/[escript]/trunk/escript/src/escriptcpp.cpp
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revision 767 by gross, Fri Jun 30 07:29:08 2006 UTC revision 2644 by jfenwick, Wed Sep 2 04:14:03 2009 UTC
# Line 1  Line 1 
1  //$Id$  
2  /*  /*******************************************************
3   ************************************************************  *
4   *          Copyright 2006 by ACcESS MNRF                   *  * Copyright (c) 2003-2009 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    #include "EscriptParams.h"
27    #include "TestDomain.h"
28    
29    
30    extern "C" {
31    #include "esysUtils/blocktimer.h"
32    }
33    
34  #include "esysUtils/esysExceptionTranslator.h"  #include "esysUtils/esysExceptionTranslator.h"
35    
36    #include <boost/version.hpp>
37  #include <boost/python.hpp>  #include <boost/python.hpp>
38  #include <boost/python/module.hpp>  #include <boost/python/module.hpp>
39  #include <boost/python/def.hpp>  #include <boost/python/def.hpp>
40  #include <boost/python/object.hpp>  #include <boost/python/object.hpp>
41  #include <boost/python/tuple.hpp>  #include <boost/python/tuple.hpp>
42  #include <boost/python/numeric.hpp>  #include <boost/python/numeric.hpp>
43    #include <boost/smart_ptr.hpp>
44    #include <boost/version.hpp>
45    
46  using namespace boost::python;  using namespace boost::python;
47    
48  /*! \mainpage Esys Documentation  /*! \mainpage Esys Documentation
49   *   *
50   * \version 1.0.0   * \version 3.0.0
51   *   *
52   * - \ref escript   * - \ref escript
53   *   *
# Line 41  using namespace boost::python; Line 55  using namespace boost::python;
55   *   *
56   * - \ref finley   * - \ref finley
57   *   *
58   * - <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>
59   *   *
60   */   */
61    
# Line 49  using namespace boost::python; Line 63  using namespace boost::python;
63   * Escript is the python module that contains the interfaces   * Escript is the python module that contains the interfaces
64   * to the C++ side of escript.   * to the C++ side of escript.
65   *   *
66   * \version 1.0.0   *
67   *   *
68   * \section class_desc Class Description:   * \section class_desc Class Description:
69   * Data   * Data
# Line 67  using namespace boost::python; Line 81  using namespace boost::python;
81    
82  BOOST_PYTHON_MODULE(escriptcpp)  BOOST_PYTHON_MODULE(escriptcpp)
83  {  {
84    def("setNumberOfThreads",escript::setNumberOfThreads);  
85    def("getNumberOfThreads",escript::getNumberOfThreads);    #if BOOST_VERSION >= 103500
86    // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
87      docstring_options docopt(true,true,false);
88      #endif
89    
90      def("setNumberOfThreads",escript::setNumberOfThreads,"Use of this method is strongly discouraged.");
91      def("getNumberOfThreads",escript::getNumberOfThreads,"Return the maximum number of threads"
92    " available to OpenMP.");
93      def("releaseUnusedMemory",escript::releaseUnusedMemory);
94      def("blocktimer_initialize",blocktimer_initialize);
95      def("blocktimer_reportSortByName",blocktimer_reportSortByName);
96      def("blocktimer_reportSortByTime",blocktimer_reportSortByTime);
97      def("blocktimer_increment",blocktimer_increment);
98      def("blocktimer_time",blocktimer_time);
99      def("getVersion",escript::getSvnVersion,"This method will only report accurate version numbers for clean checkouts.");
100      def("printParallelThreadCounts",escript::printParallelThreadCnt);
101      def("getMPISizeWorld",escript::getMPISizeWorld,"Return number of MPI processes in the job.");
102      def("getMPIRankWorld",escript::getMPIRankWorld,"Return the rank of this process in the MPI World.");
103      def("MPIBarrierWorld",escript::MPIBarrierWorld,"Wait until all MPI processes have reached this point.");
104      def("getMPIWorldMax",escript::getMPIWorldMax,"\nEach MPI process calls this function with a"
105    " value for arg1. The maximum value is computed and returned.\n\n:rtype: int");
106      def("getMPIWorldSum",escript::getMPIWorldSum,"\nEach MPI process calls this function with a"
107    " value for arg1. The values are added up and the total value is returned.\n\n:rtype: int");
108      def("getMachinePrecision",escript::getMachinePrecision);
109      def("getMaxFloat",escript::getMaxFloat);
110      def("_saveDataCSV",escript::saveDataCSV, (args("filename","arg","sep","csep"), arg("append")=false),
111    "Saves data objects passed in a python dictionary to a file.\n"
112    "The data objects must be over the same domain and be able to be interpolated to the same FunctionSpace.\n"
113    "If one of the dictionary keys is named ``mask``, then only samples where ``mask`` has a positive\n"
114    "value will be written to the file.\n\n"
115    "A header line giving the names of each column will be output first.\n"
116    "The keys given in the dictionary will be used to name columns.\n"
117    "Then the data will be output, one line per sample (for all data).\n"
118    "\n:param filename:\n:type filename: ``string``\n"
119    ":param arg: dictionary of named `Data` objects. If one is called ``mask`` it must be scalar data."
120    "\n:type arg: ``dict``\n"
121    ":param sep:separator for columns (defaults to \", \"\n:type sep:``string``\n"
122    ":param csep:separator for fields within data object (defaults to \"_\"\n:type csep:``string``\n"
123    ":param append: If True, write to the end of ``filename``\n:type append: ``string``\n");
124    
125    
126    //    //
127    // Interface for AbstractDomain    // Interface for AbstractDomain
128    //    //
129    class_<escript::AbstractDomain>("Domain",no_init)    class_<escript::AbstractDomain, escript::Domain_ptr>("Domain","Base class for all domains.",no_init)
130       .def("getX",&escript::AbstractDomain::getX)       .def("getStatus",&escript::AbstractDomain::getStatus,"The status of a domain changes whenever the domain is modified\n\n:rtype: int")
131       .def("getNormal",&escript::AbstractDomain::getNormal)       .def("setTagMap",&escript::AbstractDomain::setTagMap,args("name","tag"),
132       .def("getSize",&escript::AbstractDomain::getSize)  "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
133       .def("saveVTK",&escript::AbstractDomain::saveVTK)  ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
134       .def("saveDX",&escript::AbstractDomain::saveDX)       .def("getTag",&escript::AbstractDomain::getTag,args("name"),":return: tag id for "
135    "``name``\n:rtype: ``string``")
136         .def("isValidTagName",&escript::AbstractDomain::isValidTagName,args("name"),
137    ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
138         .def("showTagNames",&escript::AbstractDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
139         .def("getX",&escript::AbstractDomain::getX,":rtype: `Data`\n:return: Locations in the"
140    "`Domain`. FunctionSpace is chosen appropriately")
141         .def("getDim",&escript::AbstractDomain::getDim,":rtype: `int`\n:return: Spatial dimension of the `Domain`")
142         .def("getNormal",&escript::AbstractDomain::getNormal,":rtype: `escript`\n:return: Boundary normals")
143         .def("getSize",&escript::AbstractDomain::getSize,":return: the local size of samples. The function space is chosen appropriately\n:rtype: `Data`")
144         .def("saveVTK",&escript::AbstractDomain::saveVTK,args("filename","arg", "metadata"
145    , "metadata_schema"),
146    ":param filename: \n:type filename: ``string``\n:param arg: items to be added"
147    "\n:type arg: ``dict``\n:param metadata: string representing some meta data to be added\n:type metadata: ``string``"
148    "\n:param metadata_schema: schema type for metadata\n:type metadata_schema: ``string``")
149         .def("dump",&escript::AbstractDomain::dump,args("filename"),"Dumps the domain to a file"
150    ":param filename:\n:type filename: string")
151         .def("saveDX",&escript::AbstractDomain::saveDX,args("filename","arg"),"Saves a dictonary of Data objects to an OpenDX input file.\n\n:param filename:\n:type filename: ``string``"
152    "\n:param arg:\n:type arg: `dict`")
153         .def("getMPISize",&escript::AbstractDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
154         .def("getMPIRank",&escript::AbstractDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
155         .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier,"Wait until all processes have reached this point")
156         .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")
157    
158       .def(self == self)       .def(self == self)
159       .def(self != self);       .def(self != self);
160    
161    //    //
162    // Interface for AbstractContinuousDomain    // Interface for AbstractContinuousDomain
163    //    //
164    class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain",no_init)    class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain","Class representing continuous domains",no_init)
165         .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId);         .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId,
166    args("solver", "preconditioner", "package", "symmetry"),
167    ":return: the identifier of the matrix type to be used for the global stiffness matrix "
168    "when a particular solver package and symmetric matrix is used.\n"
169    ":rtype: int")
170           .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId,
171    args("solver", "preconditioner", "package", "symmetry"));
172    
173    
174      //
175      // Interface for TestDomain
176      //
177      class_ <escript::TestDomain, bases<escript::AbstractDomain> >("TestDomain", "Test Class for domains with no structure. May be removed from future releases without notice.", init<int,int>());
178    
179      // This is the only python visible way to get a TestDomain
180      def("getTestDomainFunctionSpace",&escript::getTestDomainFunctionSpace, args("dpps",
181     "samples"),
182    "For testing only. May be removed without notice.");
183    
184    //    //
185    // Interface for FunctionSpace    // Interface for FunctionSpace
186    //    //
187    class_<escript::FunctionSpace>("FunctionSpace",init<>())    class_<escript::FunctionSpace> fs_definer("FunctionSpace","A FunctionSpace describes which points from the `Domain` to use to represent functions.",init<>());    // Doco goes in the empty string param
188       .def("getDim",&escript::FunctionSpace::getDim)    fs_definer.def("getDim",&escript::FunctionSpace::getDim,":return: the spatial dimension of the underlying domain.\n:rtype: int");
189       .def("getDomain",&escript::FunctionSpace::getDomain,return_internal_reference<>())  //   fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
190       .def("getX",&escript::FunctionSpace::getX)  //                  return_internal_reference<>());
191       .def("getNormal",&escript::FunctionSpace::getNormal)    fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython,":return: the underlying `Domain` for this FunctionSpace.\n:rtype: `Domain`");
192       .def("getSize",&escript::FunctionSpace::getSize)    fs_definer.def("getX",&escript::FunctionSpace::getX,"\n:return: a function whose values are its input coordinates. ie an identity function.\n:rtype: `Data`");
193       .def("setTags",&escript::FunctionSpace::setTags)    fs_definer.def("getNormal",&escript::FunctionSpace::getNormal,":return: the surface normal field.\n\n:rtype: `Data`");
194       .def("getTagFromDataPointNo",&escript::FunctionSpace::getTagFromDataPointNo)    fs_definer.def("getSize",&escript::FunctionSpace::getSize,":return: sample size\n:rtype: `Data`");
195       .def("__str__",&escript::FunctionSpace::toString)    fs_definer.def("setTags",&escript::FunctionSpace::setTags,args("newtag","mask"),
196       .def(self == self)  "Set tags according to a mask\n\n:param newtag: tag number to set\n:type newtag: non-zero ``int``\n:param mask: Samples which correspond to positive values in the mask will be set to ``newtag``.\n:type mask: scalar `Data`");
197       .def(self != self);    fs_definer.def("getTagFromDataPointNo",
198                     &escript::FunctionSpace::getTagFromDataPointNo,":return: the tag associated with the given sample number.\n:rtype: int");
199      fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo,args("dataPointNo"),":return: the reference number associated with ``dataPointNo``\n:rtype: int ");
200      fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags,":return: a list of the tags used in this function space\n:rtype: ``list``");
201      fs_definer.def("__str__", &escript::FunctionSpace::toString);
202      fs_definer.def(self == self);
203      fs_definer.def(self != self);
204    //    //
205    // Interface for Data    // Interface for Data
206    //    //
207    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<>() )
208      // various constructors for Data objects      // various constructors for Data objects
     .def(init<const numeric::array&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))  
209      .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")))
210      .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")))
211      .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))      .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))
# Line 115  BOOST_PYTHON_MODULE(escriptcpp) Line 213  BOOST_PYTHON_MODULE(escriptcpp)
213      // 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
214      // reference. In this case return_internal_reference.      // reference. In this case return_internal_reference.
215      .def("__str__",&escript::Data::toString)      .def("__str__",&escript::Data::toString)
216      .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())      .def("getDomain",&escript::Data::getDomainPython,":rtype: `Domain`")
217      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_internal_reference<>())      .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>(),":rtype: `FunctionSpace`")
218      .def("isEmpty",&escript::Data::isEmpty)      .def("isEmpty",&escript::Data::isEmpty,"Is this object an instance of ``DataEmpty``\n\n:rtype: ``bool``\n:note: This is not the same thing as asking if the object contains datapoints.")
219      .def("getShape",&escript::Data::getShapeTuple)      .def("isProtected",&escript::Data::isProtected,"Can this instance be modified.\n:rtype: ``bool``")
220      .def("getRank",&escript::Data::getDataPointRank)      .def("setProtection",&escript::Data::setProtection,"Disallow modifications to this data object\n\n:note: This method does not allow you to undo protection.")
221      .def("copyWithMask",&escript::Data::copyWithMask)      .def("getShape",&escript::Data::getShapeTuple,"\nReturns the shape of the datapoints in this object as a python tuple. Scalar data has the shape ``()``\n\n:rtype: ``tuple``")
222      .def("setTaggedValue",&escript::Data::setTaggedValue)      .def("getRank",&escript::Data::getDataPointRank,":return: the number of indicies required to address a component of a datapoints\n:rtype: positive ``int``")
223      .def("setRefValue",&escript::Data::setRefValue)      .def("dump",&escript::Data::dump,args("fileName"),"Save the data as a netCDF file\n\n:param fileName: \n:type fileName: ``string``")
224      .def("getRefValue",&escript::Data::getRefValue)      .def("toListOfTuples",&escript::Data::toListOfTuples, (arg("scalarastuple")=false),
225      .def("expand",&escript::Data::expand)  "Return the datapoints of this object in a list. Each datapoint is stored as a tuple.\n\n"
226      .def("tag",&escript::Data::tag)  ":param scalarastuple: if True, scalar data will be wrapped as a tuple."
227      .def("copy",&escript::Data::copy)  " True => [(0), (1), (2)]; False => [0, 1, 2]")
228      .def("convertToNumArray",&escript::Data::convertToNumArray)      .def("copyWithMask",&escript::Data::copyWithMask,args("other","mask"),
229      .def("convertToNumArrayFromSampleNo",&escript::Data::convertToNumArrayFromSampleNo)  "Selectively copy values from ``other`` `Data`."
230      .def("convertToNumArrayFromDPNo",&escript::Data::convertToNumArrayFromDPNo)  "Datapoints which correspond to postive values in ``mask`` will be copied from ``other``\n"
231      .def("fillFromNumArray",&escript::Data::fillFromNumArray)  "\n:param other: source of values\n"
232      .def("interpolate",&escript::Data::interpolate)  ":type other: `Data`\n:param mask:\n:type mask: Scalar `Data`")
233      .def("mindp",&escript::Data::mindp)      .def("setTaggedValue",&escript::Data::setTaggedValue,args("tagKey","value"),
234      .def("saveDX",&escript::Data::saveDX)  "Set the value of tagged Data.\n\n:param tagKey: tag to update\n:type tagKey: ``int``\n")
235      .def("saveVTK",&escript::Data::saveVTK)      .def("setTaggedValue",&escript::Data::setTaggedValueByName,args("name","value"),":param name: tag to update\n:type name: ``string``\n"
236      .def("getTagNumber",&escript::Data::getTagNumber)  ":param value: value to set tagged data to\n:type value: ``object`` which acts like an array, ``tuple`` or ``list``\n")
237      .def("archiveData",&escript::Data::archiveData)      .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints,":rtype: ``int``\n:return: Number of datapoints in the object")
238      .def("extractData",&escript::Data::extractData)      .def("isExpanded",&escript::Data::isExpanded,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
239        .def("isTagged",&escript::Data::isTagged,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
240        .def("isConstant",&escript::Data::isConstant,":rtype: ``bool``\n:return: True if this ``Data`` is an instance of ``DataConstant``\n:note: This does not mean the data is immutable.")
241        .def("isLazy",&escript::Data::isLazy,":rtype: ``bool``\n:return: True if this ``Data`` is lazy.")
242        .def("isReady",&escript::Data::isReady,":rtype: ``bool``\n:return: True if this ``Data`` is not lazy.")
243        .def("expand",&escript::Data::expand,"Convert the data to expanded representation if it is not expanded already.")
244        .def("tag",&escript::Data::tag,"Convert data to tagged representation if it is not already tagged or expanded")
245        .def("resolve",&escript::Data::resolve,"Convert the data to non-lazy representation.")
246        .def("copy",&escript::Data::copy,args("other"),"Make this object a copy of ``other``\n"
247    "\n:note: The two objects will act independently from now on. That is, changing ``other`` "
248    "after this call will not change this object and vice versa.")
249        .def("copy",&escript::Data::copySelf,":note: In the no argument form, a new object will be returned which is an independent copy of this object.")
250        .def("delay",&escript::Data::delay,"Convert this object into lazy representation")
251        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject,args("dataPointNo","value"))
252        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
253        .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint,"\nModify the value of a single datapoint.\n\n:param dataPointNo:\n"
254    ":type dataPointNo: int\n:param value: \n:type value: ``float`` or an object which acts like an array, ``tuple`` or ``list``\n:warning: Use of this operation is discouraged. It prevents some optimisations from operating.")
255        .def("getTupleForDataPoint",&escript::Data::getValueOfDataPointAsTuple,args("dataPointNo"),
256    ":return: Value of the specified datapoint\n:rtype: ``tuple``\n:param dataPointNo: datapoint to access\n:type dataPointNo: ``int``")
257        .def("getTupleForGlobalDataPoint",&escript::Data::getValueOfGlobalDataPointAsTuple,args("procNo","dataPointNo"),"Get a specific datapoint from a specific process\n\n"
258    ":rtype: ``tuple``\n:param procNo: MPI rank of the process\n:type procNo: positive ``int``"
259    "\n:param dataPointNo: datapoint to access\n:type dataPointNo: int")
260        .def("setToZero",&escript::Data::setToZero,"After this call the object will store values of the same shape as before but all components will be zero.")
261        .def("interpolate",&escript::Data::interpolate,args("functionspace"),"Interpolate this object's values into a new functionspace.")
262        .def("interpolateTable", &escript::Data::interpolateFromTable,
263    args("table","Amin","Astep","undef", "B", "Bmin", "Bstep"),
264    "Creates a new Data object by interpolating using the source data (which are\n"
265    "looked up in ``table``)\n\n"
266    ":param table: two dimensional collection of values\n"
267    ":param Amin: The base of locations in table\n:type Amin: float\n"
268    ":param Astep: size of gap between each item in the table\n:type Astep: float\n"
269    ":param undef: upper bound on interpolated values\n:type undef: float\n"
270    ":param B: Scalar representing the second coordinate to be mapped into the table\n"
271    ":type B: `Data`\n"
272    ":param Bmin: The base of locations in table for 2nd dimension\n:type Bmin: float\n"
273    ":param Bstep: size of gap between each item in the table for 2nd dimension\n:type Bstep: float\n"
274    ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"
275    "\n:rtype: `Data`"
276    )
277    
278        .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
279        .def("maxGlobalDataPoint",&escript::Data::maxGlobalDataPoint)
280        .def("saveDX",&escript::Data::saveDX,args("fileName"),"Save the object in DX format.\n\n"
281    ":param fileName: filename\n:type fileName: string")
282        .def("saveVTK",&escript::Data::saveVTK, args("fileName"),"Save the object in VTK format.\n\n"
283    ":param fileName: \n:type fileName: string")
284        .def("getTagNumber",&escript::Data::getTagNumber,args("dpno"),"Return tag number for the specified datapoint\n\n:rtype: int\n:param dpno: datapoint number\n:type dpno: int")
285      // Unary functions for Data      // Unary functions for Data
286      .def("_interpolate",&escript::Data::interpolate)      .def("_interpolate",&escript::Data::interpolate)
287      .def("_grad",&escript::Data::gradOn)      .def("_grad",&escript::Data::gradOn)
# Line 152  BOOST_PYTHON_MODULE(escriptcpp) Line 296  BOOST_PYTHON_MODULE(escriptcpp)
296      .def("_whereNonPositive",&escript::Data::whereNonPositive)      .def("_whereNonPositive",&escript::Data::whereNonPositive)
297      .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))      .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
298      .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))      .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
299        .def("_erf",&escript::Data::erf)
300      .def("_sin",&escript::Data::sin)      .def("_sin",&escript::Data::sin)
301      .def("_cos",&escript::Data::cos)      .def("_cos",&escript::Data::cos)
302      .def("_tan",&escript::Data::tan)      .def("_tan",&escript::Data::tan)
# Line 169  BOOST_PYTHON_MODULE(escriptcpp) Line 314  BOOST_PYTHON_MODULE(escriptcpp)
314      .def("_log10",&escript::Data::log10)      .def("_log10",&escript::Data::log10)
315      .def("_log",&escript::Data::log)      .def("_log",&escript::Data::log)
316      .def("_sign",&escript::Data::sign)      .def("_sign",&escript::Data::sign)
317        .def("_symmetric",&escript::Data::symmetric)
318        .def("_nonsymmetric",&escript::Data::nonsymmetric)
319        .def("_trace",&escript::Data::trace)
320        .def("_swap_axes",&escript::Data::swapaxes)
321      .def("_eigenvalues",&escript::Data::eigenvalues)      .def("_eigenvalues",&escript::Data::eigenvalues)
322      .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))
323      // functions returning a single real number:      // functions returning a single real number:
324      .def("_Lsup",&escript::Data::Lsup)      .def("_Lsup",&escript::Data::Lsup,":return: the Lsup-norm of the object\n:rtype: float\n:note: If the ``Data`` contains no values, zero will be returned instead.")
325      .def("_sup",&escript::Data::sup)      .def("_sup",&escript::Data::sup,":return: the maximum value over all data points.\n:rtype: float\n:note: If the ``Data`` contains no values a large negative value will be returned instead.")
326      .def("_inf",&escript::Data::inf)      .def("_inf",&escript::Data::inf,":return: minimum value over all components and all data points\n:rtype: float\n:note: If the ``Data`` contains no values a large positive value will be returned instead.")
327      .def("_integrate",&escript::Data::integrate)      .def("_integrateToTuple",&escript::Data::integrateToTuple,":return: Calculate the integral over the function space domain as a python tuple\n:rtype: tuple")
   
328      // following implements the python abs operator      // following implements the python abs operator
329      .def("__abs__",&escript::Data::abs)      .def("__abs__",&escript::Data::abs,":return: absolute value\n\n:rtype: `Data`")
330      // following implements the python "-" negation operator      // following implements the python "-" negation operator
331      .def("__neg__",&escript::Data::neg)      .def("__neg__",&escript::Data::neg, ":return: negation of the values in this object\n:rtype: `Data`")
332      // following implements the python "+" identity operator      // following implements the python "+" identity operator
333      .def("__pos__",&escript::Data::pos)      .def("__pos__",&escript::Data::pos, "\nThe unary + operator\n\n:rtype: Data`")
334      // following two functions implement the python [] operator      // following two functions implement the python [] operator
335      .def("__getitem__",&escript::Data::getItem)      .def("__getitem__",&escript::Data::getItem,"Used by the python [] operator\n\n:rtype: `Data`")
336      .def("__setitem__",&escript::Data::setItemO)      .def("__setitem__",&escript::Data::setItemO,"Used by the python [] operator")
337      .def("__setitem__",&escript::Data::setItemD)      .def("__setitem__",&escript::Data::setItemD,"Used by the python [] operator")
338      // following two functions implement the python ** operator      // following two functions implement the python ** operator
339      .def("__pow__",&escript::Data::powO)      .def("__pow__",&escript::Data::powO,"Used by the python ** operator\n\n:rtype: `Data`")
340      .def("__pow__",&escript::Data::powD)      .def("__pow__",&escript::Data::powD)
341      .def("__rpow__",&escript::Data::rpowO)      .def("__rpow__",&escript::Data::rpowO,"\nUsed by the python ** operator\n\n:rtype: `Data`")
342      // NOTE:: The order of these declarations is important. Anything      // NOTE:: The order of these declarations is important. Anything
343      // declared before the generic declaration isn't found so the generic      // declared before the generic declaration isn't found so the generic
344      // version will be called.      // version will be called.
# Line 221  BOOST_PYTHON_MODULE(escriptcpp) Line 369  BOOST_PYTHON_MODULE(escriptcpp)
369      // the boost code. This calls operator << for Data.      // the boost code. This calls operator << for Data.
370      .def(self_ns::str(self));      .def(self_ns::str(self));
371    
372    
373    //    //
374    // Factory methods for function space    // Factory methods for function space
375    //    //
376    def("ContinuousFunction",escript::continuousFunction);    def("ContinuousFunction",escript::continuousFunction,args("domain"),
377    def("Function",escript::function);  ":return: a continuous FunctionSpace (overlapped node values)\n"
378    def("FunctionOnBoundary",escript::functionOnBoundary);  ":rtype: `FunctionSpace`");
379    def("FunctionOnContactZero",escript::functionOnContactZero);    def("ReducedContinuousFunction",escript::reducedContinuousFunction,args("domain"),
380    def("FunctionOnContactOne",escript::functionOnContactOne);  ":return: a continuous with reduced order FunctionSpace (overlapped node values on reduced element order)\n"
381    def("Solution",escript::solution);  ":rtype: `FunctionSpace`");
382    def("ReducedSolution",escript::reducedSolution);    def("Function",escript::function,args("domain"),":return: a function `FunctionSpace`\n"
383    def("DiracDeltaFunction",escript::diracDeltaFunction);  ":rtype: `FunctionSpace`");
384      def("ReducedFunction",escript::reducedFunction, args("domain"),":return: a function FunctionSpace with reduced integration order\n:rtype: `FunctionSpace`");
385      def("FunctionOnBoundary",escript::functionOnBoundary, args("domain"), ":return: a function on boundary FunctionSpace\n:rtype: `FunctionSpace`");
386      def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary, args("domain"),
387    ":return: a function on boundary FunctionSpace with reduced integration order\n"
388    ":rtype: `FunctionSpace`");
389      def("FunctionOnContactZero",escript::functionOnContactZero, args("domain"), ":return: Return a FunctionSpace on left side of contact\n:rtype: `FunctionSpace`");
390      def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero, args("domain"),
391     ":return: a FunctionSpace  on left side of contact with reduced integration order\n:rtype: `FunctionSpace`");
392      def("FunctionOnContactOne",escript::functionOnContactOne, args("domain"), ":return: Return a FunctionSpace on right side of contact\n:rtype: `FunctionSpace`");
393      def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne, args("domain"),
394     ":return: Return a FunctionSpace on right side of contact with reduced integration order\n"
395    ":rtype: `FunctionSpace`");
396      def("Solution",escript::solution, args("domain"), ":rtype: `FunctionSpace`");
397      def("ReducedSolution",escript::reducedSolution, args("domain"), ":rtype: `FunctionSpace`");
398      def("DiracDeltaFunction",escript::diracDeltaFunction, args("domain"), ":rtype: `FunctionSpace`");
399    
400    
401    
402    
403    
404    //    //
405    // Factory methods for Data    // Factory methods for Data
406    //    //
407      def("load",escript::load, args("fileName","domain"), "reads Data on domain from file in netCDF format\n\n:param fileName:\n:type fileName: ``string``\n:param domain:\n:type domain: `Domain`");
408      def("loadIsConfigured",escript::loadConfigured,":return: True if the load function is configured.");
409    def("Scalar",escript::Scalar,    def("Scalar",escript::Scalar,
410        (arg("value")=0.0,        (arg("value")=0.0,
411         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
412         arg("expanded")=false));         arg("expanded")=false),
413    "Construct a Data object containing scalar data-points.\n\n:param value: scalar value for all points\n"
414    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
415    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
416    ":type expanded: ``bool``");
417    def("Vector",escript::Vector,    def("Vector",escript::Vector,
418        (arg("value")=0.0,        (arg("value")=0.0,
419         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
420         arg("expanded")=false));         arg("expanded")=false),
421    "Construct a Data object containing rank1 data-points.\n\n:param value: scalar value for all points\n"
422    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
423    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
424    ":type expanded: ``bool``");
425    def("Tensor",escript::Tensor,    def("Tensor",escript::Tensor,
426        (arg("value")=0.0,        (arg("value")=0.0,
427         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
428         arg("expanded")=false));         arg("expanded")=false),
429    "Construct a Data object containing rank2 data-points.\n\n:param value: scalar value for all points\n"
430    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
431    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
432    ":type expanded: ``bool``");
433    def("Tensor3",escript::Tensor3,    def("Tensor3",escript::Tensor3,
434        (arg("value")=0.0,        (arg("value")=0.0,
435         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
436         arg("expanded")=false));         arg("expanded")=false),
437    "Construct a Data object containing rank3 data-points.\n\n:param value: scalar value for all points\n"
438    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
439    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
440    ":type expanded: ``bool``"
441    );
442    def("Tensor4",escript::Tensor4,    def("Tensor4",escript::Tensor4,
443        (arg("value")=0.0,        (arg("value")=0.0,
444         arg("what")=escript::FunctionSpace(),         arg("what")=escript::FunctionSpace(),
445         arg("expanded")=false));         arg("expanded")=false),
446    "Construct a Data object containing rank4 data-points.\n\n:param value: scalar value for all points\n"
447    "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
448    ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
449    ":type expanded: ``bool``"
450    );
451    
452      //
453      // Binary operators
454      //
455      def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
456          (arg("arg0"),
457           arg("arg1"),
458           arg("axis_offset")=0,
459           arg("transpose")=0),
460    "Compute a tensor product of two Data objects.\n\n:rtype: `Data`\n:param arg0:\n"
461    ":param arg1:\n:param axis_offset:\n:type axis_offset: ``int``\n"
462    ":param transpose: 0: transpose neither, 1: transpose arg0, 2: transpose arg1\n"
463    ":type transpose: int");
464    
465    //    //
466    // Interface for AbstractSystemMatrix    // Interface for AbstractSystemMatrix
467    //    //
468    class_<escript::AbstractSystemMatrix>("Operator",init<>())    class_<escript::AbstractSystemMatrix>("Operator","",init<>())    // Doco goes in the empty string param
469       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty)       .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty,":rtype: ``bool``\n"
470       .def("solve",&escript::AbstractSystemMatrix::solve)  ":return: True if matrix is empty")
471       .def("of",&escript::AbstractSystemMatrix::vectorMultiply)       .def("solve",&escript::AbstractSystemMatrix::solve, args("in","options"),
472       .def("saveMM",&escript::AbstractSystemMatrix::saveMM)  ":return: the solution *u* of the linear system *this*u=in*\n\n:param in:\n:type in: `Data`")
473       .def("saveHB",&escript::AbstractSystemMatrix::saveHB)       .def("of",&escript::AbstractSystemMatrix::vectorMultiply,args("right"),
474       .def("resetValues",&escript::AbstractSystemMatrix::resetValues)  "matrix*vector multiplication")
475         .def("saveMM",&escript::AbstractSystemMatrix::saveMM, args("fileName"),
476    "writes the matrix to a file using the Matrix Market file format")
477         .def("saveHB",&escript::AbstractSystemMatrix::saveHB, args("filename"),
478    "writes the matrix to a file using the Harwell-Boeing file format")
479         .def("resetValues",&escript::AbstractSystemMatrix::resetValues, "resets the matrix entries")
480       .def(self*other<escript::Data>());       .def(self*other<escript::Data>());
481      //
482      // Interface for AbstractTransportProblem
483      //
484      class_<escript::AbstractTransportProblem>("TransportProblem","",init<>())    // Doco goes in the empty string param
485         .def("isEmpty",&escript::AbstractTransportProblem::isEmpty,":rtype: ``int``")
486         .def("solve",&escript::AbstractTransportProblem::solve, args("source","dt", "options"),
487    "returns the solution *u* for a time step *dt>0*\n\n:rtype: `Data`\n"
488    ":param source:\n:type source: `Data`")
489         .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue, args("u"),
490    "sets the value for *u* at time *t=0*.")
491         .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint,
492    args("source", "q", "r","factor"),
493    "inserts constraint *u_{,t}=r* where *q>0*  into the problem using a weighting factor")
494         .def("reset",&escript::AbstractTransportProblem::resetTransport,
495    "resets the transport operator typically as they have been updated.")
496         .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
497         .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize)
498         .def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize);
499    
500      // Functions to modify global parameters
501      def("setEscriptParamInt",escript::setEscriptParamInt,
502          (arg("name"), arg("value")=0), "Modify the value of an escript tuning parameter\n\n"
503    ":param name:\n:type name: ``string``\n:param value:\n:type value: ``int``");
504      def("getEscriptParamInt",escript::getEscriptParamInt,
505          (arg("name"),arg("sentinel")=0), "Read the value of an escript tuning paramter\n\n"
506    ":param name: parameter to lookup\n:type name: ``string``\n:param sentinel: Value to be returned if ``name`` is not a known parameter\n"
507    ":type sentinel: ``int``");
508      def("listEscriptParams",escript::listEscriptParams,":return: A list of pairs (p,d) where p is the name of a parameter for escript and d is a description.");
509    
510    //    //
511    // Register esysExceptionTranslator    // Register esysExceptionTranslator
512    //    //
513    register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);    register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);
   
514  }  }

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