",&escript::Data::getValueOfGlobalDataPoint)
163        .def("setToZero",&escript::Data::setToZero)
164        .def("interpolate",&escript::Data::interpolate)
165        .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
166      .def("saveDX",&escript::Data::saveDX)      .def("saveDX",&escript::Data::saveDX)
167      .def("saveVTK",&escript::Data::saveVTK)      .def("saveVTK",&escript::Data::saveVTK)
168      .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)  
     // Unary functions for Data  
     .def("interpolate",&escript::Data::interpolate)  
     .def("grad",&escript::Data::gradOn)  
     .def("grad",&escript::Data::grad)  
     .def("convertToNumArray",&escript::Data::convertToNumArray)  
169      .def("archiveData",&escript::Data::archiveData)      .def("archiveData",&escript::Data::archiveData)
170      .def("extractData",&escript::Data::extractData)      .def("extractData",&escript::Data::extractData)
171      .def("integrate",&escript::Data::integrate)      // Unary functions for Data
172      .def("transpose",&escript::Data::transpose)      .def("_interpolate",&escript::Data::interpolate)
173      .def("trace",&escript::Data::trace)      .def("_grad",&escript::Data::gradOn)
174      .def("sin",&escript::Data::sin)      .def("_grad",&escript::Data::grad)
175      .def("cos",&escript::Data::cos)      .def("_transpose",&escript::Data::transpose)
176      .def("tan",&escript::Data::tan)      .def("_trace",&escript::Data::trace)
177      .def("log",&escript::Data::log)      .def("_maxval",&escript::Data::maxval)
178      .def("ln",&escript::Data::ln)      .def("_minval",&escript::Data::minval)
179      .def("Lsup",&escript::Data::Lsup)      .def("_wherePositive",&escript::Data::wherePositive)
180      .def("Linf",&escript::Data::Lsup)      .def("_whereNegative",&escript::Data::whereNegative)
181      .def("sup",&escript::Data::sup)      .def("_whereNonNegative",&escript::Data::whereNonNegative)
182      .def("inf",&escript::Data::inf)      .def("_whereNonPositive",&escript::Data::whereNonPositive)
183        .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
184        .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
185        .def("_erf",&escript::Data::erf)
186        .def("_sin",&escript::Data::sin)
187        .def("_cos",&escript::Data::cos)
188        .def("_tan",&escript::Data::tan)
189        .def("_asin",&escript::Data::asin)
190        .def("_acos",&escript::Data::acos)
191        .def("_atan",&escript::Data::atan)
192        .def("_sinh",&escript::Data::sinh)
193        .def("_cosh",&escript::Data::cosh)
194        .def("_tanh",&escript::Data::tanh)
195        .def("_asinh",&escript::Data::asinh)
196        .def("_acosh",&escript::Data::acosh)
197        .def("_atanh",&escript::Data::atanh)
198        .def("_exp",&escript::Data::exp)
199        .def("_sqrt",&escript::Data::sqrt)
200        .def("_log10",&escript::Data::log10)
201        .def("_log",&escript::Data::log)
202        .def("_sign",&escript::Data::sign)
203        .def("_symmetric",&escript::Data::symmetric)
204        .def("_nonsymmetric",&escript::Data::nonsymmetric)
205        .def("_trace",&escript::Data::trace)
206        .def("_swap_axes",&escript::Data::swapaxes)
207        .def("_eigenvalues",&escript::Data::eigenvalues)
208        .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
209        // functions returning a single real number:
210        .def("_Lsup",&escript::Data::Lsup)
211        .def("_sup",&escript::Data::sup)
212        .def("_inf",&escript::Data::inf)
213        .def("_integrate",&escript::Data::integrate)
214    
215        // following implements the python abs operator
216      .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("length",&escript::Data::length)  
     .def("sign",&escript::Data::sign)  
217      // following implements the python "-" negation operator      // following implements the python "-" negation operator
218      .def("__neg__",&escript::Data::neg)      .def("__neg__",&escript::Data::neg)
219      // following implements the python "+" identity operator      // following implements the python "+" identity operator
# Line 154  BOOST_PYTHON_MODULE(escriptcpp) Line 225  BOOST_PYTHON_MODULE(escriptcpp)
225      // following two functions implement the python ** operator      // following two functions implement the python ** operator
226      .def("__pow__",&escript::Data::powO)      .def("__pow__",&escript::Data::powO)
227      .def("__pow__",&escript::Data::powD)      .def("__pow__",&escript::Data::powD)
228        .def("__rpow__",&escript::Data::rpowO)
229      // NOTE:: The order of these declarations is important. Anything      // NOTE:: The order of these declarations is important. Anything
230      // declared before the generic declaration isn't found so the generic      // declared before the generic declaration isn't found so the generic
231      // version will be called.      // version will be called.
     .def(self += other<object>())  
     .def(self += self)  
232      .def(self + other<object>())      .def(self + other<object>())
233      .def(other<object>() + self)      .def(other<object>() + self)
234      .def(self + self)      .def(self + self)
235      .def(self -= other<object>())      .def(self += other<object>())
236      .def(self -= self)      .def(self += self)
237    
238      .def(self - other<object>())      .def(self - other<object>())
239      .def(other<object>() - self)      .def(other<object>() - self)
240      .def(self - self)      .def(self - self)
241      .def(self *= other<object>())      .def(self -= other<object>())
242      .def(self *= self)      .def(self -= self)
243    
244      .def(self * other<object>())      .def(self * other<object>())
245      .def(other<object>() * self)      .def(other<object>() * self)
246      .def(self * self)      .def(self * self)
247      .def(self /= other<object>())      .def(self *= other<object>())
248      .def(self /= self)      .def(self *= self)
249    
250      .def(self / other<object>())      .def(self / other<object>())
251      .def(other<object>() / self)      .def(other<object>() / self)
252      .def(self / self)      .def(self / self)
253        .def(self /= other<object>())
254        .def(self /= self)
255      // Need scope resolution due to a bug either in the compiler or      // Need scope resolution due to a bug either in the compiler or
256      // the boost code. This calls operator << for Data.      // the boost code. This calls operator << for Data.
257      .def(self_ns::str(self));      .def(self_ns::str(self));
# Line 185  BOOST_PYTHON_MODULE(escriptcpp) Line 260  BOOST_PYTHON_MODULE(escriptcpp)
260    // Factory methods for function space    // Factory methods for function space
261    //    //
262    def("ContinuousFunction",escript::continuousFunction);    def("ContinuousFunction",escript::continuousFunction);
263      def("ReducedContinuousFunction",escript::reducedContinuousFunction);
264    def("Function",escript::function);    def("Function",escript::function);
265      def("ReducedFunction",escript::reducedFunction);
266    def("FunctionOnBoundary",escript::functionOnBoundary);    def("FunctionOnBoundary",escript::functionOnBoundary);
267      def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary);
268    def("FunctionOnContactZero",escript::functionOnContactZero);    def("FunctionOnContactZero",escript::functionOnContactZero);
269      def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero);
270    def("FunctionOnContactOne",escript::functionOnContactOne);    def("FunctionOnContactOne",escript::functionOnContactOne);
271      def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne);
272    def("Solution",escript::solution);    def("Solution",escript::solution);
273    def("ReducedSolution",escript::reducedSolution);    def("ReducedSolution",escript::reducedSolution);
274    def("DiracDeltaFunction",escript::diracDeltaFunction);    def("DiracDeltaFunction",escript::diracDeltaFunction);
# Line 196  BOOST_PYTHON_MODULE(escriptcpp) Line 276  BOOST_PYTHON_MODULE(escriptcpp)
276    //    //
277    // Factory methods for Data    // Factory methods for Data
278    //    //
279      def("load",escript::load);
280      def("loadIsConfigured",escript::loadConfigured);
281    def("Scalar",escript::Scalar,    def("Scalar",escript::Scalar,
282        (arg("value")=0.0,        (arg("value")=0.0,
283         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
# Line 218  BOOST_PYTHON_MODULE(escriptcpp) Line 300  BOOST_PYTHON_MODULE(escriptcpp)
300         arg("expanded")=false));         arg("expanded")=false));
301    
302    //    //
303      // Binary operators
304      //
305      def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
306          (arg("arg0")=escript::Data(),
307           arg("arg1")=escript::Data(),
308           arg("axis_offset")=0,
309           arg("transpose")=0));
310    
311      //
312    // Interface for AbstractSystemMatrix    // Interface for AbstractSystemMatrix
313    //    //
314    class_<escript::AbstractSystemMatrix>("Operator",init<>())    class_<escript::AbstractSystemMatrix>("Operator",init<>())
# Line 225  BOOST_PYTHON_MODULE(escriptcpp) Line 316  BOOST_PYTHON_MODULE(escriptcpp)
316       .def("solve",&escript::AbstractSystemMatrix::solve)       .def("solve",&escript::AbstractSystemMatrix::solve)
317       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)
318       .def("saveMM",&escript::AbstractSystemMatrix::saveMM)       .def("saveMM",&escript::AbstractSystemMatrix::saveMM)
319       .def("setValue",&escript::AbstractSystemMatrix::setValue)       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)
320       .def("resetSolver",&escript::AbstractSystemMatrix::resetSolver)       .def("resetValues",&escript::AbstractSystemMatrix::resetValues)
321       .def(self*other<escript::Data>());       .def(self*other<escript::Data>());
322      //
323      // Interface for AbstractTransportProblem
324      //
325      class_<escript::AbstractTransportProblem>("TransportProblem",init<>())
326         .def("isEmpty",&escript::AbstractTransportProblem::isEmpty)
327         .def("solve",&escript::AbstractTransportProblem::solve)
328         .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue)
329         .def("resetTransport",&escript::AbstractTransportProblem::resetTransport);
330    
331    //    //
332    // Register esysExceptionTranslator    // Register esysExceptionTranslator

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