/[escript]/trunk/escript/src/escriptcpp.cpp
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trunk/esys2/escript/src/Data/escriptcpp.cpp revision 108 by jgs, Thu Jan 27 06:21:59 2005 UTC trunk/escript/src/escriptcpp.cpp revision 2064 by jfenwick, Thu Nov 20 04:06:34 2008 UTC
# Line 1  Line 1 
1  //$Id$  
2  /*=============================================================================  /*******************************************************
3    *
4   ******************************************************************************  * Copyright (c) 2003-2008 by University of Queensland
5   *                                                                            *  * Earth Systems Science Computational Center (ESSCC)
6   *       COPYRIGHT ACcESS 2004 -  All Rights Reserved                         *  * http://www.uq.edu.au/esscc
7   *                                                                            *  *
8   * This software is the property of ACcESS.  No part of this code             *  * Primary Business: Queensland, Australia
9   * may be copied in any form or by any means without the expressed written    *  * Licensed under the Open Software License version 3.0
10   * consent of ACcESS.  Copying, use or modification of this software          *  * http://www.opensource.org/licenses/osl-3.0.php
11   * by any unauthorised person is illegal unless that                          *  *
12   * person has a software license agreement with ACcESS.                       *  *******************************************************/
13   *                                                                            *  
14   ******************************************************************************  
15    #include "Data.h"
16  ******************************************************************************/  #include "FunctionSpace.h"
17    #include "FunctionSpaceFactory.h"
18  #include "escript/Data/Data.h"  #include "DataFactory.h"
19  #include "escript/Data/FunctionSpace.h"  #include "AbstractContinuousDomain.h"
20  #include "escript/Data/FunctionSpaceFactory.h"  #include "AbstractDomain.h"
21  #include "escript/Data/DataFactory.h"  #include "Utils.h"
22  #include "escript/Data/AbstractContinuousDomain.h"  #include "AbstractSystemMatrix.h"
23  #include "escript/Data/AbstractDomain.h"  #include "AbstractTransportProblem.h"
24    #include "DataVector.h"
25    #include "paso/Paso_MPI.h"
26    #include "EscriptParams.h"
27    
28    
29    extern "C" {
30    #include "escript/blocktimer.h"
31    }
32    
33  #include "esysUtils/esysExceptionTranslator.h"  #include "esysUtils/esysExceptionTranslator.h"
34    
35  #include <boost/python.hpp>  #include <boost/python.hpp>
# Line 28  Line 37 
37  #include <boost/python/def.hpp>  #include <boost/python/def.hpp>
38  #include <boost/python/object.hpp>  #include <boost/python/object.hpp>
39  #include <boost/python/tuple.hpp>  #include <boost/python/tuple.hpp>
40                                                                                                                                              #include <boost/python/numeric.hpp>
41  using namespace boost::python;  #include <boost/smart_ptr.hpp>
42    #include <boost/version.hpp>
 /**  
    @memo  
    escript is the python module that contains the interfaces  
    to the C++ side of escript.  
   
    @version 1.0.0  
   
    @doc  
43    
44     Class Description:  using namespace boost::python;
    Data  
   
    Class Limitations:  
    None  
   
    Class Conditions of Use:  
    None  
   
    Throws:  
    None  
45    
46  */  /*! \mainpage Esys Documentation
47     *
48     * \version 1.0.0
49     *
50     * - \ref escript
51     *
52     * - \ref esys_exception "Esys Exception"
53     *
54     * - \ref finley
55     *
56     * - <a href=http://iservo.edu.au/esys/epydoc/index.html>Python module documentation (epydoc generated)</a>
57     *
58     */
59    
60    /*! \page escript Escript
61     * Escript is the python module that contains the interfaces
62     * to the C++ side of escript.
63     *
64     * \version 1.0.0
65     *
66     * \section class_desc Class Description:
67     * Data
68     *
69     * \section class_limits Class Limitations:
70     * None
71     *
72     * \section class_conds Class Conditions of Use:
73     * None
74     *
75     * \section class_throws Throws:
76     * None
77     *
78     */
79    
80  BOOST_PYTHON_MODULE(escriptcpp)  BOOST_PYTHON_MODULE(escriptcpp)
81  {  {
82    // This feature was added in boost v1.34
83    #if ((BOOST_VERSION/100)%1000 > 33) || (BOOST_VERSION/100000 >1)
84    //#if ((BOOST_VERSION/100)%1000) > 33
85      // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
86      docstring_options docopt(true, true, false);
87    #endif
88    
89      def("setNumberOfThreads",escript::setNumberOfThreads);
90      def("getNumberOfThreads",escript::getNumberOfThreads);
91      def("releaseUnusedMemory",escript::releaseUnusedMemory);
92      def("blocktimer_initialize",blocktimer_initialize);
93      def("blocktimer_reportSortByName",blocktimer_reportSortByName);
94      def("blocktimer_reportSortByTime",blocktimer_reportSortByTime);
95      def("blocktimer_increment",blocktimer_increment);
96      def("blocktimer_time",blocktimer_time);
97      def("getVersion",escript::getSvnVersion);
98      def("printParallelThreadCounts",escript::printParallelThreadCnt);
99      def("getMPISizeWorld",escript::getMPISizeWorld);
100      def("getMPIRankWorld",escript::getMPIRankWorld);
101    
102    
103    //    //
104    // Interface for AbstractDomain    // Interface for AbstractDomain
105    //    //
106    class_<escript::AbstractDomain>("Domain",no_init)    class_<escript::AbstractDomain, escript::Domain_ptr>("Domain","Base class for all domains.",no_init)
107         .def("setTagMap",&escript::AbstractDomain::setTagMap)
108         .def("getTag",&escript::AbstractDomain::getTag)
109         .def("isValidTagName",&escript::AbstractDomain::isValidTagName)
110         .def("showTagNames",&escript::AbstractDomain::showTagNames)
111       .def("getX",&escript::AbstractDomain::getX)       .def("getX",&escript::AbstractDomain::getX)
112         .def("getDim",&escript::AbstractDomain::getDim)
113       .def("getNormal",&escript::AbstractDomain::getNormal)       .def("getNormal",&escript::AbstractDomain::getNormal)
114       .def("getSize",&escript::AbstractDomain::getSize)       .def("getSize",&escript::AbstractDomain::getSize)
115         .def("saveVTK",&escript::AbstractDomain::saveVTK)
116         .def("saveDX",&escript::AbstractDomain::saveDX)
117         .def("getMPISize",&escript::AbstractDomain::getMPISize)
118         .def("getMPIRank",&escript::AbstractDomain::getMPIRank)
119         .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier)
120         .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor)
121    
122       .def(self == self)       .def(self == self)
123       .def(self != self);       .def(self != self);
124    
125    //    //
126    // Interface for AbstractContinuousDomain    // Interface for AbstractContinuousDomain
127    //    //
128    class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain",no_init)    class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain","Class representing continuous domains",no_init)
129         .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId);         .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId)
130           .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId);
131    
132    //    //
133    // Interface for FunctionSpace    // Interface for FunctionSpace
134    //    //
135    class_<escript::FunctionSpace>("FunctionSpace",init<>())    class_<escript::FunctionSpace> fs_definer("FunctionSpace","",init<>());   // Doco goes in the empty string param
136       .def("getDim",&escript::FunctionSpace::getDim)    fs_definer.def("getDim",&escript::FunctionSpace::getDim);
137       .def("getX",&escript::FunctionSpace::getX)  //   fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
138       .def("getNormal",&escript::FunctionSpace::getNormal)  //                  return_internal_reference<>());
139       .def("getSize",&escript::FunctionSpace::getSize)    fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython);
140       .def("toString",&escript::FunctionSpace::toString)    fs_definer.def("getX",&escript::FunctionSpace::getX);
141       .def(self == self)    fs_definer.def("getNormal",&escript::FunctionSpace::getNormal);
142       .def(self != self);    fs_definer.def("getSize",&escript::FunctionSpace::getSize);
143      fs_definer.def("setTags",&escript::FunctionSpace::setTags);
144      fs_definer.def("getTagFromDataPointNo",
145                     &escript::FunctionSpace::getTagFromDataPointNo);
146      fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo);
147      fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags);
148      fs_definer.def("__str__", &escript::FunctionSpace::toString);
149      fs_definer.def(self == self);
150      fs_definer.def(self != self);
151    //    //
152    // Interface for Data    // Interface for Data
153    //    //
154    class_<escript::Data>("Data",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<>() )
155      // various constructors for Data objects      // various constructors for Data objects
156      .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")))
157      .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 160  BOOST_PYTHON_MODULE(escriptcpp)
160      .def(init<const escript::Data&>())      .def(init<const escript::Data&>())
161      // 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
162      // reference. In this case return_internal_reference.      // reference. In this case return_internal_reference.
163      .def("toString",&escript::Data::toString)      .def("__str__",&escript::Data::toString)
164      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())  //     .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())
165      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())      .def("getDomain",&escript::Data::getDomainPython)
166        .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>())
167      .def("isEmpty",&escript::Data::isEmpty)      .def("isEmpty",&escript::Data::isEmpty)
168        .def("isProtected",&escript::Data::isProtected)
169        .def("setProtection",&escript::Data::setProtection)
170      .def("getShape",&escript::Data::getShapeTuple)      .def("getShape",&escript::Data::getShapeTuple)
171      .def("getRank",&escript::Data::getDataPointRank)      .def("getRank",&escript::Data::getDataPointRank)
172        .def("dump",&escript::Data::dump)
173      .def("copyWithMask",&escript::Data::copyWithMask)      .def("copyWithMask",&escript::Data::copyWithMask)
174      .def("setTaggedValue",&escript::Data::setTaggedValue)      .def("setTaggedValue",&escript::Data::setTaggedValue)
175      //.def("expand",&escript::Data::expand)      .def("setTaggedValue",&escript::Data::setTaggedValueByName)
176      //.def("tag",&escript::Data::tag)      .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints)
177        .def("isExpanded",&escript::Data::isExpanded)
178        .def("isTagged",&escript::Data::isTagged)
179        .def("isConstant",&escript::Data::isConstant)
180        .def("isLazy",&escript::Data::isLazy)
181        .def("isReady",&escript::Data::isReady)
182        .def("expand",&escript::Data::expand)
183        .def("tag",&escript::Data::tag)
184        .def("resolve",&escript::Data::resolve)
185        .def("copy",&escript::Data::copy)
186        .def("copy",&escript::Data::copySelf,return_value_policy<manage_new_object>())
187        .def("delay",&escript::Data::delay)
188        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject)
189        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
190        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint)
191        .def("getValueOfDataPoint",&escript::Data::getValueOfDataPoint)
192        .def("getValueOfGlobalDataPoint",&escript::Data::getValueOfGlobalDataPoint)
193        .def("setToZero",&escript::Data::setToZero)
194        .def("interpolate",&escript::Data::interpolate)
195        .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
196      .def("saveDX",&escript::Data::saveDX)      .def("saveDX",&escript::Data::saveDX)
197      .def("wherePositive",&escript::Data::wherePositive)      .def("saveVTK",&escript::Data::saveVTK)
198      .def("whereNegative",&escript::Data::whereNegative)      .def("getTagNumber",&escript::Data::getTagNumber)
     .def("whereNonNegative",&escript::Data::whereNonNegative)  
     .def("whereNonPositive",&escript::Data::whereNonPositive)  
     .def("whereZero",&escript::Data::whereZero)  
     .def("whereNonZero",&escript::Data::whereNonZero)  
199      // Unary functions for Data      // Unary functions for Data
200      .def("interpolate",&escript::Data::interpolate)      .def("_interpolate",&escript::Data::interpolate)
201      .def("grad",&escript::Data::gradOn)      .def("_grad",&escript::Data::gradOn)
202      .def("grad",&escript::Data::grad)      .def("_grad",&escript::Data::grad)
203      .def("integrate",&escript::Data::integrate)      .def("_transpose",&escript::Data::transpose)
204      .def("transpose",&escript::Data::transpose)      .def("_trace",&escript::Data::trace)
205      .def("trace",&escript::Data::trace)      .def("_maxval",&escript::Data::maxval)
206      .def("sin",&escript::Data::sin)      .def("_minval",&escript::Data::minval)
207      .def("cos",&escript::Data::cos)      .def("_wherePositive",&escript::Data::wherePositive)
208      .def("tan",&escript::Data::tan)      .def("_whereNegative",&escript::Data::whereNegative)
209      .def("log",&escript::Data::log)      .def("_whereNonNegative",&escript::Data::whereNonNegative)
210      .def("ln",&escript::Data::ln)      .def("_whereNonPositive",&escript::Data::whereNonPositive)
211      .def("Lsup",&escript::Data::Lsup)      .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
212      .def("sup",&escript::Data::sup)      .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
213      .def("inf",&escript::Data::inf)      .def("_erf",&escript::Data::erf)
214        .def("_sin",&escript::Data::sin)
215        .def("_cos",&escript::Data::cos)
216        .def("_tan",&escript::Data::tan)
217        .def("_asin",&escript::Data::asin)
218        .def("_acos",&escript::Data::acos)
219        .def("_atan",&escript::Data::atan)
220        .def("_sinh",&escript::Data::sinh)
221        .def("_cosh",&escript::Data::cosh)
222        .def("_tanh",&escript::Data::tanh)
223        .def("_asinh",&escript::Data::asinh)
224        .def("_acosh",&escript::Data::acosh)
225        .def("_atanh",&escript::Data::atanh)
226        .def("_exp",&escript::Data::exp)
227        .def("_sqrt",&escript::Data::sqrt)
228        .def("_log10",&escript::Data::log10)
229        .def("_log",&escript::Data::log)
230        .def("_sign",&escript::Data::sign)
231        .def("_symmetric",&escript::Data::symmetric)
232        .def("_nonsymmetric",&escript::Data::nonsymmetric)
233        .def("_trace",&escript::Data::trace)
234        .def("_swap_axes",&escript::Data::swapaxes)
235        .def("_eigenvalues",&escript::Data::eigenvalues)
236        .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
237        // functions returning a single real number:
238        .def("_Lsup",&escript::Data::Lsup)
239        .def("_sup",&escript::Data::sup)
240        .def("_inf",&escript::Data::inf)
241        .def("_integrate",&escript::Data::integrate)
242    
243        // following implements the python abs operator
244      .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)  
245      // following implements the python "-" negation operator      // following implements the python "-" negation operator
246      .def("__neg__",&escript::Data::neg)      .def("__neg__",&escript::Data::neg)
247      // following implements the python "+" identity operator      // following implements the python "+" identity operator
# Line 147  BOOST_PYTHON_MODULE(escriptcpp) Line 253  BOOST_PYTHON_MODULE(escriptcpp)
253      // following two functions implement the python ** operator      // following two functions implement the python ** operator
254      .def("__pow__",&escript::Data::powO)      .def("__pow__",&escript::Data::powO)
255      .def("__pow__",&escript::Data::powD)      .def("__pow__",&escript::Data::powD)
256        .def("__rpow__",&escript::Data::rpowO)
257      // NOTE:: The order of these declarations is important. Anything      // NOTE:: The order of these declarations is important. Anything
258      // declared before the generic declaration isn't found so the generic      // declared before the generic declaration isn't found so the generic
259      // version will be called.      // version will be called.
     .def(self += other<object>())  
     .def(self += self)  
260      .def(self + other<object>())      .def(self + other<object>())
261      .def(other<object>() + self)      .def(other<object>() + self)
262      .def(self + self)      .def(self + self)
263      .def(self -= other<object>())      .def(self += other<object>())
264      .def(self -= self)      .def(self += self)
265    
266      .def(self - other<object>())      .def(self - other<object>())
267      .def(other<object>() - self)      .def(other<object>() - self)
268      .def(self - self)      .def(self - self)
269      .def(self *= other<object>())      .def(self -= other<object>())
270      .def(self *= self)      .def(self -= self)
271    
272      .def(self * other<object>())      .def(self * other<object>())
273      .def(other<object>() * self)      .def(other<object>() * self)
274      .def(self * self)      .def(self * self)
275      .def(self /= other<object>())      .def(self *= other<object>())
276      .def(self /= self)      .def(self *= self)
277    
278      .def(self / other<object>())      .def(self / other<object>())
279      .def(other<object>() / self)      .def(other<object>() / self)
280      .def(self / self)      .def(self / self)
281        .def(self /= other<object>())
282        .def(self /= self)
283      // Need scope resolution due to a bug either in the compiler or      // Need scope resolution due to a bug either in the compiler or
284      // the boost code. This calls operator << for Data.      // the boost code. This calls operator << for Data.
285      .def(self_ns::str(self));      .def(self_ns::str(self));
# Line 178  BOOST_PYTHON_MODULE(escriptcpp) Line 288  BOOST_PYTHON_MODULE(escriptcpp)
288    // Factory methods for function space    // Factory methods for function space
289    //    //
290    def("ContinuousFunction",escript::continuousFunction);    def("ContinuousFunction",escript::continuousFunction);
291      def("ReducedContinuousFunction",escript::reducedContinuousFunction);
292    def("Function",escript::function);    def("Function",escript::function);
293      def("ReducedFunction",escript::reducedFunction);
294    def("FunctionOnBoundary",escript::functionOnBoundary);    def("FunctionOnBoundary",escript::functionOnBoundary);
295      def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary);
296    def("FunctionOnContactZero",escript::functionOnContactZero);    def("FunctionOnContactZero",escript::functionOnContactZero);
297      def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero);
298    def("FunctionOnContactOne",escript::functionOnContactOne);    def("FunctionOnContactOne",escript::functionOnContactOne);
299      def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne);
300    def("Solution",escript::solution);    def("Solution",escript::solution);
301    def("ReducedSolution",escript::reducedSolution);    def("ReducedSolution",escript::reducedSolution);
302    def("DiracDeltaFunction",escript::diracDeltaFunction);    def("DiracDeltaFunction",escript::diracDeltaFunction);
# Line 189  BOOST_PYTHON_MODULE(escriptcpp) Line 304  BOOST_PYTHON_MODULE(escriptcpp)
304    //    //
305    // Factory methods for Data    // Factory methods for Data
306    //    //
307      def("load",escript::load);
308      def("loadIsConfigured",escript::loadConfigured);
309    def("Scalar",escript::Scalar,    def("Scalar",escript::Scalar,
310        (arg("value")=0.0,        (arg("value")=0.0,
311         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
# Line 211  BOOST_PYTHON_MODULE(escriptcpp) Line 328  BOOST_PYTHON_MODULE(escriptcpp)
328         arg("expanded")=false));         arg("expanded")=false));
329    
330    //    //
331      // Binary operators
332      //
333      def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
334          (arg("arg0")=escript::Data(),
335           arg("arg1")=escript::Data(),
336           arg("axis_offset")=0,
337           arg("transpose")=0));
338    
339      //
340    // Interface for AbstractSystemMatrix    // Interface for AbstractSystemMatrix
341    //    //
342    class_<escript::AbstractSystemMatrix>("Operator",init<>())    class_<escript::AbstractSystemMatrix>("Operator","",init<>())    // Doco goes in the empty string param
343       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty)       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty)
344       .def("solve",&escript::AbstractSystemMatrix::solve)       .def("solve",&escript::AbstractSystemMatrix::solve)
345       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)
346       .def("saveMM",&escript::AbstractSystemMatrix::saveMM)       .def("saveMM",&escript::AbstractSystemMatrix::saveMM)
347       .def("setValue",&escript::AbstractSystemMatrix::setValue)       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)
348       .def("resetSolver",&escript::AbstractSystemMatrix::resetSolver)       .def("resetValues",&escript::AbstractSystemMatrix::resetValues)
349       .def(self*other<escript::Data>());       .def(self*other<escript::Data>());
350      //
351      // Interface for AbstractTransportProblem
352      //
353      class_<escript::AbstractTransportProblem>("TransportProblem","",init<>())    // Doco goes in the empty string param
354         .def("isEmpty",&escript::AbstractTransportProblem::isEmpty)
355         .def("solve",&escript::AbstractTransportProblem::solve)
356         .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue)
357         .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint)
358         .def("reset",&escript::AbstractTransportProblem::resetTransport)
359         .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
360         .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize)
361         .def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize);
362    
363      // Functions to modify global parameters
364      def("setEscriptParamInt",escript::setEscriptParamInt,
365          (arg("value")=0));
366      def("getEscriptParamInt",escript::getEscriptParamInt,
367          (arg("sentinel")=0));
368    
369    
370    //    //
371    // Register esysExceptionTranslator    // Register esysExceptionTranslator

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