/[escript]/trunk/escript/src/escriptcpp.cpp
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revision 964 by gross, Tue Feb 13 05:10:26 2007 UTC revision 2459 by jfenwick, Thu Jun 4 06:17:54 2009 UTC
# Line 1  Line 1 
1  //$Id$  
2  /*  /*******************************************************
3   ************************************************************  *
4   *          Copyright 2006 by ACcESS MNRF                   *  * Copyright (c) 2003-2008 by University of Queensland
5   *                                                          *  * Earth Systems Science Computational Center (ESSCC)
6   *              http://www.access.edu.au                    *  * http://www.uq.edu.au/esscc
7   *       Primary Business: Queensland, Australia            *  *
8   *  Licensed under the Open Software License version 3.0    *  * Primary Business: Queensland, Australia
9   *     http://www.opensource.org/licenses/osl-3.0.php       *  * Licensed under the Open Software License version 3.0
10   *                                                          *  * http://www.opensource.org/licenses/osl-3.0.php
11   ************************************************************  *
12  */  *******************************************************/
13    
14    
15  #include "Data.h"  #include "Data.h"
16  #include "FunctionSpace.h"  #include "FunctionSpace.h"
# Line 19  Line 20 
20  #include "AbstractDomain.h"  #include "AbstractDomain.h"
21  #include "Utils.h"  #include "Utils.h"
22  #include "AbstractSystemMatrix.h"  #include "AbstractSystemMatrix.h"
23    #include "AbstractTransportProblem.h"
24  #include "DataVector.h"  #include "DataVector.h"
25    #include "paso/Paso_MPI.h"
26    #include "EscriptParams.h"
27    
28    
29    extern "C" {
30    #include "esysUtils/blocktimer.h"
31    }
32    
33  #include "esysUtils/esysExceptionTranslator.h"  #include "esysUtils/esysExceptionTranslator.h"
34    
35    #include <boost/version.hpp>
36  #include <boost/python.hpp>  #include <boost/python.hpp>
37  #include <boost/python/module.hpp>  #include <boost/python/module.hpp>
38  #include <boost/python/def.hpp>  #include <boost/python/def.hpp>
39  #include <boost/python/object.hpp>  #include <boost/python/object.hpp>
40  #include <boost/python/tuple.hpp>  #include <boost/python/tuple.hpp>
41  #include <boost/python/numeric.hpp>  #include <boost/python/numeric.hpp>
42    #include <boost/smart_ptr.hpp>
43    #include <boost/version.hpp>
44    
45  using namespace boost::python;  using namespace boost::python;
46    
47  /*! \mainpage Esys Documentation  /*! \mainpage Esys Documentation
48   *   *
49   * \version 1.0.0   * \version 2.9.0
50   *   *
51   * - \ref escript   * - \ref escript
52   *   *
# Line 42  using namespace boost::python; Line 54  using namespace boost::python;
54   *   *
55   * - \ref finley   * - \ref finley
56   *   *
57   * - <a href=http://iservo.edu.au/esys/epydoc/index.html>Python module documentation (epydoc generated)</a>   * - <a href="../../epydoc/index.html">Python module documentation (epydoc generated)</a>
58   *   *
59   */   */
60    
# Line 50  using namespace boost::python; Line 62  using namespace boost::python;
62   * Escript is the python module that contains the interfaces   * Escript is the python module that contains the interfaces
63   * to the C++ side of escript.   * to the C++ side of escript.
64   *   *
65   * \version 1.0.0   *
66   *   *
67   * \section class_desc Class Description:   * \section class_desc Class Description:
68   * Data   * Data
# Line 68  using namespace boost::python; Line 80  using namespace boost::python;
80    
81  BOOST_PYTHON_MODULE(escriptcpp)  BOOST_PYTHON_MODULE(escriptcpp)
82  {  {
83    // This feature was added in boost v1.34
84    #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
85    //#if ((BOOST_VERSION/100)%1000) > 34
86      // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
87      #if BOOST_VERSION > 103399
88      docstring_options docopt(true, true, false);
89      #endif
90    #endif
91    
92    def("setNumberOfThreads",escript::setNumberOfThreads);    def("setNumberOfThreads",escript::setNumberOfThreads);
93    def("getNumberOfThreads",escript::getNumberOfThreads);    def("getNumberOfThreads",escript::getNumberOfThreads);
94    def("releaseUnusedMemory",escript::releaseUnusedMemory);    def("releaseUnusedMemory",escript::releaseUnusedMemory);
95      def("blocktimer_initialize",blocktimer_initialize);
96      def("blocktimer_reportSortByName",blocktimer_reportSortByName);
97      def("blocktimer_reportSortByTime",blocktimer_reportSortByTime);
98      def("blocktimer_increment",blocktimer_increment);
99      def("blocktimer_time",blocktimer_time);
100      def("getVersion",escript::getSvnVersion);
101      def("printParallelThreadCounts",escript::printParallelThreadCnt);
102      def("getMPISizeWorld",escript::getMPISizeWorld);
103      def("getMPIRankWorld",escript::getMPIRankWorld);
104      def("MPIBarrierWorld",escript::MPIBarrierWorld);
105      def("getMPIWorldMax",escript::getMPIWorldMax);
106      def("getMachinePrecision",escript::getMachinePrecision);
107      def("getMaxFloat",escript::getMaxFloat);
108    //    //
109    // Interface for AbstractDomain    // Interface for AbstractDomain
110    //    //
111    class_<escript::AbstractDomain>("Domain",no_init)    class_<escript::AbstractDomain, escript::Domain_ptr>("Domain","Base class for all domains.",no_init)
112         .def("setTagMap",&escript::AbstractDomain::setTagMap)
113         .def("getTag",&escript::AbstractDomain::getTag)
114         .def("isValidTagName",&escript::AbstractDomain::isValidTagName)
115         .def("showTagNames",&escript::AbstractDomain::showTagNames)
116       .def("getX",&escript::AbstractDomain::getX)       .def("getX",&escript::AbstractDomain::getX)
117         .def("getDim",&escript::AbstractDomain::getDim)
118       .def("getNormal",&escript::AbstractDomain::getNormal)       .def("getNormal",&escript::AbstractDomain::getNormal)
119       .def("getSize",&escript::AbstractDomain::getSize)       .def("getSize",&escript::AbstractDomain::getSize)
120       .def("saveVTK",&escript::AbstractDomain::saveVTK)       .def("saveVTK",&escript::AbstractDomain::saveVTK)
121         .def("dump",&escript::AbstractDomain::dump)
122       .def("saveDX",&escript::AbstractDomain::saveDX)       .def("saveDX",&escript::AbstractDomain::saveDX)
123         .def("getMPISize",&escript::AbstractDomain::getMPISize)
124         .def("getMPIRank",&escript::AbstractDomain::getMPIRank)
125         .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier)
126         .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor)
127    
128       .def(self == self)       .def(self == self)
129       .def(self != self);       .def(self != self);
130    
131    //    //
132    // Interface for AbstractContinuousDomain    // Interface for AbstractContinuousDomain
133    //    //
134    class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain",no_init)    class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain","Class representing continuous domains",no_init)
135         .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId);         .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId)
136           .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId);
137    
138    //    //
139    // Interface for FunctionSpace    // Interface for FunctionSpace
140    //    //
141    class_<escript::FunctionSpace>("FunctionSpace",init<>())    class_<escript::FunctionSpace> fs_definer("FunctionSpace","",init<>());   // Doco goes in the empty string param
142       .def("getDim",&escript::FunctionSpace::getDim)    fs_definer.def("getDim",&escript::FunctionSpace::getDim);
143       .def("getDomain",&escript::FunctionSpace::getDomain,return_internal_reference<>())  //   fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
144       .def("getX",&escript::FunctionSpace::getX)  //                  return_internal_reference<>());
145       .def("getNormal",&escript::FunctionSpace::getNormal)    fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython);
146       .def("getSize",&escript::FunctionSpace::getSize)    fs_definer.def("getX",&escript::FunctionSpace::getX);
147       .def("setTags",&escript::FunctionSpace::setTags)    fs_definer.def("getNormal",&escript::FunctionSpace::getNormal);
148       .def("getTagFromDataPointNo",&escript::FunctionSpace::getTagFromDataPointNo)    fs_definer.def("getSize",&escript::FunctionSpace::getSize);
149       .def("__str__",&escript::FunctionSpace::toString)    fs_definer.def("setTags",&escript::FunctionSpace::setTags);
150       .def(self == self)    fs_definer.def("getTagFromDataPointNo",
151       .def(self != self);                   &escript::FunctionSpace::getTagFromDataPointNo);
152      fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo);
153      fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags);
154      fs_definer.def("__str__", &escript::FunctionSpace::toString);
155      fs_definer.def(self == self);
156      fs_definer.def(self != self);
157    //    //
158    // Interface for Data    // Interface for Data
159    //    //
160    class_<escript::Data>("Data","TEST DOCUMENTATION",init<>())    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<>() )
161      // various constructors for Data objects      // various constructors for Data objects
     .def(init<const numeric::array&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))  
162      .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")))
163      .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))      .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))
164      .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))      .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))
# Line 118  BOOST_PYTHON_MODULE(escriptcpp) Line 166  BOOST_PYTHON_MODULE(escriptcpp)
166      // 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
167      // reference. In this case return_internal_reference.      // reference. In this case return_internal_reference.
168      .def("__str__",&escript::Data::toString)      .def("__str__",&escript::Data::toString)
169      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())      .def("getDomain",&escript::Data::getDomainPython)
170      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>())
171      .def("isEmpty",&escript::Data::isEmpty)      .def("isEmpty",&escript::Data::isEmpty)
172      .def("isProtected",&escript::Data::isProtected)      .def("isProtected",&escript::Data::isProtected)
173      .def("setProtection",&escript::Data::setProtection)      .def("setProtection",&escript::Data::setProtection)
174      .def("getShape",&escript::Data::getShapeTuple)      .def("getShape",&escript::Data::getShapeTuple)
175      .def("getRank",&escript::Data::getDataPointRank)      .def("getRank",&escript::Data::getDataPointRank)
176      .def("dump",&escript::Data::dump)      .def("dump",&escript::Data::dump)
177        .def("toListOfTuples",&escript::Data::toListOfTuples, (arg("scalarastuple")=false))
178      .def("copyWithMask",&escript::Data::copyWithMask)      .def("copyWithMask",&escript::Data::copyWithMask)
179      .def("setTaggedValue",&escript::Data::setTaggedValue)      .def("setTaggedValue",&escript::Data::setTaggedValue)
180        .def("setTaggedValue",&escript::Data::setTaggedValueByName)
181      .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints)      .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints)
182        .def("isExpanded",&escript::Data::isExpanded)
183        .def("isTagged",&escript::Data::isTagged)
184        .def("isConstant",&escript::Data::isConstant)
185        .def("isLazy",&escript::Data::isLazy)
186        .def("isReady",&escript::Data::isReady)
187      .def("expand",&escript::Data::expand)      .def("expand",&escript::Data::expand)
188      .def("tag",&escript::Data::tag)      .def("tag",&escript::Data::tag)
189        .def("resolve",&escript::Data::resolve)
190      .def("copy",&escript::Data::copy)      .def("copy",&escript::Data::copy)
191      .def("convertToNumArray",&escript::Data::convertToNumArray)      .def("copy",&escript::Data::copySelf)
192      .def("fillFromNumArray",&escript::Data::fillFromNumArray)      .def("delay",&escript::Data::delay)
193      .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint)      .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject)
194      .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)      .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
195      .def("getValueOfDataPoint",&escript::Data::getValueOfDataPoint)      .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint)
196      .def("getValueOfGlobalDataPoint",&escript::Data::getValueOfGlobalDataPoint)      .def("getTupleForDataPoint",&escript::Data::getValueOfDataPointAsTuple)
197        .def("getTupleForGlobalDataPoint",&escript::Data::getValueOfGlobalDataPointAsTuple)
198        .def("setToZero",&escript::Data::setToZero)
199      .def("interpolate",&escript::Data::interpolate)      .def("interpolate",&escript::Data::interpolate)
200      .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)      .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
201      .def("saveDX",&escript::Data::saveDX)      .def("saveDX",&escript::Data::saveDX)
202      .def("saveVTK",&escript::Data::saveVTK)      .def("saveVTK",&escript::Data::saveVTK)
203      .def("getTagNumber",&escript::Data::getTagNumber)      .def("getTagNumber",&escript::Data::getTagNumber)
     .def("archiveData",&escript::Data::archiveData)  
     .def("extractData",&escript::Data::extractData)  
204      // Unary functions for Data      // Unary functions for Data
205      .def("_interpolate",&escript::Data::interpolate)      .def("_interpolate",&escript::Data::interpolate)
206      .def("_grad",&escript::Data::gradOn)      .def("_grad",&escript::Data::gradOn)
# Line 187  BOOST_PYTHON_MODULE(escriptcpp) Line 243  BOOST_PYTHON_MODULE(escriptcpp)
243      .def("_Lsup",&escript::Data::Lsup)      .def("_Lsup",&escript::Data::Lsup)
244      .def("_sup",&escript::Data::sup)      .def("_sup",&escript::Data::sup)
245      .def("_inf",&escript::Data::inf)      .def("_inf",&escript::Data::inf)
246      .def("_integrate",&escript::Data::integrate)      .def("_integrateToTuple",&escript::Data::integrateToTuple)
247    
248      // following implements the python abs operator      // following implements the python abs operator
249      .def("__abs__",&escript::Data::abs)      .def("__abs__",&escript::Data::abs)
# Line 237  BOOST_PYTHON_MODULE(escriptcpp) Line 293  BOOST_PYTHON_MODULE(escriptcpp)
293    // Factory methods for function space    // Factory methods for function space
294    //    //
295    def("ContinuousFunction",escript::continuousFunction);    def("ContinuousFunction",escript::continuousFunction);
296      def("ReducedContinuousFunction",escript::reducedContinuousFunction);
297    def("Function",escript::function);    def("Function",escript::function);
298      def("ReducedFunction",escript::reducedFunction);
299    def("FunctionOnBoundary",escript::functionOnBoundary);    def("FunctionOnBoundary",escript::functionOnBoundary);
300      def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary);
301    def("FunctionOnContactZero",escript::functionOnContactZero);    def("FunctionOnContactZero",escript::functionOnContactZero);
302      def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero);
303    def("FunctionOnContactOne",escript::functionOnContactOne);    def("FunctionOnContactOne",escript::functionOnContactOne);
304      def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne);
305    def("Solution",escript::solution);    def("Solution",escript::solution);
306    def("ReducedSolution",escript::reducedSolution);    def("ReducedSolution",escript::reducedSolution);
307    def("DiracDeltaFunction",escript::diracDeltaFunction);    def("DiracDeltaFunction",escript::diracDeltaFunction);
# Line 249  BOOST_PYTHON_MODULE(escriptcpp) Line 310  BOOST_PYTHON_MODULE(escriptcpp)
310    // Factory methods for Data    // Factory methods for Data
311    //    //
312    def("load",escript::load);    def("load",escript::load);
313      def("loadIsConfigured",escript::loadConfigured);
314    def("Scalar",escript::Scalar,    def("Scalar",escript::Scalar,
315        (arg("value")=0.0,        (arg("value")=0.0,
316         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
# Line 282  BOOST_PYTHON_MODULE(escriptcpp) Line 344  BOOST_PYTHON_MODULE(escriptcpp)
344    //    //
345    // Interface for AbstractSystemMatrix    // Interface for AbstractSystemMatrix
346    //    //
347    class_<escript::AbstractSystemMatrix>("Operator",init<>())    class_<escript::AbstractSystemMatrix>("Operator","",init<>())    // Doco goes in the empty string param
348       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty)       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty)
349       .def("solve",&escript::AbstractSystemMatrix::solve)       .def("solve",&escript::AbstractSystemMatrix::solve)
350       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)
# Line 290  BOOST_PYTHON_MODULE(escriptcpp) Line 352  BOOST_PYTHON_MODULE(escriptcpp)
352       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)
353       .def("resetValues",&escript::AbstractSystemMatrix::resetValues)       .def("resetValues",&escript::AbstractSystemMatrix::resetValues)
354       .def(self*other<escript::Data>());       .def(self*other<escript::Data>());
355      //
356      // Interface for AbstractTransportProblem
357      //
358      class_<escript::AbstractTransportProblem>("TransportProblem","",init<>())    // Doco goes in the empty string param
359         .def("isEmpty",&escript::AbstractTransportProblem::isEmpty)
360         .def("solve",&escript::AbstractTransportProblem::solve)
361         .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue)
362         .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint)
363         .def("reset",&escript::AbstractTransportProblem::resetTransport)
364         .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
365         .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize)
366         .def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize);
367    
368      // Functions to modify global parameters
369      def("setEscriptParamInt",escript::setEscriptParamInt,
370          (arg("value")=0));
371      def("getEscriptParamInt",escript::getEscriptParamInt,
372          (arg("sentinel")=0));
373      def("listEscriptParams",escript::listEscriptParams);
374    
375    //    //
376    // Register esysExceptionTranslator    // Register esysExceptionTranslator

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