/[escript]/trunk/escript/src/escriptcpp.cpp
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Contents of /trunk/escript/src/escriptcpp.cpp

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Revision 2766 - (show annotations)
Mon Nov 23 05:10:53 2009 UTC (9 years, 11 months ago) by jfenwick
File size: 32211 byte(s)
inf, sup and Lsup now correctly handle +-infinity.
They also will return NaN if any part of their input is NaN.

This will break unit tests since it exposes the hidden bug (#447 in mantis)

This code relies on the ability to test for NaNs.
To do this it makes use of macros and functions from C99.
If you do not have a C99 compiler, then you will probably get the old behaviour.
That is, you won't know when you have NaNs.


Also did minor tweak to saveDataCSV doco.
1
2 /*******************************************************
3 *
4 * Copyright (c) 2003-2009 by University of Queensland
5 * 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
14
15 #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 #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"
35
36 #include <boost/version.hpp>
37 #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 #include <boost/smart_ptr.hpp>
43 #include <boost/version.hpp>
44
45 using namespace boost::python;
46
47 /*! \mainpage Esys Documentation
48 *
49 * \version 3.0.0
50 *
51 * - \ref escript
52 *
53 * - \ref esys_exception "Esys Exception"
54 *
55 * - \ref finley
56 *
57 * - <a href="../../epydoc/index.html">Python module documentation (epydoc generated)</a>
58 *
59 */
60
61 /*! \page escript Escript
62 * Escript is the python module that contains the interfaces
63 * to the C++ side of escript.
64 *
65 *
66 *
67 * \section class_desc Class Description:
68 * Data
69 *
70 * \section class_limits Class Limitations:
71 * None
72 *
73 * \section class_conds Class Conditions of Use:
74 * None
75 *
76 * \section class_throws Throws:
77 * None
78 *
79 */
80
81 BOOST_PYTHON_MODULE(escriptcpp)
82 {
83
84 #if BOOST_VERSION >= 103500
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,"Use of this method is strongly discouraged.");
90 def("getNumberOfThreads",escript::getNumberOfThreads,"Return the maximum number of threads"
91 " available to OpenMP.");
92 def("releaseUnusedMemory",escript::releaseUnusedMemory);
93 def("blocktimer_initialize",blocktimer_initialize);
94 def("blocktimer_reportSortByName",blocktimer_reportSortByName);
95 def("blocktimer_reportSortByTime",blocktimer_reportSortByTime);
96 def("blocktimer_increment",blocktimer_increment);
97 def("blocktimer_time",blocktimer_time);
98 def("getVersion",escript::getSvnVersion,"This method will only report accurate version numbers for clean checkouts.");
99 def("printParallelThreadCounts",escript::printParallelThreadCnt);
100 def("getMPISizeWorld",escript::getMPISizeWorld,"Return number of MPI processes in the job.");
101 def("getMPIRankWorld",escript::getMPIRankWorld,"Return the rank of this process in the MPI World.");
102 def("MPIBarrierWorld",escript::MPIBarrierWorld,"Wait until all MPI processes have reached this point.");
103 def("getMPIWorldMax",escript::getMPIWorldMax,"\nEach MPI process calls this function with a"
104 " value for arg1. The maximum value is computed and returned.\n\n:rtype: int");
105 def("getMPIWorldSum",escript::getMPIWorldSum,"\nEach MPI process calls this function with a"
106 " value for arg1. The values are added up and the total value is returned.\n\n:rtype: int");
107 def("getMachinePrecision",escript::getMachinePrecision);
108 def("getMaxFloat",escript::getMaxFloat);
109 def("_saveDataCSV",escript::saveDataCSV, (args("filename","arg","sep","csep"), arg("append")=false),
110 "Saves data objects passed in a python dictionary to a file.\n"
111 "The data objects must be over the same domain and be able to be interpolated to the same FunctionSpace.\n"
112 "If one of the dictionary keys is named ``mask``, then only samples where ``mask`` has a positive\n"
113 "value will be written to the file.\n\n"
114 "A header line giving the names of each column will be output first.\n"
115 "The keys given in the dictionary will be used to name columns.\n"
116 "Then the data will be output, one line per sample (for all data).\n"
117 "That is, items in each column will be printed in the same order.\n"
118 "So you can be sure that values in the same row correspond to the same input value.\n"
119 "\n:param filename:\n:type filename: ``string``\n"
120 ":param arg: dictionary of named `Data` objects. If one is called ``mask`` it must be scalar data."
121 "\n:type arg: ``dict``\n"
122 ":param sep:separator for columns (defaults to \", \"\n:type sep:``string``\n"
123 ":param csep:separator for fields within data object (defaults to \"_\"\n:type csep:``string``\n"
124 ":param append: If True, write to the end of ``filename``\n:type append: ``string``\n");
125
126
127 //
128 // Interface for AbstractDomain
129 //
130 class_<escript::AbstractDomain, escript::Domain_ptr>("Domain","Base class for all domains.",no_init)
131 .def("getStatus",&escript::AbstractDomain::getStatus,"The status of a domain changes whenever the domain is modified\n\n:rtype: int")
132 .def("setTagMap",&escript::AbstractDomain::setTagMap,args("name","tag"),
133 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
134 ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
135 .def("getTag",&escript::AbstractDomain::getTag,args("name"),":return: tag id for "
136 "``name``\n:rtype: ``string``")
137 .def("isValidTagName",&escript::AbstractDomain::isValidTagName,args("name"),
138 ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
139 .def("showTagNames",&escript::AbstractDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
140 .def("getX",&escript::AbstractDomain::getX,":rtype: `Data`\n:return: Locations in the"
141 "`Domain`. FunctionSpace is chosen appropriately")
142 .def("getDim",&escript::AbstractDomain::getDim,":rtype: `int`\n:return: Spatial dimension of the `Domain`")
143 .def("getNormal",&escript::AbstractDomain::getNormal,":rtype: `escript`\n:return: Boundary normals")
144 .def("getSize",&escript::AbstractDomain::getSize,":return: the local size of samples. The function space is chosen appropriately\n:rtype: `Data`")
145 .def("saveVTK",&escript::AbstractDomain::saveVTK,args("filename","arg", "metadata"
146 , "metadata_schema"),
147 ":param filename: \n:type filename: ``string``\n:param arg: items to be added"
148 "\n:type arg: ``dict``\n:param metadata: string representing some meta data to be added\n:type metadata: ``string``"
149 "\n:param metadata_schema: schema type for metadata\n:type metadata_schema: ``string``")
150 .def("dump",&escript::AbstractDomain::dump,args("filename"),"Dumps the domain to a file"
151 ":param filename:\n:type filename: string")
152 .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``"
153 "\n:param arg:\n:type arg: `dict`")
154 .def("getMPISize",&escript::AbstractDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
155 .def("getMPIRank",&escript::AbstractDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
156 .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier,"Wait until all processes have reached this point")
157 .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")
158
159 .def(self == self)
160 .def(self != self);
161
162 //
163 // Interface for AbstractContinuousDomain
164 //
165 class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain","Class representing continuous domains",no_init)
166 .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId,
167 args("solver", "preconditioner", "package", "symmetry"),
168 ":return: the identifier of the matrix type to be used for the global stiffness matrix "
169 "when a particular solver package and symmetric matrix is used.\n"
170 ":rtype: int")
171 .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId,
172 args("solver", "preconditioner", "package", "symmetry"));
173
174
175 //
176 // Interface for TestDomain
177 //
178 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>());
179
180 // This is the only python visible way to get a TestDomain
181 def("getTestDomainFunctionSpace",&escript::getTestDomainFunctionSpace, args("dpps",
182 "samples"),
183 "For testing only. May be removed without notice.");
184
185 //
186 // Interface for FunctionSpace
187 //
188 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
189 fs_definer.def("getDim",&escript::FunctionSpace::getDim,":return: the spatial dimension of the underlying domain.\n:rtype: int");
190 // fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
191 // return_internal_reference<>());
192 fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython,":return: the underlying `Domain` for this FunctionSpace.\n:rtype: `Domain`");
193 fs_definer.def("getX",&escript::FunctionSpace::getX,"\n:return: a function whose values are its input coordinates. ie an identity function.\n:rtype: `Data`");
194 fs_definer.def("getNormal",&escript::FunctionSpace::getNormal,":return: the surface normal field.\n\n:rtype: `Data`");
195 fs_definer.def("getSize",&escript::FunctionSpace::getSize,":return: sample size\n:rtype: `Data`");
196 fs_definer.def("setTags",&escript::FunctionSpace::setTags,args("newtag","mask"),
197 "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`");
198 fs_definer.def("getTagFromDataPointNo",
199 &escript::FunctionSpace::getTagFromDataPointNo,":return: the tag associated with the given sample number.\n:rtype: int");
200 fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo,args("dataPointNo"),":return: the reference number associated with ``dataPointNo``\n:rtype: int ");
201 fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags,":return: a list of the tags used in this function space\n:rtype: ``list``");
202 fs_definer.def("__str__", &escript::FunctionSpace::toString);
203 fs_definer.def(self == self);
204 fs_definer.def(self != self);
205 //
206 // Interface for Data
207 //
208 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<>() )
209 // various constructors for Data objects
210 .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
211 .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))
212 .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))
213 .def(init<const escript::Data&>())
214 // Note for Lutz, Need to specify the call policy in order to return a
215 // reference. In this case return_internal_reference.
216 .def("__str__",&escript::Data::toString)
217 .def("getDomain",&escript::Data::getDomainPython,":rtype: `Domain`")
218 .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>(),":rtype: `FunctionSpace`")
219 .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.")
220 .def("isProtected",&escript::Data::isProtected,"Can this instance be modified.\n:rtype: ``bool``")
221 .def("setProtection",&escript::Data::setProtection,"Disallow modifications to this data object\n\n:note: This method does not allow you to undo protection.")
222 .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``")
223 .def("getRank",&escript::Data::getDataPointRank,":return: the number of indicies required to address a component of a datapoints\n:rtype: positive ``int``")
224 .def("dump",&escript::Data::dump,args("fileName"),"Save the data as a netCDF file\n\n:param fileName: \n:type fileName: ``string``")
225 .def("toListOfTuples",&escript::Data::toListOfTuples, (arg("scalarastuple")=false),
226 "Return the datapoints of this object in a list. Each datapoint is stored as a tuple.\n\n"
227 ":param scalarastuple: if True, scalar data will be wrapped as a tuple."
228 " True => [(0), (1), (2)]; False => [0, 1, 2]")
229 .def("copyWithMask",&escript::Data::copyWithMask,args("other","mask"),
230 "Selectively copy values from ``other`` `Data`."
231 "Datapoints which correspond to postive values in ``mask`` will be copied from ``other``\n"
232 "\n:param other: source of values\n"
233 ":type other: `Data`\n:param mask:\n:type mask: Scalar `Data`")
234 .def("setTaggedValue",&escript::Data::setTaggedValue,args("tagKey","value"),
235 "Set the value of tagged Data.\n\n:param tagKey: tag to update\n:type tagKey: ``int``\n")
236 .def("setTaggedValue",&escript::Data::setTaggedValueByName,args("name","value"),":param name: tag to update\n:type name: ``string``\n"
237 ":param value: value to set tagged data to\n:type value: ``object`` which acts like an array, ``tuple`` or ``list``\n")
238 .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints,":rtype: ``int``\n:return: Number of datapoints in the object")
239 .def("isExpanded",&escript::Data::isExpanded,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
240 .def("isTagged",&escript::Data::isTagged,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
241 .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.")
242 .def("isLazy",&escript::Data::isLazy,":rtype: ``bool``\n:return: True if this ``Data`` is lazy.")
243 .def("isReady",&escript::Data::isReady,":rtype: ``bool``\n:return: True if this ``Data`` is not lazy.")
244 .def("expand",&escript::Data::expand,"Convert the data to expanded representation if it is not expanded already.")
245 .def("tag",&escript::Data::tag,"Convert data to tagged representation if it is not already tagged or expanded")
246 .def("resolve",&escript::Data::resolve,"Convert the data to non-lazy representation.")
247 .def("copy",&escript::Data::copy,args("other"),"Make this object a copy of ``other``\n"
248 "\n:note: The two objects will act independently from now on. That is, changing ``other`` "
249 "after this call will not change this object and vice versa.")
250 .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.")
251 .def("delay",&escript::Data::delay,"Convert this object into lazy representation")
252 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject,args("dataPointNo","value"))
253 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
254 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint,"\nModify the value of a single datapoint.\n\n:param dataPointNo:\n"
255 ":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.")
256 .def("getTupleForDataPoint",&escript::Data::getValueOfDataPointAsTuple,args("dataPointNo"),
257 ":return: Value of the specified datapoint\n:rtype: ``tuple``\n:param dataPointNo: datapoint to access\n:type dataPointNo: ``int``")
258 .def("getTupleForGlobalDataPoint",&escript::Data::getValueOfGlobalDataPointAsTuple,args("procNo","dataPointNo"),"Get a specific datapoint from a specific process\n\n"
259 ":rtype: ``tuple``\n:param procNo: MPI rank of the process\n:type procNo: positive ``int``"
260 "\n:param dataPointNo: datapoint to access\n:type dataPointNo: int")
261 .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.")
262 .def("interpolate",&escript::Data::interpolate,args("functionspace"),"Interpolate this object's values into a new functionspace.")
263 .def("interpolateTable", &escript::Data::interpolateFromTable2DP,
264 (arg("table"),arg("Amin"),arg("Astep"), arg("B"), arg("Bmin"), arg("Bstep"), arg("undef")=1.e50, arg("check_boundaries")=false),
265 "Creates a new Data object by interpolating using the source data (which are\n"
266 "looked up in ``table``)\n``A`` must be the outer dimension on the table\n\n"
267 ":param table: two dimensional collection of values\n"
268 ":param Amin: The base of locations in table\n:type Amin: float\n"
269 ":param Astep: size of gap between each item in the table\n:type Astep: float\n"
270 ":param undef: upper bound on interpolated values\n:type undef: float\n"
271 ":param B: Scalar representing the second coordinate to be mapped into the table\n"
272 ":type B: `Data`\n"
273 ":param Bmin: The base of locations in table for 2nd dimension\n:type Bmin: float\n"
274 ":param Bstep: size of gap between each item in the table for 2nd dimension\n:type Bstep: float\n"
275 ":param check_boundaries: if true, then values outside the boundaries will be rejected. If false, then boundary values will be used.\n"
276 ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"
277 "\n:rtype: `Data`"
278 )
279 .def("interpolateTable", &escript::Data::interpolateFromTable1DP,
280 (arg("table"),arg("Amin"),arg("Astep"), arg("undef")=1.e50, arg("check_boundaries")=false),
281 "Creates a new Data object by interpolating using the source data (which are\n"
282 "looked up in ``table``)\n\n"
283 ":param table: one dimensional collection of values\n"
284 ":param Amin: The base of locations in table\n:type Amin: float\n"
285 ":param Astep: size of gap between each item in the table\n:type Astep: float\n"
286 ":param undef: upper bound on interpolated values\n:type undef: float\n"
287 ":param check_boundaries: if true, then values outside the boundaries will be rejected. If false, then boundary values will be used.\n"
288 ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"
289 "\n:rtype: `Data`"
290 )
291
292
293 .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
294 .def("maxGlobalDataPoint",&escript::Data::maxGlobalDataPoint)
295 .def("saveDX",&escript::Data::saveDX,args("fileName"),"Save the object in DX format.\n\n"
296 ":param fileName: filename\n:type fileName: string")
297 .def("saveVTK",&escript::Data::saveVTK, args("fileName"),"Save the object in VTK format.\n\n"
298 ":param fileName: \n:type fileName: string")
299 .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")
300 // Unary functions for Data
301 .def("_interpolate",&escript::Data::interpolate)
302 .def("_grad",&escript::Data::gradOn)
303 .def("_grad",&escript::Data::grad)
304 .def("_transpose",&escript::Data::transpose)
305 .def("_trace",&escript::Data::trace)
306 .def("_maxval",&escript::Data::maxval)
307 .def("_minval",&escript::Data::minval)
308 .def("_wherePositive",&escript::Data::wherePositive)
309 .def("_whereNegative",&escript::Data::whereNegative)
310 .def("_whereNonNegative",&escript::Data::whereNonNegative)
311 .def("_whereNonPositive",&escript::Data::whereNonPositive)
312 .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
313 .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
314 .def("_erf",&escript::Data::erf)
315 .def("_sin",&escript::Data::sin)
316 .def("_cos",&escript::Data::cos)
317 .def("_tan",&escript::Data::tan)
318 .def("_asin",&escript::Data::asin)
319 .def("_acos",&escript::Data::acos)
320 .def("_atan",&escript::Data::atan)
321 .def("_sinh",&escript::Data::sinh)
322 .def("_cosh",&escript::Data::cosh)
323 .def("_tanh",&escript::Data::tanh)
324 .def("_asinh",&escript::Data::asinh)
325 .def("_acosh",&escript::Data::acosh)
326 .def("_atanh",&escript::Data::atanh)
327 .def("_exp",&escript::Data::exp)
328 .def("_sqrt",&escript::Data::sqrt)
329 .def("_log10",&escript::Data::log10)
330 .def("_log",&escript::Data::log)
331 .def("_sign",&escript::Data::sign)
332 .def("_symmetric",&escript::Data::symmetric)
333 .def("_nonsymmetric",&escript::Data::nonsymmetric)
334 .def("_trace",&escript::Data::trace)
335 .def("_swap_axes",&escript::Data::swapaxes)
336 .def("_eigenvalues",&escript::Data::eigenvalues)
337 .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
338 // functions returning a single real number:
339 .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.")
340 .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.")
341 .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.")
342 .def("_integrateToTuple",&escript::Data::integrateToTuple,":return: Calculate the integral over the function space domain as a python tuple\n:rtype: tuple")
343 // following implements the python abs operator
344 .def("__abs__",&escript::Data::abs,":return: absolute value\n\n:rtype: `Data`")
345 // following implements the python "-" negation operator
346 .def("__neg__",&escript::Data::neg, ":return: negation of the values in this object\n:rtype: `Data`")
347 // following implements the python "+" identity operator
348 .def("__pos__",&escript::Data::pos, "\nThe unary + operator\n\n:rtype: `Data`")
349 // following two functions implement the python [] operator
350 .def("__getitem__",&escript::Data::getItem,"Used by the python [] operator\n\n:rtype: `Data`")
351 .def("__setitem__",&escript::Data::setItemO,"Used by the python [] operator")
352 .def("__setitem__",&escript::Data::setItemD,"Used by the python [] operator")
353 // following two functions implement the python ** operator
354 .def("__pow__",&escript::Data::powO,"Used by the python ** operator\n\n:rtype: `Data`")
355 .def("__pow__",&escript::Data::powD)
356 .def("__rpow__",&escript::Data::rpowO,"\nUsed by the python ** operator\n\n:rtype: `Data`")
357 // NOTE:: The order of these declarations is important. Anything
358 // declared before the generic declaration isn't found so the generic
359 // version will be called.
360 .def(self + other<object>())
361 .def(other<object>() + self)
362 .def(self + self)
363 .def(self += other<object>())
364 .def(self += self)
365
366 .def(self - other<object>())
367 .def(other<object>() - self)
368 .def(self - self)
369 .def(self -= other<object>())
370 .def(self -= self)
371
372 .def(self * other<object>())
373 .def(other<object>() * self)
374 .def(self * self)
375 .def(self *= other<object>())
376 .def(self *= self)
377
378 .def(self / other<object>())
379 .def(other<object>() / self)
380 .def(self / self)
381 .def(self /= other<object>())
382 .def(self /= self)
383 // Need scope resolution due to a bug either in the compiler or
384 // the boost code. This calls operator << for Data.
385 .def(self_ns::str(self))
386 .def("_inverse", &escript::Data::matrixInverse, ":return: inverse of square matricies\n");
387
388
389 //
390 // Factory methods for function space
391 //
392 def("ContinuousFunction",escript::continuousFunction,args("domain"),
393 ":return: a continuous FunctionSpace (overlapped node values)\n"
394 ":rtype: `FunctionSpace`");
395 def("ReducedContinuousFunction",escript::reducedContinuousFunction,args("domain"),
396 ":return: a continuous with reduced order FunctionSpace (overlapped node values on reduced element order)\n"
397 ":rtype: `FunctionSpace`");
398 def("Function",escript::function,args("domain"),":return: a function `FunctionSpace`\n"
399 ":rtype: `FunctionSpace`");
400 def("ReducedFunction",escript::reducedFunction, args("domain"),":return: a function FunctionSpace with reduced integration order\n:rtype: `FunctionSpace`");
401 def("FunctionOnBoundary",escript::functionOnBoundary, args("domain"), ":return: a function on boundary FunctionSpace\n:rtype: `FunctionSpace`");
402 def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary, args("domain"),
403 ":return: a function on boundary FunctionSpace with reduced integration order\n"
404 ":rtype: `FunctionSpace`");
405 def("FunctionOnContactZero",escript::functionOnContactZero, args("domain"), ":return: Return a FunctionSpace on left side of contact\n:rtype: `FunctionSpace`");
406 def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero, args("domain"),
407 ":return: a FunctionSpace on left side of contact with reduced integration order\n:rtype: `FunctionSpace`");
408 def("FunctionOnContactOne",escript::functionOnContactOne, args("domain"), ":return: Return a FunctionSpace on right side of contact\n:rtype: `FunctionSpace`");
409 def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne, args("domain"),
410 ":return: Return a FunctionSpace on right side of contact with reduced integration order\n"
411 ":rtype: `FunctionSpace`");
412 def("Solution",escript::solution, args("domain"), ":rtype: `FunctionSpace`");
413 def("ReducedSolution",escript::reducedSolution, args("domain"), ":rtype: `FunctionSpace`");
414 def("DiracDeltaFunction",escript::diracDeltaFunction, args("domain"), ":rtype: `FunctionSpace`");
415
416
417
418
419
420 //
421 // Factory methods for Data
422 //
423 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`");
424 def("loadIsConfigured",escript::loadConfigured,":return: True if the load function is configured.");
425 def("Scalar",escript::Scalar,
426 (arg("value")=0.0,
427 arg("what")=escript::FunctionSpace(),
428 arg("expanded")=false),
429 "Construct a Data object containing scalar 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("Vector",escript::Vector,
434 (arg("value")=0.0,
435 arg("what")=escript::FunctionSpace(),
436 arg("expanded")=false),
437 "Construct a Data object containing rank1 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 def("Tensor",escript::Tensor,
442 (arg("value")=0.0,
443 arg("what")=escript::FunctionSpace(),
444 arg("expanded")=false),
445 "Construct a Data object containing rank2 data-points.\n\n:param value: scalar value for all points\n"
446 "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
447 ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
448 ":type expanded: ``bool``");
449 def("Tensor3",escript::Tensor3,
450 (arg("value")=0.0,
451 arg("what")=escript::FunctionSpace(),
452 arg("expanded")=false),
453 "Construct a Data object containing rank3 data-points.\n\n:param value: scalar value for all points\n"
454 "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
455 ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
456 ":type expanded: ``bool``"
457 );
458 def("Tensor4",escript::Tensor4,
459 (arg("value")=0.0,
460 arg("what")=escript::FunctionSpace(),
461 arg("expanded")=false),
462 "Construct a Data object containing rank4 data-points.\n\n:param value: scalar value for all points\n"
463 "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
464 ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
465 ":type expanded: ``bool``"
466 );
467
468 //
469 // Binary operators
470 //
471 def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
472 (arg("arg0"),
473 arg("arg1"),
474 arg("axis_offset")=0,
475 arg("transpose")=0),
476 "Compute a tensor product of two Data objects.\n\n:rtype: `Data`\n:param arg0:\n"
477 ":param arg1:\n:param axis_offset:\n:type axis_offset: ``int``\n"
478 ":param transpose: 0: transpose neither, 1: transpose arg0, 2: transpose arg1\n"
479 ":type transpose: int");
480
481 //
482 // Interface for AbstractSystemMatrix
483 //
484 class_<escript::AbstractSystemMatrix>("Operator","",init<>()) // Doco goes in the empty string param
485 .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty,":rtype: ``bool``\n"
486 ":return: True if matrix is empty")
487 .def("solve",&escript::AbstractSystemMatrix::solve, args("in","options"),
488 ":return: the solution *u* of the linear system *this*u=in*\n\n:param in:\n:type in: `Data`")
489 .def("of",&escript::AbstractSystemMatrix::vectorMultiply,args("right"),
490 "matrix*vector multiplication")
491 .def("saveMM",&escript::AbstractSystemMatrix::saveMM, args("fileName"),
492 "writes the matrix to a file using the Matrix Market file format")
493 .def("saveHB",&escript::AbstractSystemMatrix::saveHB, args("filename"),
494 "writes the matrix to a file using the Harwell-Boeing file format")
495 .def("resetValues",&escript::AbstractSystemMatrix::resetValues, "resets the matrix entries")
496 .def(self*other<escript::Data>());
497 //
498 // Interface for AbstractTransportProblem
499 //
500 class_<escript::AbstractTransportProblem>("TransportProblem","",init<>()) // Doco goes in the empty string param
501 .def("isEmpty",&escript::AbstractTransportProblem::isEmpty,":rtype: ``int``")
502 .def("solve",&escript::AbstractTransportProblem::solve, args("source","dt", "options"),
503 "returns the solution *u* for a time step *dt>0*\n\n:rtype: `Data`\n"
504 ":param source:\n:type source: `Data`")
505 .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue, args("u"),
506 "sets the value for *u* at time *t=0*.")
507 .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint,
508 args("source", "q", "r","factor"),
509 "inserts constraint *u_{,t}=r* where *q>0* into the problem using a weighting factor")
510 .def("reset",&escript::AbstractTransportProblem::resetTransport,
511 "resets the transport operator typically as they have been updated.")
512 .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
513 .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize)
514 .def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize);
515
516 // Functions to modify global parameters
517 def("setEscriptParamInt",escript::setEscriptParamInt,
518 (arg("name"), arg("value")=0), "Modify the value of an escript tuning parameter\n\n"
519 ":param name:\n:type name: ``string``\n:param value:\n:type value: ``int``");
520 def("getEscriptParamInt",escript::getEscriptParamInt,
521 (arg("name"),arg("sentinel")=0), "Read the value of an escript tuning paramter\n\n"
522 ":param name: parameter to lookup\n:type name: ``string``\n:param sentinel: Value to be returned if ``name`` is not a known parameter\n"
523 ":type sentinel: ``int``");
524 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.");
525
526 //
527 // Register esysExceptionTranslator
528 //
529 register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);
530 }

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