/[escript]/trunk/escript/src/escriptcpp.cpp
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revision 699 by gross, Fri Mar 31 06:27:56 2006 UTC revision 1841 by gross, Fri Oct 3 03:57:52 2008 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"
25    #include "paso/Paso_MPI.h"
26    
27    extern "C" {
28    #include "escript/blocktimer.h"
29    }
30    
31  #include "esysUtils/esysExceptionTranslator.h"  #include "esysUtils/esysExceptionTranslator.h"
32    
# Line 69  BOOST_PYTHON_MODULE(escriptcpp) Line 77  BOOST_PYTHON_MODULE(escriptcpp)
77  {  {
78    def("setNumberOfThreads",escript::setNumberOfThreads);    def("setNumberOfThreads",escript::setNumberOfThreads);
79    def("getNumberOfThreads",escript::getNumberOfThreads);    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      def("getMPISizeWorld",escript::getMPISizeWorld);
89      def("getMPIRankWorld",escript::getMPIRankWorld);
90    
91    
92    //    //
93    // Interface for AbstractDomain    // Interface for AbstractDomain
94    //    //
95    class_<escript::AbstractDomain>("Domain",no_init)    class_<escript::AbstractDomain>("Domain",no_init)
96         .def("setTagMap",&escript::AbstractDomain::setTagMap)
97         .def("getTag",&escript::AbstractDomain::getTag)
98         .def("isValidTagName",&escript::AbstractDomain::isValidTagName)
99         .def("showTagNames",&escript::AbstractDomain::showTagNames)
100       .def("getX",&escript::AbstractDomain::getX)       .def("getX",&escript::AbstractDomain::getX)
101         .def("getDim",&escript::AbstractDomain::getDim)
102       .def("getNormal",&escript::AbstractDomain::getNormal)       .def("getNormal",&escript::AbstractDomain::getNormal)
103       .def("getSize",&escript::AbstractDomain::getSize)       .def("getSize",&escript::AbstractDomain::getSize)
104       .def("saveVTK",&escript::AbstractDomain::saveVTK)       .def("saveVTK",&escript::AbstractDomain::saveVTK)
105       .def("saveDX",&escript::AbstractDomain::saveDX)       .def("saveDX",&escript::AbstractDomain::saveDX)
106         .def("getMPISize",&escript::AbstractDomain::getMPISize)
107         .def("getMPIRank",&escript::AbstractDomain::getMPIRank)
108    
109       .def(self == self)       .def(self == self)
110       .def(self != self);       .def(self != self);
111    
# Line 91  BOOST_PYTHON_MODULE(escriptcpp) Line 118  BOOST_PYTHON_MODULE(escriptcpp)
118    //    //
119    // Interface for FunctionSpace    // Interface for FunctionSpace
120    //    //
121    class_<escript::FunctionSpace>("FunctionSpace",init<>())    class_<escript::FunctionSpace> fs_definer("FunctionSpace",init<>());
122       .def("getDim",&escript::FunctionSpace::getDim)    fs_definer.def("getDim",&escript::FunctionSpace::getDim);
123       .def("getDomain",&escript::FunctionSpace::getDomain,return_internal_reference<>())    fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
124       .def("getX",&escript::FunctionSpace::getX)                   return_internal_reference<>());
125       .def("getNormal",&escript::FunctionSpace::getNormal)    fs_definer.def("getX",&escript::FunctionSpace::getX);
126       .def("getSize",&escript::FunctionSpace::getSize)    fs_definer.def("getNormal",&escript::FunctionSpace::getNormal);
127       .def("getTagFromDataPointNo",&escript::FunctionSpace::getTagFromDataPointNo)    fs_definer.def("getSize",&escript::FunctionSpace::getSize);
128       .def("__str__",&escript::FunctionSpace::toString)    fs_definer.def("setTags",&escript::FunctionSpace::setTags);
129       .def(self == self)    fs_definer.def("getTagFromDataPointNo",
130       .def(self != self);                   &escript::FunctionSpace::getTagFromDataPointNo);
131      fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo);
132      fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags);
133      fs_definer.def("__str__", &escript::FunctionSpace::toString);
134      fs_definer.def(self == self);
135      fs_definer.def(self != self);
136    //    //
137    // Interface for Data    // Interface for Data
138    //    //
# Line 117  BOOST_PYTHON_MODULE(escriptcpp) Line 149  BOOST_PYTHON_MODULE(escriptcpp)
149      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())
150      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())
151      .def("isEmpty",&escript::Data::isEmpty)      .def("isEmpty",&escript::Data::isEmpty)
152        .def("isProtected",&escript::Data::isProtected)
153        .def("setProtection",&escript::Data::setProtection)
154      .def("getShape",&escript::Data::getShapeTuple)      .def("getShape",&escript::Data::getShapeTuple)
155      .def("getRank",&escript::Data::getDataPointRank)      .def("getRank",&escript::Data::getDataPointRank)
156        .def("dump",&escript::Data::dump)
157      .def("copyWithMask",&escript::Data::copyWithMask)      .def("copyWithMask",&escript::Data::copyWithMask)
158      .def("setTaggedValue",&escript::Data::setTaggedValue)      .def("setTaggedValue",&escript::Data::setTaggedValue)
159      .def("setRefValue",&escript::Data::setRefValue)      .def("setTaggedValue",&escript::Data::setTaggedValueByName)
160      .def("getRefValue",&escript::Data::getRefValue)      .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints)
161        .def("isExpanded",&escript::Data::isExpanded)
162        .def("isTagged",&escript::Data::isTagged)
163      .def("expand",&escript::Data::expand)      .def("expand",&escript::Data::expand)
164      .def("tag",&escript::Data::tag)      .def("tag",&escript::Data::tag)
165      .def("copy",&escript::Data::copy)      .def("copy",&escript::Data::copy)
166      .def("convertToNumArray",&escript::Data::convertToNumArray)      .def("copy",&escript::Data::copySelf,return_value_policy<manage_new_object>())
167      .def("convertToNumArrayFromSampleNo",&escript::Data::convertToNumArrayFromSampleNo)      .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject)
168      .def("convertToNumArrayFromDPNo",&escript::Data::convertToNumArrayFromDPNo)      .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
169      .def("fillFromNumArray",&escript::Data::fillFromNumArray)      .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint)
170        .def("getValueOfDataPoint",&escript::Data::getValueOfDataPoint)
171        .def("getValueOfGlobalDataPoint",&escript::Data::getValueOfGlobalDataPoint)
172        .def("setToZero",&escript::Data::setToZero)
173      .def("interpolate",&escript::Data::interpolate)      .def("interpolate",&escript::Data::interpolate)
174      .def("mindp",&escript::Data::mindp)      .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
175      .def("saveDX",&escript::Data::saveDX)      .def("saveDX",&escript::Data::saveDX)
176      .def("saveVTK",&escript::Data::saveVTK)      .def("saveVTK",&escript::Data::saveVTK)
177      .def("getTagNumber",&escript::Data::getTagNumber)      .def("getTagNumber",&escript::Data::getTagNumber)
     .def("archiveData",&escript::Data::archiveData)  
     .def("extractData",&escript::Data::extractData)  
178      // Unary functions for Data      // Unary functions for Data
179      .def("_interpolate",&escript::Data::interpolate)      .def("_interpolate",&escript::Data::interpolate)
180      .def("_grad",&escript::Data::gradOn)      .def("_grad",&escript::Data::gradOn)
# Line 151  BOOST_PYTHON_MODULE(escriptcpp) Line 189  BOOST_PYTHON_MODULE(escriptcpp)
189      .def("_whereNonPositive",&escript::Data::whereNonPositive)      .def("_whereNonPositive",&escript::Data::whereNonPositive)
190      .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))      .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
191      .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))      .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
192        .def("_erf",&escript::Data::erf)
193      .def("_sin",&escript::Data::sin)      .def("_sin",&escript::Data::sin)
194      .def("_cos",&escript::Data::cos)      .def("_cos",&escript::Data::cos)
195      .def("_tan",&escript::Data::tan)      .def("_tan",&escript::Data::tan)
# Line 168  BOOST_PYTHON_MODULE(escriptcpp) Line 207  BOOST_PYTHON_MODULE(escriptcpp)
207      .def("_log10",&escript::Data::log10)      .def("_log10",&escript::Data::log10)
208      .def("_log",&escript::Data::log)      .def("_log",&escript::Data::log)
209      .def("_sign",&escript::Data::sign)      .def("_sign",&escript::Data::sign)
210        .def("_symmetric",&escript::Data::symmetric)
211        .def("_nonsymmetric",&escript::Data::nonsymmetric)
212        .def("_trace",&escript::Data::trace)
213        .def("_swap_axes",&escript::Data::swapaxes)
214      .def("_eigenvalues",&escript::Data::eigenvalues)      .def("_eigenvalues",&escript::Data::eigenvalues)
215      .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))      .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
216      // functions returning a single real number:      // functions returning a single real number:
# Line 224  BOOST_PYTHON_MODULE(escriptcpp) Line 267  BOOST_PYTHON_MODULE(escriptcpp)
267    // Factory methods for function space    // Factory methods for function space
268    //    //
269    def("ContinuousFunction",escript::continuousFunction);    def("ContinuousFunction",escript::continuousFunction);
270      def("ReducedContinuousFunction",escript::reducedContinuousFunction);
271    def("Function",escript::function);    def("Function",escript::function);
272      def("ReducedFunction",escript::reducedFunction);
273    def("FunctionOnBoundary",escript::functionOnBoundary);    def("FunctionOnBoundary",escript::functionOnBoundary);
274      def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary);
275    def("FunctionOnContactZero",escript::functionOnContactZero);    def("FunctionOnContactZero",escript::functionOnContactZero);
276      def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero);
277    def("FunctionOnContactOne",escript::functionOnContactOne);    def("FunctionOnContactOne",escript::functionOnContactOne);
278      def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne);
279    def("Solution",escript::solution);    def("Solution",escript::solution);
280    def("ReducedSolution",escript::reducedSolution);    def("ReducedSolution",escript::reducedSolution);
281    def("DiracDeltaFunction",escript::diracDeltaFunction);    def("DiracDeltaFunction",escript::diracDeltaFunction);
# Line 235  BOOST_PYTHON_MODULE(escriptcpp) Line 283  BOOST_PYTHON_MODULE(escriptcpp)
283    //    //
284    // Factory methods for Data    // Factory methods for Data
285    //    //
286      def("load",escript::load);
287      def("loadIsConfigured",escript::loadConfigured);
288    def("Scalar",escript::Scalar,    def("Scalar",escript::Scalar,
289        (arg("value")=0.0,        (arg("value")=0.0,
290         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
# Line 257  BOOST_PYTHON_MODULE(escriptcpp) Line 307  BOOST_PYTHON_MODULE(escriptcpp)
307         arg("expanded")=false));         arg("expanded")=false));
308    
309    //    //
310      // Binary operators
311      //
312      def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
313          (arg("arg0")=escript::Data(),
314           arg("arg1")=escript::Data(),
315           arg("axis_offset")=0,
316           arg("transpose")=0));
317    
318      //
319    // Interface for AbstractSystemMatrix    // Interface for AbstractSystemMatrix
320    //    //
321    class_<escript::AbstractSystemMatrix>("Operator",init<>())    class_<escript::AbstractSystemMatrix>("Operator",init<>())
# Line 267  BOOST_PYTHON_MODULE(escriptcpp) Line 326  BOOST_PYTHON_MODULE(escriptcpp)
326       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)
327       .def("resetValues",&escript::AbstractSystemMatrix::resetValues)       .def("resetValues",&escript::AbstractSystemMatrix::resetValues)
328       .def(self*other<escript::Data>());       .def(self*other<escript::Data>());
329      //
330      // Interface for AbstractTransportProblem
331      //
332      class_<escript::AbstractTransportProblem>("TransportProblem",init<>())
333         .def("isEmpty",&escript::AbstractTransportProblem::isEmpty)
334         .def("solve",&escript::AbstractTransportProblem::solve)
335         .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue)
336         .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint)
337         .def("reset",&escript::AbstractTransportProblem::resetTransport)
338         .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
339         .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize);
340    
341    //    //
342    // Register esysExceptionTranslator    // Register esysExceptionTranslator

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