/[escript]/trunk/escript/src/escriptcpp.cpp
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Thu Dec 2 00:34:37 2010 UTC (8 years, 9 months ago) by jfenwick
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1 jgs 102
2 ksteube 1312 /*******************************************************
3 ksteube 1811 *
4 jfenwick 2881 * Copyright (c) 2003-2010 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 jfenwick 3259 #include "esysUtils/Esys_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 jfenwick 1872 #include <boost/smart_ptr.hpp>
43 jfenwick 2064 #include <boost/version.hpp>
44 gross 285
45 jgs 102 using namespace boost::python;
46    
47 jgs 121 /*! \mainpage Esys Documentation
48     *
49 jfenwick 2602 * \version 3.0.0
50 jgs 121 *
51     * - \ref escript
52     *
53     * - \ref esys_exception "Esys Exception"
54     *
55 jfenwick 3259 * - \ref dudley
56 jgs 121 *
57 jfenwick 2283 * - <a href="../../epydoc/index.html">Python module documentation (epydoc generated)</a>
58 jgs 122 *
59 jgs 121 */
60 jgs 102
61 jgs 121 /*! \page escript Escript
62     * Escript is the python module that contains the interfaces
63     * to the C++ side of escript.
64     *
65 jfenwick 2459 *
66 jgs 121 *
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 jgs 102
81     BOOST_PYTHON_MODULE(escriptcpp)
82     {
83 jfenwick 2625
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 gross 2100 #endif
88 jfenwick 2061
89 jfenwick 2607 def("setNumberOfThreads",escript::setNumberOfThreads,"Use of this method is strongly discouraged.");
90 jfenwick 2625 def("getNumberOfThreads",escript::getNumberOfThreads,"Return the maximum number of threads"
91     " available to OpenMP.");
92 gross 797 def("releaseUnusedMemory",escript::releaseUnusedMemory);
93 ksteube 1312 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 jfenwick 2607 def("getVersion",escript::getSvnVersion,"This method will only report accurate version numbers for clean checkouts.");
99 ksteube 1561 def("printParallelThreadCounts",escript::printParallelThreadCnt);
100 jfenwick 2625 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 gross 2100 def("getMachinePrecision",escript::getMachinePrecision);
108     def("getMaxFloat",escript::getMaxFloat);
109 jfenwick 2644 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 jfenwick 2766 "That is, items in each column will be printed in the same order.\n"
118 jfenwick 3360 "So you can be sure that values in the same row correspond to the same input value.\n\n"
119 jfenwick 2644 "\n:param filename:\n:type filename: ``string``\n"
120 jfenwick 3360 ":param arg: dictionary of named `Data` objects. If one is called ``mask`` it must be scalar data.\n"
121     ":type arg: ``dict``\n"
122     ":param sep: separator for columns (defaults to ',')\n"
123     ":type sep: ``string``\n"
124     ":param csep: separator for fields within data object (defaults to \"_\")\n:type csep: ``string``\n"
125 jfenwick 2644 ":param append: If True, write to the end of ``filename``\n:type append: ``string``\n");
126 jfenwick 2635
127    
128 jgs 102 //
129     // Interface for AbstractDomain
130     //
131 jfenwick 2061 class_<escript::AbstractDomain, escript::Domain_ptr>("Domain","Base class for all domains.",no_init)
132 jfenwick 2625 .def("getStatus",&escript::AbstractDomain::getStatus,"The status of a domain changes whenever the domain is modified\n\n:rtype: int")
133     .def("setTagMap",&escript::AbstractDomain::setTagMap,args("name","tag"),
134     "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
135     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
136     .def("getTag",&escript::AbstractDomain::getTag,args("name"),":return: tag id for "
137     "``name``\n:rtype: ``string``")
138     .def("isValidTagName",&escript::AbstractDomain::isValidTagName,args("name"),
139     ":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
140     .def("showTagNames",&escript::AbstractDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
141     .def("getX",&escript::AbstractDomain::getX,":rtype: `Data`\n:return: Locations in the"
142     "`Domain`. FunctionSpace is chosen appropriately")
143     .def("getDim",&escript::AbstractDomain::getDim,":rtype: `int`\n:return: Spatial dimension of the `Domain`")
144     .def("getNormal",&escript::AbstractDomain::getNormal,":rtype: `escript`\n:return: Boundary normals")
145     .def("getSize",&escript::AbstractDomain::getSize,":return: the local size of samples. The function space is chosen appropriately\n:rtype: `Data`")
146     .def("saveVTK",&escript::AbstractDomain::saveVTK,args("filename","arg", "metadata"
147     , "metadata_schema"),
148     ":param filename: \n:type filename: ``string``\n:param arg: items to be added"
149     "\n:type arg: ``dict``\n:param metadata: string representing some meta data to be added\n:type metadata: ``string``"
150     "\n:param metadata_schema: schema type for metadata\n:type metadata_schema: ``string``")
151     .def("dump",&escript::AbstractDomain::dump,args("filename"),"Dumps the domain to a file"
152     ":param filename:\n:type filename: string")
153     .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``"
154     "\n:param arg:\n:type arg: `dict`")
155     .def("getMPISize",&escript::AbstractDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
156     .def("getMPIRank",&escript::AbstractDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
157     .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier,"Wait until all processes have reached this point")
158     .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`")
159 jfenwick 3259 .def("supportsContactElements", &escript::AbstractDomain::supportsContactElements,"Does this domain support contact elements.")
160 jgs 102 .def(self == self)
161     .def(self != self);
162    
163     //
164     // Interface for AbstractContinuousDomain
165     //
166 jfenwick 2061 class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain","Class representing continuous domains",no_init)
167 jfenwick 2625 .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId,
168     args("solver", "preconditioner", "package", "symmetry"),
169     ":return: the identifier of the matrix type to be used for the global stiffness matrix "
170     "when a particular solver package and symmetric matrix is used.\n"
171     ":rtype: int")
172     .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId,
173 jfenwick 3259 args("solver", "preconditioner", "package", "symmetry"))
174 jgs 102
175 jfenwick 3259 .def("addPDEToSystem",&escript::AbstractContinuousDomain::addPDEToSystem,
176     args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
177     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
178     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
179     ":param A:\n:type A: `Data`\n"
180     ":param B:\n:type B: `Data`\n"
181     ":param C:\n:type C: `Data`\n"
182     ":param D:\n:type D: `Data`\n"
183     ":param X:\n:type X: `Data`\n"
184     ":param Y:\n:type Y: `Data`\n"
185     ":param d:\n:type d: `Data`\n"
186     ":param d_contact:\n:type d_contact: `Data`\n"
187     ":param y_contact:\n:type y_contact: `Data`\n"
188     )
189     .def("addPDEToRHS",&escript::AbstractContinuousDomain::addPDEToRHS,
190     args("rhs", "X", "Y", "y", "y_contact"),
191     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
192     ":param rhs:\n:type rhs: `Data`\n"
193     ":param X:\n:type X: `Data`\n"
194     ":param Y:\n:type Y: `Data`\n"
195     ":param y:\n:type y: `Data`\n"
196     ":param y_contact:\n:type y_contact: `Data`"
197     )
198     .def("addPDEToTransportProblem",&escript::AbstractContinuousDomain::addPDEToTransportProblem,
199     args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
200     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
201     ":param source:\n:type source: `Data`\n"
202     ":param M:\n:type M: `Data`\n"
203     ":param A:\n:type A: `Data`\n"
204     ":param B:\n:type B: `Data`\n"
205     ":param C:\n:type C: `Data`\n"
206     ":param D:\n:type D: `Data`\n"
207     ":param X:\n:type X: `Data`\n"
208     ":param Y:\n:type Y: `Data`\n"
209     ":param d:\n:type d: `Data`\n"
210     ":param y:\n:type y: `Data`\n"
211     ":param d_contact:\n:type d_contact: `Data`\n"
212     ":param y_contact:\n:type y_contact: `Data`\n"
213     )
214     .def("newOperator",&escript::AbstractContinuousDomain::newSystemMatrix,
215     args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
216     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
217     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
218     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
219     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
220     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
221     ":param type:\n:type type: ``int``\n"
222     )
223     .def("newTransportProblem",&escript::AbstractContinuousDomain::newTransportProblem,
224     args("theta", "blocksize", "functionspace", "type"),
225     "creates a TransportProblemAdapter\n\n"
226     ":param theta:\n:type theta: ``float``\n"
227     ":param blocksize:\n:type blocksize: ``int``\n"
228     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
229     ":param type:\n:type type: ``int``\n"
230     )
231     .def("getDataShape",&escript::AbstractContinuousDomain::getDataShape, args("functionSpaceCode"),
232     ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
233     .def("print_mesh_info",&escript::AbstractContinuousDomain::Print_Mesh_Info,(arg("full")=false),
234     ":param full:\n:type full: ``bool``")
235     .def("getDescription",&escript::AbstractContinuousDomain::getDescription,
236     ":return: a description for this domain\n:rtype: ``string``")
237     .def("setX",&escript::AbstractContinuousDomain::setNewX,
238     args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
239     .def("getNumDataPointsGlobal",&escript::AbstractContinuousDomain::getNumDataPointsGlobal,
240     ":return: the number of data points summed across all MPI processes\n"
241     ":rtype: ``int``");
242 jfenwick 2482
243 jfenwick 3259
244    
245    
246 jgs 102 //
247 jfenwick 2482 // Interface for TestDomain
248     //
249     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>());
250    
251     // This is the only python visible way to get a TestDomain
252 jfenwick 2625 def("getTestDomainFunctionSpace",&escript::getTestDomainFunctionSpace, args("dpps",
253     "samples"),
254     "For testing only. May be removed without notice.");
255 jfenwick 2482
256     //
257 jgs 102 // Interface for FunctionSpace
258     //
259 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
260     fs_definer.def("getDim",&escript::FunctionSpace::getDim,":return: the spatial dimension of the underlying domain.\n:rtype: int");
261 jfenwick 1872 // fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
262     // return_internal_reference<>());
263 jfenwick 2625 fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython,":return: the underlying `Domain` for this FunctionSpace.\n:rtype: `Domain`");
264     fs_definer.def("getX",&escript::FunctionSpace::getX,"\n:return: a function whose values are its input coordinates. ie an identity function.\n:rtype: `Data`");
265     fs_definer.def("getNormal",&escript::FunctionSpace::getNormal,":return: the surface normal field.\n\n:rtype: `Data`");
266     fs_definer.def("getSize",&escript::FunctionSpace::getSize,":return: sample size\n:rtype: `Data`");
267     fs_definer.def("setTags",&escript::FunctionSpace::setTags,args("newtag","mask"),
268 jfenwick 3360 "Set tags according to a mask\n\n:param newtag: tag number to set\n:type newtag: string, 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`");
269     fs_definer.def("setTags",&escript::FunctionSpace::setTagsByString,args("newtag","mask"));
270 trankine 1426 fs_definer.def("getTagFromDataPointNo",
271 jfenwick 2625 &escript::FunctionSpace::getTagFromDataPointNo,":return: the tag associated with the given sample number.\n:rtype: int");
272     fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo,args("dataPointNo"),":return: the reference number associated with ``dataPointNo``\n:rtype: int ");
273     fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags,":return: a list of the tags used in this function space\n:rtype: ``list``");
274 gross 2856 fs_definer.def("getApproximationOrder", &escript::FunctionSpace::getApproximationOrder,":return: the approximation order refering to the maximum degree of a polynomial which can be represenred exactly in interplation and/or integration.\n:rtype: ``int``");
275 phornby 1628 fs_definer.def("__str__", &escript::FunctionSpace::toString);
276 trankine 1426 fs_definer.def(self == self);
277     fs_definer.def(self != self);
278 jgs 102 //
279     // Interface for Data
280     //
281 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<>() )
282 jgs 102 // various constructors for Data objects
283     .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
284     .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))
285     .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))
286     .def(init<const escript::Data&>())
287     // Note for Lutz, Need to specify the call policy in order to return a
288     // reference. In this case return_internal_reference.
289 ksteube 1312 .def("__str__",&escript::Data::toString)
290 jfenwick 2625 .def("getDomain",&escript::Data::getDomainPython,":rtype: `Domain`")
291     .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>(),":rtype: `FunctionSpace`")
292     .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.")
293     .def("isProtected",&escript::Data::isProtected,"Can this instance be modified.\n:rtype: ``bool``")
294     .def("setProtection",&escript::Data::setProtection,"Disallow modifications to this data object\n\n:note: This method does not allow you to undo protection.")
295     .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``")
296     .def("getRank",&escript::Data::getDataPointRank,":return: the number of indicies required to address a component of a datapoints\n:rtype: positive ``int``")
297     .def("dump",&escript::Data::dump,args("fileName"),"Save the data as a netCDF file\n\n:param fileName: \n:type fileName: ``string``")
298     .def("toListOfTuples",&escript::Data::toListOfTuples, (arg("scalarastuple")=false),
299     "Return the datapoints of this object in a list. Each datapoint is stored as a tuple.\n\n"
300     ":param scalarastuple: if True, scalar data will be wrapped as a tuple."
301     " True => [(0), (1), (2)]; False => [0, 1, 2]")
302     .def("copyWithMask",&escript::Data::copyWithMask,args("other","mask"),
303     "Selectively copy values from ``other`` `Data`."
304     "Datapoints which correspond to postive values in ``mask`` will be copied from ``other``\n"
305     "\n:param other: source of values\n"
306     ":type other: `Data`\n:param mask:\n:type mask: Scalar `Data`")
307     .def("setTaggedValue",&escript::Data::setTaggedValue,args("tagKey","value"),
308     "Set the value of tagged Data.\n\n:param tagKey: tag to update\n:type tagKey: ``int``\n")
309     .def("setTaggedValue",&escript::Data::setTaggedValueByName,args("name","value"),":param name: tag to update\n:type name: ``string``\n"
310     ":param value: value to set tagged data to\n:type value: ``object`` which acts like an array, ``tuple`` or ``list``\n")
311     .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints,":rtype: ``int``\n:return: Number of datapoints in the object")
312     .def("isExpanded",&escript::Data::isExpanded,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
313     .def("isTagged",&escript::Data::isTagged,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.")
314     .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.")
315     .def("isLazy",&escript::Data::isLazy,":rtype: ``bool``\n:return: True if this ``Data`` is lazy.")
316     .def("isReady",&escript::Data::isReady,":rtype: ``bool``\n:return: True if this ``Data`` is not lazy.")
317     .def("expand",&escript::Data::expand,"Convert the data to expanded representation if it is not expanded already.")
318     .def("tag",&escript::Data::tag,"Convert data to tagged representation if it is not already tagged or expanded")
319     .def("resolve",&escript::Data::resolve,"Convert the data to non-lazy representation.")
320     .def("copy",&escript::Data::copy,args("other"),"Make this object a copy of ``other``\n"
321     "\n:note: The two objects will act independently from now on. That is, changing ``other`` "
322     "after this call will not change this object and vice versa.")
323     .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.")
324     .def("delay",&escript::Data::delay,"Convert this object into lazy representation")
325     .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject,args("dataPointNo","value"))
326 gross 1034 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
327 jfenwick 2625 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint,"\nModify the value of a single datapoint.\n\n:param dataPointNo:\n"
328     ":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.")
329     .def("getTupleForDataPoint",&escript::Data::getValueOfDataPointAsTuple,args("dataPointNo"),
330     ":return: Value of the specified datapoint\n:rtype: ``tuple``\n:param dataPointNo: datapoint to access\n:type dataPointNo: ``int``")
331     .def("getTupleForGlobalDataPoint",&escript::Data::getValueOfGlobalDataPointAsTuple,args("procNo","dataPointNo"),"Get a specific datapoint from a specific process\n\n"
332     ":rtype: ``tuple``\n:param procNo: MPI rank of the process\n:type procNo: positive ``int``"
333     "\n:param dataPointNo: datapoint to access\n:type dataPointNo: int")
334     .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.")
335     .def("interpolate",&escript::Data::interpolate,args("functionspace"),"Interpolate this object's values into a new functionspace.")
336 jfenwick 3368 .def("_interpolateTable3d", &escript::Data::interpolateFromTable3DP,
337     (arg("table"),arg("Amin"),arg("Astep"), arg("B"), arg("Bmin"), arg("Bstep"), arg("C"), arg("Cmin"), arg("Cstep"), arg("undef")=1.e50, arg("check_boundaries")=false, "For internal use only. Please use the interpolateTable function.")
338     )
339    
340 jfenwick 2646 .def("interpolateTable", &escript::Data::interpolateFromTable2DP,
341 gross 2668 (arg("table"),arg("Amin"),arg("Astep"), arg("B"), arg("Bmin"), arg("Bstep"), arg("undef")=1.e50, arg("check_boundaries")=false),
342 jfenwick 2628 "Creates a new Data object by interpolating using the source data (which are\n"
343 jfenwick 2646 "looked up in ``table``)\n``A`` must be the outer dimension on the table\n\n"
344 jfenwick 2628 ":param table: two dimensional collection of values\n"
345     ":param Amin: The base of locations in table\n:type Amin: float\n"
346     ":param Astep: size of gap between each item in the table\n:type Astep: float\n"
347     ":param undef: upper bound on interpolated values\n:type undef: float\n"
348     ":param B: Scalar representing the second coordinate to be mapped into the table\n"
349     ":type B: `Data`\n"
350     ":param Bmin: The base of locations in table for 2nd dimension\n:type Bmin: float\n"
351     ":param Bstep: size of gap between each item in the table for 2nd dimension\n:type Bstep: float\n"
352 jfenwick 2673 ":param check_boundaries: if true, then values outside the boundaries will be rejected. If false, then boundary values will be used.\n"
353 jfenwick 2628 ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"
354     "\n:rtype: `Data`"
355     )
356 jfenwick 2646 .def("interpolateTable", &escript::Data::interpolateFromTable1DP,
357 jfenwick 3360 (arg("table"),arg("Amin"),arg("Astep"), arg("undef")=1.e50, arg("check_boundaries")=false)/*,
358 jfenwick 2646 "Creates a new Data object by interpolating using the source data (which are\n"
359     "looked up in ``table``)\n\n"
360     ":param table: one dimensional collection of values\n"
361     ":param Amin: The base of locations in table\n:type Amin: float\n"
362     ":param Astep: size of gap between each item in the table\n:type Astep: float\n"
363     ":param undef: upper bound on interpolated values\n:type undef: float\n"
364 jfenwick 2673 ":param check_boundaries: if true, then values outside the boundaries will be rejected. If false, then boundary values will be used.\n"
365 jfenwick 2646 ":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``"
366     "\n:rtype: `Data`"
367 jfenwick 3360 */
368 jfenwick 2646 )
369 jfenwick 2628
370 jfenwick 2646
371 jfenwick 2770 .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint,"Please consider using getInfLocator() from pdetools instead.")
372     .def("maxGlobalDataPoint",&escript::Data::maxGlobalDataPoint, "Please consider using getSupLocator() from pdetools instead.")
373 jfenwick 2625 .def("saveDX",&escript::Data::saveDX,args("fileName"),"Save the object in DX format.\n\n"
374     ":param fileName: filename\n:type fileName: string")
375     .def("saveVTK",&escript::Data::saveVTK, args("fileName"),"Save the object in VTK format.\n\n"
376     ":param fileName: \n:type fileName: string")
377     .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")
378 gross 285 // Unary functions for Data
379     .def("_interpolate",&escript::Data::interpolate)
380     .def("_grad",&escript::Data::gradOn)
381     .def("_grad",&escript::Data::grad)
382     .def("_transpose",&escript::Data::transpose)
383     .def("_trace",&escript::Data::trace)
384     .def("_maxval",&escript::Data::maxval)
385     .def("_minval",&escript::Data::minval)
386 gross 698 .def("_wherePositive",&escript::Data::wherePositive)
387     .def("_whereNegative",&escript::Data::whereNegative)
388     .def("_whereNonNegative",&escript::Data::whereNonNegative)
389     .def("_whereNonPositive",&escript::Data::whereNonPositive)
390 jgs 571 .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
391     .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
392 ksteube 876 .def("_erf",&escript::Data::erf)
393 gross 285 .def("_sin",&escript::Data::sin)
394     .def("_cos",&escript::Data::cos)
395     .def("_tan",&escript::Data::tan)
396     .def("_asin",&escript::Data::asin)
397     .def("_acos",&escript::Data::acos)
398     .def("_atan",&escript::Data::atan)
399     .def("_sinh",&escript::Data::sinh)
400     .def("_cosh",&escript::Data::cosh)
401     .def("_tanh",&escript::Data::tanh)
402     .def("_asinh",&escript::Data::asinh)
403     .def("_acosh",&escript::Data::acosh)
404     .def("_atanh",&escript::Data::atanh)
405     .def("_exp",&escript::Data::exp)
406     .def("_sqrt",&escript::Data::sqrt)
407     .def("_log10",&escript::Data::log10)
408     .def("_log",&escript::Data::log)
409     .def("_sign",&escript::Data::sign)
410 ksteube 775 .def("_symmetric",&escript::Data::symmetric)
411     .def("_nonsymmetric",&escript::Data::nonsymmetric)
412 gross 800 .def("_trace",&escript::Data::trace)
413 gross 804 .def("_swap_axes",&escript::Data::swapaxes)
414 gross 576 .def("_eigenvalues",&escript::Data::eigenvalues)
415     .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
416 gross 285 // functions returning a single real number:
417 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.")
418     .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.")
419     .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.")
420     .def("_integrateToTuple",&escript::Data::integrateToTuple,":return: Calculate the integral over the function space domain as a python tuple\n:rtype: tuple")
421 gross 285 // following implements the python abs operator
422 jfenwick 2625 .def("__abs__",&escript::Data::abs,":return: absolute value\n\n:rtype: `Data`")
423 jgs 102 // following implements the python "-" negation operator
424 jfenwick 2625 .def("__neg__",&escript::Data::neg, ":return: negation of the values in this object\n:rtype: `Data`")
425 jgs 102 // following implements the python "+" identity operator
426 jfenwick 2646 .def("__pos__",&escript::Data::pos, "\nThe unary + operator\n\n:rtype: `Data`")
427 jgs 102 // following two functions implement the python [] operator
428 jfenwick 2625 .def("__getitem__",&escript::Data::getItem,"Used by the python [] operator\n\n:rtype: `Data`")
429     .def("__setitem__",&escript::Data::setItemO,"Used by the python [] operator")
430     .def("__setitem__",&escript::Data::setItemD,"Used by the python [] operator")
431 jgs 102 // following two functions implement the python ** operator
432 jfenwick 2625 .def("__pow__",&escript::Data::powO,"Used by the python ** operator\n\n:rtype: `Data`")
433 jgs 102 .def("__pow__",&escript::Data::powD)
434 jfenwick 2625 .def("__rpow__",&escript::Data::rpowO,"\nUsed by the python ** operator\n\n:rtype: `Data`")
435 jgs 102 // NOTE:: The order of these declarations is important. Anything
436     // declared before the generic declaration isn't found so the generic
437     // version will be called.
438     .def(self + other<object>())
439     .def(other<object>() + self)
440     .def(self + self)
441 gross 285 .def(self += other<object>())
442     .def(self += self)
443    
444 jgs 102 .def(self - other<object>())
445     .def(other<object>() - self)
446     .def(self - self)
447 gross 285 .def(self -= other<object>())
448     .def(self -= self)
449    
450 jgs 102 .def(self * other<object>())
451     .def(other<object>() * self)
452     .def(self * self)
453 gross 285 .def(self *= other<object>())
454     .def(self *= self)
455    
456 jgs 102 .def(self / other<object>())
457     .def(other<object>() / self)
458     .def(self / self)
459 gross 285 .def(self /= other<object>())
460     .def(self /= self)
461 jgs 102 // Need scope resolution due to a bug either in the compiler or
462     // the boost code. This calls operator << for Data.
463 jfenwick 2742 .def(self_ns::str(self))
464     .def("_inverse", &escript::Data::matrixInverse, ":return: inverse of square matricies\n");
465 jgs 102
466 jfenwick 2635
467 jgs 102 //
468     // Factory methods for function space
469     //
470 jfenwick 2625 def("ContinuousFunction",escript::continuousFunction,args("domain"),
471     ":return: a continuous FunctionSpace (overlapped node values)\n"
472     ":rtype: `FunctionSpace`");
473     def("ReducedContinuousFunction",escript::reducedContinuousFunction,args("domain"),
474     ":return: a continuous with reduced order FunctionSpace (overlapped node values on reduced element order)\n"
475     ":rtype: `FunctionSpace`");
476     def("Function",escript::function,args("domain"),":return: a function `FunctionSpace`\n"
477     ":rtype: `FunctionSpace`");
478     def("ReducedFunction",escript::reducedFunction, args("domain"),":return: a function FunctionSpace with reduced integration order\n:rtype: `FunctionSpace`");
479     def("FunctionOnBoundary",escript::functionOnBoundary, args("domain"), ":return: a function on boundary FunctionSpace\n:rtype: `FunctionSpace`");
480     def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary, args("domain"),
481     ":return: a function on boundary FunctionSpace with reduced integration order\n"
482     ":rtype: `FunctionSpace`");
483     def("FunctionOnContactZero",escript::functionOnContactZero, args("domain"), ":return: Return a FunctionSpace on left side of contact\n:rtype: `FunctionSpace`");
484     def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero, args("domain"),
485     ":return: a FunctionSpace on left side of contact with reduced integration order\n:rtype: `FunctionSpace`");
486     def("FunctionOnContactOne",escript::functionOnContactOne, args("domain"), ":return: Return a FunctionSpace on right side of contact\n:rtype: `FunctionSpace`");
487     def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne, args("domain"),
488     ":return: Return a FunctionSpace on right side of contact with reduced integration order\n"
489     ":rtype: `FunctionSpace`");
490     def("Solution",escript::solution, args("domain"), ":rtype: `FunctionSpace`");
491     def("ReducedSolution",escript::reducedSolution, args("domain"), ":rtype: `FunctionSpace`");
492     def("DiracDeltaFunction",escript::diracDeltaFunction, args("domain"), ":rtype: `FunctionSpace`");
493 jgs 102
494 jfenwick 2635
495    
496    
497    
498 jgs 102 //
499     // Factory methods for Data
500     //
501 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`");
502     def("loadIsConfigured",escript::loadConfigured,":return: True if the load function is configured.");
503 jgs 102 def("Scalar",escript::Scalar,
504     (arg("value")=0.0,
505     arg("what")=escript::FunctionSpace(),
506 jfenwick 2625 arg("expanded")=false),
507     "Construct a Data object containing scalar data-points.\n\n:param value: scalar value for all points\n"
508     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
509     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
510     ":type expanded: ``bool``");
511 jgs 102 def("Vector",escript::Vector,
512     (arg("value")=0.0,
513     arg("what")=escript::FunctionSpace(),
514 jfenwick 2625 arg("expanded")=false),
515     "Construct a Data object containing rank1 data-points.\n\n:param value: scalar value for all points\n"
516     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
517     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
518     ":type expanded: ``bool``");
519 jfenwick 2838 def("Vector", escript::VectorFromObj,
520     (arg("value"),
521     arg("what")=escript::FunctionSpace(),
522     arg("expanded")=false));
523 jgs 102 def("Tensor",escript::Tensor,
524     (arg("value")=0.0,
525     arg("what")=escript::FunctionSpace(),
526 jfenwick 2625 arg("expanded")=false),
527     "Construct a Data object containing rank2 data-points.\n\n:param value: scalar value for all points\n"
528     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
529     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
530     ":type expanded: ``bool``");
531 jfenwick 2838 def("Tensor", escript::TensorFromObj,
532     (arg("value"),
533     arg("what")=escript::FunctionSpace(),
534     arg("expanded")=false));
535 jgs 102 def("Tensor3",escript::Tensor3,
536     (arg("value")=0.0,
537     arg("what")=escript::FunctionSpace(),
538 jfenwick 2625 arg("expanded")=false),
539     "Construct a Data object containing rank3 data-points.\n\n:param value: scalar value for all points\n"
540     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
541     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
542     ":type expanded: ``bool``"
543     );
544 jfenwick 2838 def("Tensor3", escript::Tensor3FromObj,
545     (arg("value"),
546     arg("what")=escript::FunctionSpace(),
547     arg("expanded")=false));
548 jgs 102 def("Tensor4",escript::Tensor4,
549     (arg("value")=0.0,
550     arg("what")=escript::FunctionSpace(),
551 jfenwick 2625 arg("expanded")=false),
552     "Construct a Data object containing rank4 data-points.\n\n:param value: scalar value for all points\n"
553     "\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n"
554     ":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n"
555     ":type expanded: ``bool``"
556     );
557 jfenwick 2838 def("Tensor4", escript::Tensor4FromObj,
558     (arg("value"),
559     arg("what")=escript::FunctionSpace(),
560     arg("expanded")=false));
561 jgs 102
562 jfenwick 3390
563     def("RandomData", escript::randomData, (arg("shape"), arg("fs"), arg("seed")=0.0),
564     "Creates a new expanded Data object containing (not very) random values.\n\n"
565     ":param shape: datapoint shape\n:type shape: tuple\n"
566     ":param fs: function space for data object.\n:type fs: `FunctionSpace`\n"
567     ":param seed: seed for random number generator.\n:type seed: double\n");
568    
569 jgs 102 //
570 ksteube 813 // Binary operators
571     //
572     def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
573 jfenwick 2626 (arg("arg0"),
574     arg("arg1"),
575 ksteube 813 arg("axis_offset")=0,
576 jfenwick 2625 arg("transpose")=0),
577     "Compute a tensor product of two Data objects.\n\n:rtype: `Data`\n:param arg0:\n"
578     ":param arg1:\n:param axis_offset:\n:type axis_offset: ``int``\n"
579     ":param transpose: 0: transpose neither, 1: transpose arg0, 2: transpose arg1\n"
580     ":type transpose: int");
581 ksteube 813
582     //
583 jgs 102 // Interface for AbstractSystemMatrix
584     //
585 jfenwick 3259 class_<escript::AbstractSystemMatrix,escript::ASM_ptr>("Operator","",init<>()) // Doco goes in the empty string param
586 jfenwick 2625 .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty,":rtype: ``bool``\n"
587     ":return: True if matrix is empty")
588     .def("solve",&escript::AbstractSystemMatrix::solve, args("in","options"),
589     ":return: the solution *u* of the linear system *this*u=in*\n\n:param in:\n:type in: `Data`")
590     .def("of",&escript::AbstractSystemMatrix::vectorMultiply,args("right"),
591     "matrix*vector multiplication")
592     .def("saveMM",&escript::AbstractSystemMatrix::saveMM, args("fileName"),
593     "writes the matrix to a file using the Matrix Market file format")
594     .def("saveHB",&escript::AbstractSystemMatrix::saveHB, args("filename"),
595     "writes the matrix to a file using the Harwell-Boeing file format")
596     .def("resetValues",&escript::AbstractSystemMatrix::resetValues, "resets the matrix entries")
597 jgs 102 .def(self*other<escript::Data>());
598 gross 1364 //
599     // Interface for AbstractTransportProblem
600     //
601 jfenwick 3259 class_<escript::AbstractTransportProblem, escript::ATP_ptr>("TransportProblem","",init<>()) // Doco goes in the empty string param
602 jfenwick 2625 .def("isEmpty",&escript::AbstractTransportProblem::isEmpty,":rtype: ``int``")
603 gross 2987 .def("solve",&escript::AbstractTransportProblem::solve, args("u0","source","dt", "options"),
604     "returns the solution *u* for a time step *dt>0* with initial value u0\n\n:rtype: `Data`\n"
605 jfenwick 2625 ":param source:\n:type source: `Data`")
606     .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint,
607     args("source", "q", "r","factor"),
608     "inserts constraint *u_{,t}=r* where *q>0* into the problem using a weighting factor")
609     .def("reset",&escript::AbstractTransportProblem::resetTransport,
610     "resets the transport operator typically as they have been updated.")
611 gross 1841 .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
612 gross 1859 .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize)
613     .def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize);
614 jgs 102
615 jfenwick 1897 // Functions to modify global parameters
616     def("setEscriptParamInt",escript::setEscriptParamInt,
617 jfenwick 2625 (arg("name"), arg("value")=0), "Modify the value of an escript tuning parameter\n\n"
618     ":param name:\n:type name: ``string``\n:param value:\n:type value: ``int``");
619 jfenwick 1897 def("getEscriptParamInt",escript::getEscriptParamInt,
620 jfenwick 2625 (arg("name"),arg("sentinel")=0), "Read the value of an escript tuning paramter\n\n"
621     ":param name: parameter to lookup\n:type name: ``string``\n:param sentinel: Value to be returned if ``name`` is not a known parameter\n"
622     ":type sentinel: ``int``");
623     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.");
624 jfenwick 1897
625 jfenwick 2799
626     def("resolveGroup", escript::resolveGroup);
627 jfenwick 2827
628     #ifdef IKNOWWHATIMDOING
629    
630     def("applyBinaryCFunction", escript::applyBinaryCFunction, (arg("function"), arg("outshape"),
631     arg("in1"),
632     arg("in2"))
633     );
634     #endif
635    
636 jfenwick 3059 def("_condEval", escript::condEval, (arg("mask"), arg("trueval"), arg("falseval")));
637 jfenwick 3031
638 jgs 102 //
639     // Register esysExceptionTranslator
640     //
641     register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);
642     }

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