/[escript]/trunk/escript/src/escriptcpp.cpp
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Revision 2628 - (hide annotations)
Tue Aug 25 03:50:00 2009 UTC (10 years, 1 month ago) by jfenwick
File size: 29828 byte(s)
Fixed linkage on getTestDomainFunctionSpace.

added Data.interpolateTable to perform 2D interpolation.
It needs better unit tests though.
1 jgs 102
2 ksteube 1312 /*******************************************************
3 ksteube 1811 *
4 jfenwick 2548 * Copyright (c) 2003-2009 by University of Queensland
5 ksteube 1811 * Earth Systems Science Computational Center (ESSCC)
6     * http://www.uq.edu.au/esscc
7     *
8     * Primary Business: Queensland, Australia
9     * Licensed under the Open Software License version 3.0
10     * http://www.opensource.org/licenses/osl-3.0.php
11     *
12     *******************************************************/
13 ksteube 1312
14 ksteube 1811
15 jgs 474 #include "Data.h"
16     #include "FunctionSpace.h"
17     #include "FunctionSpaceFactory.h"
18     #include "DataFactory.h"
19     #include "AbstractContinuousDomain.h"
20     #include "AbstractDomain.h"
21     #include "Utils.h"
22 jgs 480 #include "AbstractSystemMatrix.h"
23 gross 1364 #include "AbstractTransportProblem.h"
24 gross 797 #include "DataVector.h"
25 ksteube 1800 #include "paso/Paso_MPI.h"
26 jfenwick 1897 #include "EscriptParams.h"
27 jfenwick 2482 #include "TestDomain.h"
28 jgs 474
29 jfenwick 1872
30 ksteube 1312 extern "C" {
31 phornby 2078 #include "esysUtils/blocktimer.h"
32 ksteube 1312 }
33    
34 robwdcock 682 #include "esysUtils/esysExceptionTranslator.h"
35 jgs 102
36 gross 2100 #include <boost/version.hpp>
37 jgs 102 #include <boost/python.hpp>
38     #include <boost/python/module.hpp>
39     #include <boost/python/def.hpp>
40     #include <boost/python/object.hpp>
41     #include <boost/python/tuple.hpp>
42 gross 285 #include <boost/python/numeric.hpp>
43 jfenwick 1872 #include <boost/smart_ptr.hpp>
44 jfenwick 2064 #include <boost/version.hpp>
45 gross 285
46 jgs 102 using namespace boost::python;
47    
48 jgs 121 /*! \mainpage Esys Documentation
49     *
50 jfenwick 2602 * \version 3.0.0
51 jgs 121 *
52     * - \ref escript
53     *
54     * - \ref esys_exception "Esys Exception"
55     *
56     * - \ref finley
57     *
58 jfenwick 2283 * - <a href="../../epydoc/index.html">Python module documentation (epydoc generated)</a>
59 jgs 122 *
60 jgs 121 */
61 jgs 102
62 jgs 121 /*! \page escript Escript
63     * Escript is the python module that contains the interfaces
64     * to the C++ side of escript.
65     *
66 jfenwick 2459 *
67 jgs 121 *
68     * \section class_desc Class Description:
69     * Data
70     *
71     * \section class_limits Class Limitations:
72     * None
73     *
74     * \section class_conds Class Conditions of Use:
75     * None
76     *
77     * \section class_throws Throws:
78     * None
79     *
80     */
81 jgs 102
82     BOOST_PYTHON_MODULE(escriptcpp)
83     {
84 jfenwick 2625
85     #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 gross 2100 #endif
89 jfenwick 2061
90 jfenwick 2607 def("setNumberOfThreads",escript::setNumberOfThreads,"Use of this method is strongly discouraged.");
91 jfenwick 2625 def("getNumberOfThreads",escript::getNumberOfThreads,"Return the maximum number of threads"
92     " available to OpenMP.");
93 gross 797 def("releaseUnusedMemory",escript::releaseUnusedMemory);
94 ksteube 1312 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 jfenwick 2607 def("getVersion",escript::getSvnVersion,"This method will only report accurate version numbers for clean checkouts.");
100 ksteube 1561 def("printParallelThreadCounts",escript::printParallelThreadCnt);
101 jfenwick 2625 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 gross 2100 def("getMachinePrecision",escript::getMachinePrecision);
109     def("getMaxFloat",escript::getMaxFloat);
110 jgs 102 //
111     // Interface for AbstractDomain
112     //
113 jfenwick 2061 class_<escript::AbstractDomain, escript::Domain_ptr>("Domain","Base class for all domains.",no_init)
114 jfenwick 2625 .def("getStatus",&escript::AbstractDomain::getStatus,"The status of a domain changes whenever the domain is modified\n\n:rtype: int")
115     .def("setTagMap",&escript::AbstractDomain::setTagMap,args("name","tag"),
116     "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
117     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
118     .def("getTag",&escript::AbstractDomain::getTag,args("name"),":return: tag id for "
119     "``name``\n:rtype: ``string``")
120     .def("isValidTagName",&escript::AbstractDomain::isValidTagName,args("name"),
121     ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
122     .def("showTagNames",&escript::AbstractDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
123     .def("getX",&escript::AbstractDomain::getX,":rtype: `Data`\n:return: Locations in the"
124     "`Domain`. FunctionSpace is chosen appropriately")
125     .def("getDim",&escript::AbstractDomain::getDim,":rtype: `int`\n:return: Spatial dimension of the `Domain`")
126     .def("getNormal",&escript::AbstractDomain::getNormal,":rtype: `escript`\n:return: Boundary normals")
127     .def("getSize",&escript::AbstractDomain::getSize,":return: the local size of samples. The function space is chosen appropriately\n:rtype: `Data`")
128     .def("saveVTK",&escript::AbstractDomain::saveVTK,args("filename","arg", "metadata"
129     , "metadata_schema"),
130     ":param filename: \n:type filename: ``string``\n:param arg: items to be added"
131     "\n:type arg: ``dict``\n:param metadata: string representing some meta data to be added\n:type metadata: ``string``"
132     "\n:param metadata_schema: schema type for metadata\n:type metadata_schema: ``string``")
133     .def("dump",&escript::AbstractDomain::dump,args("filename"),"Dumps the domain to a file"
134     ":param filename:\n:type filename: string")
135     .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``"
136     "\n:param arg:\n:type arg: `dict`")
137     .def("getMPISize",&escript::AbstractDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
138     .def("getMPIRank",&escript::AbstractDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
139     .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier,"Wait until all processes have reached this point")
140     .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")
141 ksteube 1312
142 jgs 102 .def(self == self)
143     .def(self != self);
144    
145     //
146     // Interface for AbstractContinuousDomain
147     //
148 jfenwick 2061 class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain","Class representing continuous domains",no_init)
149 jfenwick 2625 .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId,
150     args("solver", "preconditioner", "package", "symmetry"),
151     ":return: the identifier of the matrix type to be used for the global stiffness matrix "
152     "when a particular solver package and symmetric matrix is used.\n"
153     ":rtype: int")
154     .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId,
155     args("solver", "preconditioner", "package", "symmetry"));
156 jgs 102
157 jfenwick 2482
158 jgs 102 //
159 jfenwick 2482 // Interface for TestDomain
160     //
161     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>());
162    
163     // This is the only python visible way to get a TestDomain
164 jfenwick 2625 def("getTestDomainFunctionSpace",&escript::getTestDomainFunctionSpace, args("dpps",
165     "samples"),
166     "For testing only. May be removed without notice.");
167 jfenwick 2482
168     //
169 jgs 102 // Interface for FunctionSpace
170     //
171 jfenwick 2625 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
172     fs_definer.def("getDim",&escript::FunctionSpace::getDim,":return: the spatial dimension of the underlying domain.\n:rtype: int");
173 jfenwick 1872 // fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
174     // return_internal_reference<>());
175 jfenwick 2625 fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython,":return: the underlying `Domain` for this FunctionSpace.\n:rtype: `Domain`");
176     fs_definer.def("getX",&escript::FunctionSpace::getX,"\n:return: a function whose values are its input coordinates. ie an identity function.\n:rtype: `Data`");
177     fs_definer.def("getNormal",&escript::FunctionSpace::getNormal,":return: the surface normal field.\n\n:rtype: `Data`");
178     fs_definer.def("getSize",&escript::FunctionSpace::getSize,":return: sample size\n:rtype: `Data`");
179     fs_definer.def("setTags",&escript::FunctionSpace::setTags,args("newtag","mask"),
180     "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`");
181 trankine 1426 fs_definer.def("getTagFromDataPointNo",
182 jfenwick 2625 &escript::FunctionSpace::getTagFromDataPointNo,":return: the tag associated with the given sample number.\n:rtype: int");
183     fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo,args("dataPointNo"),":return: the reference number associated with ``dataPointNo``\n:rtype: int ");
184     fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags,":return: a list of the tags used in this function space\n:rtype: ``list``");
185 phornby 1628 fs_definer.def("__str__", &escript::FunctionSpace::toString);
186 trankine 1426 fs_definer.def(self == self);
187     fs_definer.def(self != self);
188 jgs 102 //
189     // Interface for Data
190     //
191 jfenwick 2061 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<>() )
192 jgs 102 // various constructors for Data objects
193     .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
194     .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))
195     .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))
196     .def(init<const escript::Data&>())
197     // Note for Lutz, Need to specify the call policy in order to return a
198     // reference. In this case return_internal_reference.
199 ksteube 1312 .def("__str__",&escript::Data::toString)
200 jfenwick 2625 .def("getDomain",&escript::Data::getDomainPython,":rtype: `Domain`")
201     .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>(),":rtype: `FunctionSpace`")
202     .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.")
203     .def("isProtected",&escript::Data::isProtected,"Can this instance be modified.\n:rtype: ``bool``")
204     .def("setProtection",&escript::Data::setProtection,"Disallow modifications to this data object\n\n:note: This method does not allow you to undo protection.")
205     .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``")
206     .def("getRank",&escript::Data::getDataPointRank,":return: the number of indicies required to address a component of a datapoints\n:rtype: positive ``int``")
207     .def("dump",&escript::Data::dump,args("fileName"),"Save the data as a netCDF file\n\n:param fileName: \n:type fileName: ``string``")
208     .def("toListOfTuples",&escript::Data::toListOfTuples, (arg("scalarastuple")=false),
209     "Return the datapoints of this object in a list. Each datapoint is stored as a tuple.\n\n"
210     ":param scalarastuple: if True, scalar data will be wrapped as a tuple."
211     " True => [(0), (1), (2)]; False => [0, 1, 2]")
212     .def("copyWithMask",&escript::Data::copyWithMask,args("other","mask"),
213     "Selectively copy values from ``other`` `Data`."
214     "Datapoints which correspond to postive values in ``mask`` will be copied from ``other``\n"
215     "\n:param other: source of values\n"
216     ":type other: `Data`\n:param mask:\n:type mask: Scalar `Data`")
217     .def("setTaggedValue",&escript::Data::setTaggedValue,args("tagKey","value"),
218     "Set the value of tagged Data.\n\n:param tagKey: tag to update\n:type tagKey: ``int``\n")
219     .def("setTaggedValue",&escript::Data::setTaggedValueByName,args("name","value"),":param name: tag to update\n:type name: ``string``\n"
220     ":param value: value to set tagged data to\n:type value: ``object`` which acts like an array, ``tuple`` or ``list``\n")
221     .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints,":rtype: ``int``\n:return: Number of datapoints in the object")
222     .def("isExpanded",&escript::Data::isExpanded,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
223     .def("isTagged",&escript::Data::isTagged,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
224     .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.")
225     .def("isLazy",&escript::Data::isLazy,":rtype: ``bool``\n:return: True if this ``Data`` is lazy.")
226     .def("isReady",&escript::Data::isReady,":rtype: ``bool``\n:return: True if this ``Data`` is not lazy.")
227     .def("expand",&escript::Data::expand,"Convert the data to expanded representation if it is not expanded already.")
228     .def("tag",&escript::Data::tag,"Convert data to tagged representation if it is not already tagged or expanded")
229     .def("resolve",&escript::Data::resolve,"Convert the data to non-lazy representation.")
230     .def("copy",&escript::Data::copy,args("other"),"Make this object a copy of ``other``\n"
231     "\n:note: The two objects will act independently from now on. That is, changing ``other`` "
232     "after this call will not change this object and vice versa.")
233     .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.")
234     .def("delay",&escript::Data::delay,"Convert this object into lazy representation")
235     .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject,args("dataPointNo","value"))
236 gross 1034 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
237 jfenwick 2625 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint,"\nModify the value of a single datapoint.\n\n:param dataPointNo:\n"
238     ":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.")
239     .def("getTupleForDataPoint",&escript::Data::getValueOfDataPointAsTuple,args("dataPointNo"),
240     ":return: Value of the specified datapoint\n:rtype: ``tuple``\n:param dataPointNo: datapoint to access\n:type dataPointNo: ``int``")
241     .def("getTupleForGlobalDataPoint",&escript::Data::getValueOfGlobalDataPointAsTuple,args("procNo","dataPointNo"),"Get a specific datapoint from a specific process\n\n"
242     ":rtype: ``tuple``\n:param procNo: MPI rank of the process\n:type procNo: positive ``int``"
243     "\n:param dataPointNo: datapoint to access\n:type dataPointNo: int")
244     .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.")
245     .def("interpolate",&escript::Data::interpolate,args("functionspace"),"Interpolate this object's values into a new functionspace.")
246 jfenwick 2628 .def("interpolateTable", &escript::Data::interpolateFromTable,
247     args("table","Amin","Astep","undef", "B", "Bmin", "Bstep"),
248     "Creates a new Data object by interpolating using the source data (which are\n"
249     "looked up in ``table``)\n\n"
250     ":param table: two dimensional collection of values\n"
251     ":param Amin: The base of locations in table\n:type Amin: float\n"
252     ":param Astep: size of gap between each item in the table\n:type Astep: float\n"
253     ":param undef: upper bound on interpolated values\n:type undef: float\n"
254     ":param B: Scalar representing the second coordinate to be mapped into the table\n"
255     ":type B: `Data`\n"
256     ":param Bmin: The base of locations in table for 2nd dimension\n:type Bmin: float\n"
257     ":param Bstep: size of gap between each item in the table for 2nd dimension\n:type Bstep: float\n"
258     ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"
259     "\n:rtype: `Data`"
260     )
261    
262 gross 921 .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
263 jfenwick 2476 .def("maxGlobalDataPoint",&escript::Data::maxGlobalDataPoint)
264 jfenwick 2625 .def("saveDX",&escript::Data::saveDX,args("fileName"),"Save the object in DX format.\n\n"
265     ":param fileName: filename\n:type fileName: string")
266     .def("saveVTK",&escript::Data::saveVTK, args("fileName"),"Save the object in VTK format.\n\n"
267     ":param fileName: \n:type fileName: string")
268     .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")
269 gross 285 // Unary functions for Data
270     .def("_interpolate",&escript::Data::interpolate)
271     .def("_grad",&escript::Data::gradOn)
272     .def("_grad",&escript::Data::grad)
273     .def("_transpose",&escript::Data::transpose)
274     .def("_trace",&escript::Data::trace)
275     .def("_maxval",&escript::Data::maxval)
276     .def("_minval",&escript::Data::minval)
277 gross 698 .def("_wherePositive",&escript::Data::wherePositive)
278     .def("_whereNegative",&escript::Data::whereNegative)
279     .def("_whereNonNegative",&escript::Data::whereNonNegative)
280     .def("_whereNonPositive",&escript::Data::whereNonPositive)
281 jgs 571 .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
282     .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
283 ksteube 876 .def("_erf",&escript::Data::erf)
284 gross 285 .def("_sin",&escript::Data::sin)
285     .def("_cos",&escript::Data::cos)
286     .def("_tan",&escript::Data::tan)
287     .def("_asin",&escript::Data::asin)
288     .def("_acos",&escript::Data::acos)
289     .def("_atan",&escript::Data::atan)
290     .def("_sinh",&escript::Data::sinh)
291     .def("_cosh",&escript::Data::cosh)
292     .def("_tanh",&escript::Data::tanh)
293     .def("_asinh",&escript::Data::asinh)
294     .def("_acosh",&escript::Data::acosh)
295     .def("_atanh",&escript::Data::atanh)
296     .def("_exp",&escript::Data::exp)
297     .def("_sqrt",&escript::Data::sqrt)
298     .def("_log10",&escript::Data::log10)
299     .def("_log",&escript::Data::log)
300     .def("_sign",&escript::Data::sign)
301 ksteube 775 .def("_symmetric",&escript::Data::symmetric)
302     .def("_nonsymmetric",&escript::Data::nonsymmetric)
303 gross 800 .def("_trace",&escript::Data::trace)
304 gross 804 .def("_swap_axes",&escript::Data::swapaxes)
305 gross 576 .def("_eigenvalues",&escript::Data::eigenvalues)
306     .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
307 gross 285 // functions returning a single real number:
308 jfenwick 2625 .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.")
309     .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.")
310     .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.")
311     .def("_integrateToTuple",&escript::Data::integrateToTuple,":return: Calculate the integral over the function space domain as a python tuple\n:rtype: tuple")
312 gross 285
313     // following implements the python abs operator
314 jfenwick 2625 .def("__abs__",&escript::Data::abs,":return: absolute value\n\n:rtype: `Data`")
315 jgs 102 // following implements the python "-" negation operator
316 jfenwick 2625 .def("__neg__",&escript::Data::neg, ":return: negation of the values in this object\n:rtype: `Data`")
317 jgs 102 // following implements the python "+" identity operator
318 jfenwick 2625 .def("__pos__",&escript::Data::pos, "\nThe unary + operator\n\n:rtype: Data`")
319 jgs 102 // following two functions implement the python [] operator
320 jfenwick 2625 .def("__getitem__",&escript::Data::getItem,"Used by the python [] operator\n\n:rtype: `Data`")
321     .def("__setitem__",&escript::Data::setItemO,"Used by the python [] operator")
322     .def("__setitem__",&escript::Data::setItemD,"Used by the python [] operator")
323 jgs 102 // following two functions implement the python ** operator
324 jfenwick 2625 .def("__pow__",&escript::Data::powO,"Used by the python ** operator\n\n:rtype: `Data`")
325 jgs 102 .def("__pow__",&escript::Data::powD)
326 jfenwick 2625 .def("__rpow__",&escript::Data::rpowO,"\nUsed by the python ** operator\n\n:rtype: `Data`")
327 jgs 102 // NOTE:: The order of these declarations is important. Anything
328     // declared before the generic declaration isn't found so the generic
329     // version will be called.
330     .def(self + other<object>())
331     .def(other<object>() + self)
332     .def(self + self)
333 gross 285 .def(self += other<object>())
334     .def(self += self)
335    
336 jgs 102 .def(self - other<object>())
337     .def(other<object>() - self)
338     .def(self - self)
339 gross 285 .def(self -= other<object>())
340     .def(self -= self)
341    
342 jgs 102 .def(self * other<object>())
343     .def(other<object>() * self)
344     .def(self * self)
345 gross 285 .def(self *= other<object>())
346     .def(self *= self)
347    
348 jgs 102 .def(self / other<object>())
349     .def(other<object>() / self)
350     .def(self / self)
351 gross 285 .def(self /= other<object>())
352     .def(self /= self)
353 jgs 102 // Need scope resolution due to a bug either in the compiler or
354     // the boost code. This calls operator << for Data.
355     .def(self_ns::str(self));
356    
357     //
358     // Factory methods for function space
359     //
360 jfenwick 2625 def("ContinuousFunction",escript::continuousFunction,args("domain"),
361     ":return: a continuous FunctionSpace (overlapped node values)\n"
362     ":rtype: `FunctionSpace`");
363     def("ReducedContinuousFunction",escript::reducedContinuousFunction,args("domain"),
364     ":return: a continuous with reduced order FunctionSpace (overlapped node values on reduced element order)\n"
365     ":rtype: `FunctionSpace`");
366     def("Function",escript::function,args("domain"),":return: a function `FunctionSpace`\n"
367     ":rtype: `FunctionSpace`");
368     def("ReducedFunction",escript::reducedFunction, args("domain"),":return: a function FunctionSpace with reduced integration order\n:rtype: `FunctionSpace`");
369     def("FunctionOnBoundary",escript::functionOnBoundary, args("domain"), ":return: a function on boundary FunctionSpace\n:rtype: `FunctionSpace`");
370     def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary, args("domain"),
371     ":return: a function on boundary FunctionSpace with reduced integration order\n"
372     ":rtype: `FunctionSpace`");
373     def("FunctionOnContactZero",escript::functionOnContactZero, args("domain"), ":return: Return a FunctionSpace on left side of contact\n:rtype: `FunctionSpace`");
374     def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero, args("domain"),
375     ":return: a FunctionSpace on left side of contact with reduced integration order\n:rtype: `FunctionSpace`");
376     def("FunctionOnContactOne",escript::functionOnContactOne, args("domain"), ":return: Return a FunctionSpace on right side of contact\n:rtype: `FunctionSpace`");
377     def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne, args("domain"),
378     ":return: Return a FunctionSpace on right side of contact with reduced integration order\n"
379     ":rtype: `FunctionSpace`");
380     def("Solution",escript::solution, args("domain"), ":rtype: `FunctionSpace`");
381     def("ReducedSolution",escript::reducedSolution, args("domain"), ":rtype: `FunctionSpace`");
382     def("DiracDeltaFunction",escript::diracDeltaFunction, args("domain"), ":rtype: `FunctionSpace`");
383 jgs 102
384     //
385     // Factory methods for Data
386     //
387 jfenwick 2625 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`");
388     def("loadIsConfigured",escript::loadConfigured,":return: True if the load function is configured.");
389 jgs 102 def("Scalar",escript::Scalar,
390     (arg("value")=0.0,
391     arg("what")=escript::FunctionSpace(),
392 jfenwick 2625 arg("expanded")=false),
393     "Construct a Data object containing scalar data-points.\n\n:param value: scalar value for all points\n"
394     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
395     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
396     ":type expanded: ``bool``");
397 jgs 102 def("Vector",escript::Vector,
398     (arg("value")=0.0,
399     arg("what")=escript::FunctionSpace(),
400 jfenwick 2625 arg("expanded")=false),
401     "Construct a Data object containing rank1 data-points.\n\n:param value: scalar value for all points\n"
402     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
403     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
404     ":type expanded: ``bool``");
405 jgs 102 def("Tensor",escript::Tensor,
406     (arg("value")=0.0,
407     arg("what")=escript::FunctionSpace(),
408 jfenwick 2625 arg("expanded")=false),
409     "Construct a Data object containing rank2 data-points.\n\n:param value: scalar value for all points\n"
410     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
411     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
412     ":type expanded: ``bool``");
413 jgs 102 def("Tensor3",escript::Tensor3,
414     (arg("value")=0.0,
415     arg("what")=escript::FunctionSpace(),
416 jfenwick 2625 arg("expanded")=false),
417     "Construct a Data object containing rank3 data-points.\n\n:param value: scalar value for all points\n"
418     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
419     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
420     ":type expanded: ``bool``"
421     );
422 jgs 102 def("Tensor4",escript::Tensor4,
423     (arg("value")=0.0,
424     arg("what")=escript::FunctionSpace(),
425 jfenwick 2625 arg("expanded")=false),
426     "Construct a Data object containing rank4 data-points.\n\n:param value: scalar value for all points\n"
427     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
428     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
429     ":type expanded: ``bool``"
430     );
431 jgs 102
432     //
433 ksteube 813 // Binary operators
434     //
435     def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
436 jfenwick 2626 (arg("arg0"),
437     arg("arg1"),
438 ksteube 813 arg("axis_offset")=0,
439 jfenwick 2625 arg("transpose")=0),
440     "Compute a tensor product of two Data objects.\n\n:rtype: `Data`\n:param arg0:\n"
441     ":param arg1:\n:param axis_offset:\n:type axis_offset: ``int``\n"
442     ":param transpose: 0: transpose neither, 1: transpose arg0, 2: transpose arg1\n"
443     ":type transpose: int");
444 ksteube 813
445     //
446 jgs 102 // Interface for AbstractSystemMatrix
447     //
448 jfenwick 2061 class_<escript::AbstractSystemMatrix>("Operator","",init<>()) // Doco goes in the empty string param
449 jfenwick 2625 .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty,":rtype: ``bool``\n"
450     ":return: True if matrix is empty")
451     .def("solve",&escript::AbstractSystemMatrix::solve, args("in","options"),
452     ":return: the solution *u* of the linear system *this*u=in*\n\n:param in:\n:type in: `Data`")
453     .def("of",&escript::AbstractSystemMatrix::vectorMultiply,args("right"),
454     "matrix*vector multiplication")
455     .def("saveMM",&escript::AbstractSystemMatrix::saveMM, args("fileName"),
456     "writes the matrix to a file using the Matrix Market file format")
457     .def("saveHB",&escript::AbstractSystemMatrix::saveHB, args("filename"),
458     "writes the matrix to a file using the Harwell-Boeing file format")
459     .def("resetValues",&escript::AbstractSystemMatrix::resetValues, "resets the matrix entries")
460 jgs 102 .def(self*other<escript::Data>());
461 gross 1364 //
462     // Interface for AbstractTransportProblem
463     //
464 jfenwick 2061 class_<escript::AbstractTransportProblem>("TransportProblem","",init<>()) // Doco goes in the empty string param
465 jfenwick 2625 .def("isEmpty",&escript::AbstractTransportProblem::isEmpty,":rtype: ``int``")
466     .def("solve",&escript::AbstractTransportProblem::solve, args("source","dt", "options"),
467     "returns the solution *u* for a time step *dt>0*\n\n:rtype: `Data`\n"
468     ":param source:\n:type source: `Data`")
469     .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue, args("u"),
470     "sets the value for *u* at time *t=0*.")
471     .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint,
472     args("source", "q", "r","factor"),
473     "inserts constraint *u_{,t}=r* where *q>0* into the problem using a weighting factor")
474     .def("reset",&escript::AbstractTransportProblem::resetTransport,
475     "resets the transport operator typically as they have been updated.")
476 gross 1841 .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
477 gross 1859 .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize)
478     .def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize);
479 jgs 102
480 jfenwick 1897 // Functions to modify global parameters
481     def("setEscriptParamInt",escript::setEscriptParamInt,
482 jfenwick 2625 (arg("name"), arg("value")=0), "Modify the value of an escript tuning parameter\n\n"
483     ":param name:\n:type name: ``string``\n:param value:\n:type value: ``int``");
484 jfenwick 1897 def("getEscriptParamInt",escript::getEscriptParamInt,
485 jfenwick 2625 (arg("name"),arg("sentinel")=0), "Read the value of an escript tuning paramter\n\n"
486     ":param name: parameter to lookup\n:type name: ``string``\n:param sentinel: Value to be returned if ``name`` is not a known parameter\n"
487     ":type sentinel: ``int``");
488     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.");
489 jfenwick 1897
490 jgs 102 //
491     // Register esysExceptionTranslator
492     //
493     register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);
494     }

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