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/******************************************************* |
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* |
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* Copyright (c) 2003-2009 by University of Queensland |
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* Earth Systems Science Computational Center (ESSCC) |
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* http://www.uq.edu.au/esscc |
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* |
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* Primary Business: Queensland, Australia |
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* Licensed under the Open Software License version 3.0 |
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* http://www.opensource.org/licenses/osl-3.0.php |
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* |
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*******************************************************/ |
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#include "Data.h" |
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#include "FunctionSpace.h" |
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#include "FunctionSpaceFactory.h" |
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#include "DataFactory.h" |
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#include "AbstractContinuousDomain.h" |
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#include "AbstractDomain.h" |
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#include "Utils.h" |
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jgs |
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#include "AbstractSystemMatrix.h" |
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gross |
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#include "AbstractTransportProblem.h" |
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#include "DataVector.h" |
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ksteube |
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#include "paso/Paso_MPI.h" |
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#include "EscriptParams.h" |
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#include "TestDomain.h" |
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extern "C" { |
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#include "esysUtils/blocktimer.h" |
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} |
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robwdcock |
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#include "esysUtils/esysExceptionTranslator.h" |
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gross |
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#include <boost/version.hpp> |
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#include <boost/python.hpp> |
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#include <boost/python/module.hpp> |
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#include <boost/python/def.hpp> |
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#include <boost/python/object.hpp> |
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#include <boost/python/tuple.hpp> |
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gross |
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#include <boost/python/numeric.hpp> |
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#include <boost/smart_ptr.hpp> |
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#include <boost/version.hpp> |
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using namespace boost::python; |
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/*! \mainpage Esys Documentation |
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* |
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* \version 3.0.0 |
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* |
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* - \ref escript |
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* |
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* - \ref esys_exception "Esys Exception" |
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* |
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* - \ref finley |
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* |
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* - <a href="../../epydoc/index.html">Python module documentation (epydoc generated)</a> |
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* |
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*/ |
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|
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/*! \page escript Escript |
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* Escript is the python module that contains the interfaces |
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* to the C++ side of escript. |
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* |
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* |
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* |
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* \section class_desc Class Description: |
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* Data |
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* |
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* \section class_limits Class Limitations: |
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* None |
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* |
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* \section class_conds Class Conditions of Use: |
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* None |
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* |
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* \section class_throws Throws: |
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* None |
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* |
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*/ |
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BOOST_PYTHON_MODULE(escriptcpp) |
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{ |
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#if BOOST_VERSION >= 103500 |
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// params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures |
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docstring_options docopt(true,true,false); |
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#endif |
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def("setNumberOfThreads",escript::setNumberOfThreads,"Use of this method is strongly discouraged."); |
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def("getNumberOfThreads",escript::getNumberOfThreads,"Return the maximum number of threads" |
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" available to OpenMP."); |
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def("releaseUnusedMemory",escript::releaseUnusedMemory); |
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def("blocktimer_initialize",blocktimer_initialize); |
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def("blocktimer_reportSortByName",blocktimer_reportSortByName); |
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def("blocktimer_reportSortByTime",blocktimer_reportSortByTime); |
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def("blocktimer_increment",blocktimer_increment); |
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def("blocktimer_time",blocktimer_time); |
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def("getVersion",escript::getSvnVersion,"This method will only report accurate version numbers for clean checkouts."); |
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def("printParallelThreadCounts",escript::printParallelThreadCnt); |
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def("getMPISizeWorld",escript::getMPISizeWorld,"Return number of MPI processes in the job."); |
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def("getMPIRankWorld",escript::getMPIRankWorld,"Return the rank of this process in the MPI World."); |
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def("MPIBarrierWorld",escript::MPIBarrierWorld,"Wait until all MPI processes have reached this point."); |
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def("getMPIWorldMax",escript::getMPIWorldMax,"\nEach MPI process calls this function with a" |
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" value for arg1. The maximum value is computed and returned.\n\n:rtype: int"); |
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def("getMPIWorldSum",escript::getMPIWorldSum,"\nEach MPI process calls this function with a" |
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" value for arg1. The values are added up and the total value is returned.\n\n:rtype: int"); |
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def("getMachinePrecision",escript::getMachinePrecision); |
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def("getMaxFloat",escript::getMaxFloat); |
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def("_saveDataCSV",escript::saveDataCSV, (args("filename","arg","sep","csep"), arg("append")=false), |
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"Saves data objects passed in a python dictionary to a file.\n" |
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"The data objects must be over the same domain and be able to be interpolated to the same FunctionSpace.\n" |
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"If one of the dictionary keys is named ``mask``, then only samples where ``mask`` has a positive\n" |
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"value will be written to the file.\n\n" |
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"A header line giving the names of each column will be output first.\n" |
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"The keys given in the dictionary will be used to name columns.\n" |
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"Then the data will be output, one line per sample (for all data).\n" |
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"\n:param filename:\n:type filename: ``string``\n" |
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":param arg: dictionary of named `Data` objects. If one is called ``mask`` it must be scalar data." |
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"\n:type arg: ``dict``\n" |
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":param sep:separator for columns (defaults to \", \"\n:type sep:``string``\n" |
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":param csep:separator for fields within data object (defaults to \"_\"\n:type csep:``string``\n" |
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":param append: If True, write to the end of ``filename``\n:type append: ``string``\n"); |
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// |
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// Interface for AbstractDomain |
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// |
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class_<escript::AbstractDomain, escript::Domain_ptr>("Domain","Base class for all domains.",no_init) |
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.def("getStatus",&escript::AbstractDomain::getStatus,"The status of a domain changes whenever the domain is modified\n\n:rtype: int") |
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.def("setTagMap",&escript::AbstractDomain::setTagMap,args("name","tag"), |
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"Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n" |
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":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain") |
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.def("getTag",&escript::AbstractDomain::getTag,args("name"),":return: tag id for " |
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"``name``\n:rtype: ``string``") |
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.def("isValidTagName",&escript::AbstractDomain::isValidTagName,args("name"), |
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":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``") |
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.def("showTagNames",&escript::AbstractDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``") |
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.def("getX",&escript::AbstractDomain::getX,":rtype: `Data`\n:return: Locations in the" |
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"`Domain`. FunctionSpace is chosen appropriately") |
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.def("getDim",&escript::AbstractDomain::getDim,":rtype: `int`\n:return: Spatial dimension of the `Domain`") |
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.def("getNormal",&escript::AbstractDomain::getNormal,":rtype: `escript`\n:return: Boundary normals") |
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.def("getSize",&escript::AbstractDomain::getSize,":return: the local size of samples. The function space is chosen appropriately\n:rtype: `Data`") |
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.def("saveVTK",&escript::AbstractDomain::saveVTK,args("filename","arg", "metadata" |
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, "metadata_schema"), |
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":param filename: \n:type filename: ``string``\n:param arg: items to be added" |
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"\n:type arg: ``dict``\n:param metadata: string representing some meta data to be added\n:type metadata: ``string``" |
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"\n:param metadata_schema: schema type for metadata\n:type metadata_schema: ``string``") |
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.def("dump",&escript::AbstractDomain::dump,args("filename"),"Dumps the domain to a file" |
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":param filename:\n:type filename: string") |
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.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``" |
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"\n:param arg:\n:type arg: `dict`") |
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.def("getMPISize",&escript::AbstractDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``") |
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.def("getMPIRank",&escript::AbstractDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``") |
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.def("MPIBarrier",&escript::AbstractDomain::MPIBarrier,"Wait until all processes have reached this point") |
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.def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`") |
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.def(self == self) |
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.def(self != self); |
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// |
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// Interface for AbstractContinuousDomain |
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// |
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class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain","Class representing continuous domains",no_init) |
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.def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId, |
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args("solver", "preconditioner", "package", "symmetry"), |
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":return: the identifier of the matrix type to be used for the global stiffness matrix " |
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"when a particular solver package and symmetric matrix is used.\n" |
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":rtype: int") |
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.def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId, |
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args("solver", "preconditioner", "package", "symmetry")); |
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jgs |
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// |
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jfenwick |
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// Interface for TestDomain |
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// |
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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>()); |
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// This is the only python visible way to get a TestDomain |
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jfenwick |
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def("getTestDomainFunctionSpace",&escript::getTestDomainFunctionSpace, args("dpps", |
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"samples"), |
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"For testing only. May be removed without notice."); |
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// |
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// Interface for FunctionSpace |
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// |
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jfenwick |
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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 |
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fs_definer.def("getDim",&escript::FunctionSpace::getDim,":return: the spatial dimension of the underlying domain.\n:rtype: int"); |
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// fs_definer.def("getDomain",&escript::FunctionSpace::getDomain, |
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// return_internal_reference<>()); |
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jfenwick |
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fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython,":return: the underlying `Domain` for this FunctionSpace.\n:rtype: `Domain`"); |
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fs_definer.def("getX",&escript::FunctionSpace::getX,"\n:return: a function whose values are its input coordinates. ie an identity function.\n:rtype: `Data`"); |
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fs_definer.def("getNormal",&escript::FunctionSpace::getNormal,":return: the surface normal field.\n\n:rtype: `Data`"); |
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fs_definer.def("getSize",&escript::FunctionSpace::getSize,":return: sample size\n:rtype: `Data`"); |
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fs_definer.def("setTags",&escript::FunctionSpace::setTags,args("newtag","mask"), |
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"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`"); |
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fs_definer.def("getTagFromDataPointNo", |
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jfenwick |
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&escript::FunctionSpace::getTagFromDataPointNo,":return: the tag associated with the given sample number.\n:rtype: int"); |
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fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo,args("dataPointNo"),":return: the reference number associated with ``dataPointNo``\n:rtype: int "); |
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fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags,":return: a list of the tags used in this function space\n:rtype: ``list``"); |
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phornby |
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fs_definer.def("__str__", &escript::FunctionSpace::toString); |
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trankine |
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fs_definer.def(self == self); |
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fs_definer.def(self != self); |
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jgs |
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// |
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// Interface for Data |
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// |
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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<>() ) |
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// various constructors for Data objects |
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.def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand"))) |
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.def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand"))) |
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.def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what"))) |
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.def(init<const escript::Data&>()) |
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// Note for Lutz, Need to specify the call policy in order to return a |
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// reference. In this case return_internal_reference. |
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.def("__str__",&escript::Data::toString) |
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.def("getDomain",&escript::Data::getDomainPython,":rtype: `Domain`") |
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.def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>(),":rtype: `FunctionSpace`") |
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.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.") |
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.def("isProtected",&escript::Data::isProtected,"Can this instance be modified.\n:rtype: ``bool``") |
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.def("setProtection",&escript::Data::setProtection,"Disallow modifications to this data object\n\n:note: This method does not allow you to undo protection.") |
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.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``") |
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.def("getRank",&escript::Data::getDataPointRank,":return: the number of indicies required to address a component of a datapoints\n:rtype: positive ``int``") |
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.def("dump",&escript::Data::dump,args("fileName"),"Save the data as a netCDF file\n\n:param fileName: \n:type fileName: ``string``") |
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.def("toListOfTuples",&escript::Data::toListOfTuples, (arg("scalarastuple")=false), |
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"Return the datapoints of this object in a list. Each datapoint is stored as a tuple.\n\n" |
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":param scalarastuple: if True, scalar data will be wrapped as a tuple." |
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" True => [(0), (1), (2)]; False => [0, 1, 2]") |
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.def("copyWithMask",&escript::Data::copyWithMask,args("other","mask"), |
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"Selectively copy values from ``other`` `Data`." |
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"Datapoints which correspond to postive values in ``mask`` will be copied from ``other``\n" |
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"\n:param other: source of values\n" |
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":type other: `Data`\n:param mask:\n:type mask: Scalar `Data`") |
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.def("setTaggedValue",&escript::Data::setTaggedValue,args("tagKey","value"), |
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"Set the value of tagged Data.\n\n:param tagKey: tag to update\n:type tagKey: ``int``\n") |
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.def("setTaggedValue",&escript::Data::setTaggedValueByName,args("name","value"),":param name: tag to update\n:type name: ``string``\n" |
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":param value: value to set tagged data to\n:type value: ``object`` which acts like an array, ``tuple`` or ``list``\n") |
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.def("getNumberOfDataPoints",&escript::Data::getNumDataPoints,":rtype: ``int``\n:return: Number of datapoints in the object") |
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.def("isExpanded",&escript::Data::isExpanded,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.") |
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.def("isTagged",&escript::Data::isTagged,":rtype: ``bool``\n:return: True if this ``Data`` is expanded.") |
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.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.") |
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.def("isLazy",&escript::Data::isLazy,":rtype: ``bool``\n:return: True if this ``Data`` is lazy.") |
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.def("isReady",&escript::Data::isReady,":rtype: ``bool``\n:return: True if this ``Data`` is not lazy.") |
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jfenwick |
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.def("hasNoSamples", &escript::Data::hasNoSamples,":rtype: ``bool``\n:return: True if this ``Data`` (locally)" |
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" contains no samples.") |
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jfenwick |
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.def("expand",&escript::Data::expand,"Convert the data to expanded representation if it is not expanded already.") |
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.def("tag",&escript::Data::tag,"Convert data to tagged representation if it is not already tagged or expanded") |
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.def("resolve",&escript::Data::resolve,"Convert the data to non-lazy representation.") |
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.def("copy",&escript::Data::copy,args("other"),"Make this object a copy of ``other``\n" |
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"\n:note: The two objects will act independently from now on. That is, changing ``other`` " |
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"after this call will not change this object and vice versa.") |
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.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.") |
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.def("delay",&escript::Data::delay,"Convert this object into lazy representation") |
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|
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.def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject,args("dataPointNo","value")) |
| 254 |
gross |
1034 |
.def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray) |
| 255 |
jfenwick |
2625 |
.def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint,"\nModify the value of a single datapoint.\n\n:param dataPointNo:\n" |
| 256 |
|
|
":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.") |
| 257 |
|
|
.def("getTupleForDataPoint",&escript::Data::getValueOfDataPointAsTuple,args("dataPointNo"), |
| 258 |
|
|
":return: Value of the specified datapoint\n:rtype: ``tuple``\n:param dataPointNo: datapoint to access\n:type dataPointNo: ``int``") |
| 259 |
|
|
.def("getTupleForGlobalDataPoint",&escript::Data::getValueOfGlobalDataPointAsTuple,args("procNo","dataPointNo"),"Get a specific datapoint from a specific process\n\n" |
| 260 |
|
|
":rtype: ``tuple``\n:param procNo: MPI rank of the process\n:type procNo: positive ``int``" |
| 261 |
|
|
"\n:param dataPointNo: datapoint to access\n:type dataPointNo: int") |
| 262 |
|
|
.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.") |
| 263 |
|
|
.def("interpolate",&escript::Data::interpolate,args("functionspace"),"Interpolate this object's values into a new functionspace.") |
| 264 |
jfenwick |
2646 |
.def("interpolateTable", &escript::Data::interpolateFromTable2DP, |
| 265 |
gross |
2649 |
(arg("table"),arg("Amin"),arg("Astep"), arg("B"), arg("Bmin"), arg("Bstep"), arg("undef")=1.e50), |
| 266 |
jfenwick |
2628 |
"Creates a new Data object by interpolating using the source data (which are\n" |
| 267 |
jfenwick |
2646 |
"looked up in ``table``)\n``A`` must be the outer dimension on the table\n\n" |
| 268 |
jfenwick |
2628 |
":param table: two dimensional collection of values\n" |
| 269 |
|
|
":param Amin: The base of locations in table\n:type Amin: float\n" |
| 270 |
|
|
":param Astep: size of gap between each item in the table\n:type Astep: float\n" |
| 271 |
|
|
":param undef: upper bound on interpolated values\n:type undef: float\n" |
| 272 |
|
|
":param B: Scalar representing the second coordinate to be mapped into the table\n" |
| 273 |
|
|
":type B: `Data`\n" |
| 274 |
|
|
":param Bmin: The base of locations in table for 2nd dimension\n:type Bmin: float\n" |
| 275 |
|
|
":param Bstep: size of gap between each item in the table for 2nd dimension\n:type Bstep: float\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 |
jfenwick |
2646 |
.def("interpolateTable", &escript::Data::interpolateFromTable1DP, |
| 280 |
gross |
2649 |
(arg("table"),arg("Amin"),arg("Astep"), arg("undef")=1.e50), |
| 281 |
jfenwick |
2646 |
"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 |
|
|
":raise RuntimeError(DataException): if the cordinates do not map into the table or if the interpolated value is above ``undef``" |
| 288 |
|
|
"\n:rtype: `Data`" |
| 289 |
|
|
) |
| 290 |
jfenwick |
2628 |
|
| 291 |
jfenwick |
2646 |
|
| 292 |
gross |
921 |
.def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint) |
| 293 |
jfenwick |
2476 |
.def("maxGlobalDataPoint",&escript::Data::maxGlobalDataPoint) |
| 294 |
jfenwick |
2625 |
.def("saveDX",&escript::Data::saveDX,args("fileName"),"Save the object in DX format.\n\n" |
| 295 |
|
|
":param fileName: filename\n:type fileName: string") |
| 296 |
|
|
.def("saveVTK",&escript::Data::saveVTK, args("fileName"),"Save the object in VTK format.\n\n" |
| 297 |
|
|
":param fileName: \n:type fileName: string") |
| 298 |
|
|
.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") |
| 299 |
gross |
285 |
// Unary functions for Data |
| 300 |
|
|
.def("_interpolate",&escript::Data::interpolate) |
| 301 |
|
|
.def("_grad",&escript::Data::gradOn) |
| 302 |
|
|
.def("_grad",&escript::Data::grad) |
| 303 |
|
|
.def("_transpose",&escript::Data::transpose) |
| 304 |
|
|
.def("_trace",&escript::Data::trace) |
| 305 |
|
|
.def("_maxval",&escript::Data::maxval) |
| 306 |
|
|
.def("_minval",&escript::Data::minval) |
| 307 |
gross |
698 |
.def("_wherePositive",&escript::Data::wherePositive) |
| 308 |
|
|
.def("_whereNegative",&escript::Data::whereNegative) |
| 309 |
|
|
.def("_whereNonNegative",&escript::Data::whereNonNegative) |
| 310 |
|
|
.def("_whereNonPositive",&escript::Data::whereNonPositive) |
| 311 |
jgs |
571 |
.def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0)) |
| 312 |
|
|
.def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0)) |
| 313 |
ksteube |
876 |
.def("_erf",&escript::Data::erf) |
| 314 |
gross |
285 |
.def("_sin",&escript::Data::sin) |
| 315 |
|
|
.def("_cos",&escript::Data::cos) |
| 316 |
|
|
.def("_tan",&escript::Data::tan) |
| 317 |
|
|
.def("_asin",&escript::Data::asin) |
| 318 |
|
|
.def("_acos",&escript::Data::acos) |
| 319 |
|
|
.def("_atan",&escript::Data::atan) |
| 320 |
|
|
.def("_sinh",&escript::Data::sinh) |
| 321 |
|
|
.def("_cosh",&escript::Data::cosh) |
| 322 |
|
|
.def("_tanh",&escript::Data::tanh) |
| 323 |
|
|
.def("_asinh",&escript::Data::asinh) |
| 324 |
|
|
.def("_acosh",&escript::Data::acosh) |
| 325 |
|
|
.def("_atanh",&escript::Data::atanh) |
| 326 |
|
|
.def("_exp",&escript::Data::exp) |
| 327 |
|
|
.def("_sqrt",&escript::Data::sqrt) |
| 328 |
|
|
.def("_log10",&escript::Data::log10) |
| 329 |
|
|
.def("_log",&escript::Data::log) |
| 330 |
|
|
.def("_sign",&escript::Data::sign) |
| 331 |
ksteube |
775 |
.def("_symmetric",&escript::Data::symmetric) |
| 332 |
|
|
.def("_nonsymmetric",&escript::Data::nonsymmetric) |
| 333 |
gross |
800 |
.def("_trace",&escript::Data::trace) |
| 334 |
gross |
804 |
.def("_swap_axes",&escript::Data::swapaxes) |
| 335 |
gross |
576 |
.def("_eigenvalues",&escript::Data::eigenvalues) |
| 336 |
|
|
.def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13)) |
| 337 |
gross |
285 |
// functions returning a single real number: |
| 338 |
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.") |
| 339 |
|
|
.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.") |
| 340 |
|
|
.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.") |
| 341 |
|
|
.def("_integrateToTuple",&escript::Data::integrateToTuple,":return: Calculate the integral over the function space domain as a python tuple\n:rtype: tuple") |
| 342 |
gross |
285 |
// following implements the python abs operator |
| 343 |
jfenwick |
2625 |
.def("__abs__",&escript::Data::abs,":return: absolute value\n\n:rtype: `Data`") |
| 344 |
jgs |
102 |
// following implements the python "-" negation operator |
| 345 |
jfenwick |
2625 |
.def("__neg__",&escript::Data::neg, ":return: negation of the values in this object\n:rtype: `Data`") |
| 346 |
jgs |
102 |
// following implements the python "+" identity operator |
| 347 |
jfenwick |
2646 |
.def("__pos__",&escript::Data::pos, "\nThe unary + operator\n\n:rtype: `Data`") |
| 348 |
jgs |
102 |
// following two functions implement the python [] operator |
| 349 |
jfenwick |
2625 |
.def("__getitem__",&escript::Data::getItem,"Used by the python [] operator\n\n:rtype: `Data`") |
| 350 |
|
|
.def("__setitem__",&escript::Data::setItemO,"Used by the python [] operator") |
| 351 |
|
|
.def("__setitem__",&escript::Data::setItemD,"Used by the python [] operator") |
| 352 |
jgs |
102 |
// following two functions implement the python ** operator |
| 353 |
jfenwick |
2625 |
.def("__pow__",&escript::Data::powO,"Used by the python ** operator\n\n:rtype: `Data`") |
| 354 |
jgs |
102 |
.def("__pow__",&escript::Data::powD) |
| 355 |
jfenwick |
2625 |
.def("__rpow__",&escript::Data::rpowO,"\nUsed by the python ** operator\n\n:rtype: `Data`") |
| 356 |
jgs |
102 |
// NOTE:: The order of these declarations is important. Anything |
| 357 |
|
|
// declared before the generic declaration isn't found so the generic |
| 358 |
|
|
// version will be called. |
| 359 |
|
|
.def(self + other<object>()) |
| 360 |
|
|
.def(other<object>() + self) |
| 361 |
|
|
.def(self + self) |
| 362 |
gross |
285 |
.def(self += other<object>()) |
| 363 |
|
|
.def(self += self) |
| 364 |
|
|
|
| 365 |
jgs |
102 |
.def(self - other<object>()) |
| 366 |
|
|
.def(other<object>() - self) |
| 367 |
|
|
.def(self - self) |
| 368 |
gross |
285 |
.def(self -= other<object>()) |
| 369 |
|
|
.def(self -= self) |
| 370 |
|
|
|
| 371 |
jgs |
102 |
.def(self * other<object>()) |
| 372 |
|
|
.def(other<object>() * self) |
| 373 |
|
|
.def(self * self) |
| 374 |
gross |
285 |
.def(self *= other<object>()) |
| 375 |
|
|
.def(self *= self) |
| 376 |
|
|
|
| 377 |
jgs |
102 |
.def(self / other<object>()) |
| 378 |
|
|
.def(other<object>() / self) |
| 379 |
|
|
.def(self / self) |
| 380 |
gross |
285 |
.def(self /= other<object>()) |
| 381 |
|
|
.def(self /= self) |
| 382 |
jgs |
102 |
// Need scope resolution due to a bug either in the compiler or |
| 383 |
|
|
// the boost code. This calls operator << for Data. |
| 384 |
|
|
.def(self_ns::str(self)); |
| 385 |
|
|
|
| 386 |
jfenwick |
2635 |
|
| 387 |
jgs |
102 |
// |
| 388 |
|
|
// Factory methods for function space |
| 389 |
|
|
// |
| 390 |
jfenwick |
2625 |
def("ContinuousFunction",escript::continuousFunction,args("domain"), |
| 391 |
|
|
":return: a continuous FunctionSpace (overlapped node values)\n" |
| 392 |
|
|
":rtype: `FunctionSpace`"); |
| 393 |
|
|
def("ReducedContinuousFunction",escript::reducedContinuousFunction,args("domain"), |
| 394 |
|
|
":return: a continuous with reduced order FunctionSpace (overlapped node values on reduced element order)\n" |
| 395 |
|
|
":rtype: `FunctionSpace`"); |
| 396 |
|
|
def("Function",escript::function,args("domain"),":return: a function `FunctionSpace`\n" |
| 397 |
|
|
":rtype: `FunctionSpace`"); |
| 398 |
|
|
def("ReducedFunction",escript::reducedFunction, args("domain"),":return: a function FunctionSpace with reduced integration order\n:rtype: `FunctionSpace`"); |
| 399 |
|
|
def("FunctionOnBoundary",escript::functionOnBoundary, args("domain"), ":return: a function on boundary FunctionSpace\n:rtype: `FunctionSpace`"); |
| 400 |
|
|
def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary, args("domain"), |
| 401 |
|
|
":return: a function on boundary FunctionSpace with reduced integration order\n" |
| 402 |
|
|
":rtype: `FunctionSpace`"); |
| 403 |
|
|
def("FunctionOnContactZero",escript::functionOnContactZero, args("domain"), ":return: Return a FunctionSpace on left side of contact\n:rtype: `FunctionSpace`"); |
| 404 |
|
|
def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero, args("domain"), |
| 405 |
|
|
":return: a FunctionSpace on left side of contact with reduced integration order\n:rtype: `FunctionSpace`"); |
| 406 |
|
|
def("FunctionOnContactOne",escript::functionOnContactOne, args("domain"), ":return: Return a FunctionSpace on right side of contact\n:rtype: `FunctionSpace`"); |
| 407 |
|
|
def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne, args("domain"), |
| 408 |
|
|
":return: Return a FunctionSpace on right side of contact with reduced integration order\n" |
| 409 |
|
|
":rtype: `FunctionSpace`"); |
| 410 |
|
|
def("Solution",escript::solution, args("domain"), ":rtype: `FunctionSpace`"); |
| 411 |
|
|
def("ReducedSolution",escript::reducedSolution, args("domain"), ":rtype: `FunctionSpace`"); |
| 412 |
|
|
def("DiracDeltaFunction",escript::diracDeltaFunction, args("domain"), ":rtype: `FunctionSpace`"); |
| 413 |
jgs |
102 |
|
| 414 |
jfenwick |
2635 |
|
| 415 |
|
|
|
| 416 |
|
|
|
| 417 |
|
|
|
| 418 |
jgs |
102 |
// |
| 419 |
|
|
// Factory methods for Data |
| 420 |
|
|
// |
| 421 |
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`"); |
| 422 |
|
|
def("loadIsConfigured",escript::loadConfigured,":return: True if the load function is configured."); |
| 423 |
jgs |
102 |
def("Scalar",escript::Scalar, |
| 424 |
|
|
(arg("value")=0.0, |
| 425 |
|
|
arg("what")=escript::FunctionSpace(), |
| 426 |
jfenwick |
2625 |
arg("expanded")=false), |
| 427 |
|
|
"Construct a Data object containing scalar data-points.\n\n:param value: scalar value for all points\n" |
| 428 |
|
|
"\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n" |
| 429 |
|
|
":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n" |
| 430 |
|
|
":type expanded: ``bool``"); |
| 431 |
jgs |
102 |
def("Vector",escript::Vector, |
| 432 |
|
|
(arg("value")=0.0, |
| 433 |
|
|
arg("what")=escript::FunctionSpace(), |
| 434 |
jfenwick |
2625 |
arg("expanded")=false), |
| 435 |
|
|
"Construct a Data object containing rank1 data-points.\n\n:param value: scalar value for all points\n" |
| 436 |
|
|
"\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n" |
| 437 |
|
|
":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n" |
| 438 |
|
|
":type expanded: ``bool``"); |
| 439 |
jgs |
102 |
def("Tensor",escript::Tensor, |
| 440 |
|
|
(arg("value")=0.0, |
| 441 |
|
|
arg("what")=escript::FunctionSpace(), |
| 442 |
jfenwick |
2625 |
arg("expanded")=false), |
| 443 |
|
|
"Construct a Data object containing rank2 data-points.\n\n:param value: scalar value for all points\n" |
| 444 |
|
|
"\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n" |
| 445 |
|
|
":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n" |
| 446 |
|
|
":type expanded: ``bool``"); |
| 447 |
jgs |
102 |
def("Tensor3",escript::Tensor3, |
| 448 |
|
|
(arg("value")=0.0, |
| 449 |
|
|
arg("what")=escript::FunctionSpace(), |
| 450 |
jfenwick |
2625 |
arg("expanded")=false), |
| 451 |
|
|
"Construct a Data object containing rank3 data-points.\n\n:param value: scalar value for all points\n" |
| 452 |
|
|
"\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n" |
| 453 |
|
|
":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n" |
| 454 |
|
|
":type expanded: ``bool``" |
| 455 |
|
|
); |
| 456 |
jgs |
102 |
def("Tensor4",escript::Tensor4, |
| 457 |
|
|
(arg("value")=0.0, |
| 458 |
|
|
arg("what")=escript::FunctionSpace(), |
| 459 |
jfenwick |
2625 |
arg("expanded")=false), |
| 460 |
|
|
"Construct a Data object containing rank4 data-points.\n\n:param value: scalar value for all points\n" |
| 461 |
|
|
"\n:rtype: `Data`\n:type value: float\n:param what: FunctionSpace for Data\n:type what: `FunctionSpace`\n" |
| 462 |
|
|
":param expanded: If True, a value is stored for each point. If False, more efficient representations may be used\n" |
| 463 |
|
|
":type expanded: ``bool``" |
| 464 |
|
|
); |
| 465 |
jgs |
102 |
|
| 466 |
|
|
// |
| 467 |
ksteube |
813 |
// Binary operators |
| 468 |
|
|
// |
| 469 |
|
|
def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct, |
| 470 |
jfenwick |
2626 |
(arg("arg0"), |
| 471 |
|
|
arg("arg1"), |
| 472 |
ksteube |
813 |
arg("axis_offset")=0, |
| 473 |
jfenwick |
2625 |
arg("transpose")=0), |
| 474 |
|
|
"Compute a tensor product of two Data objects.\n\n:rtype: `Data`\n:param arg0:\n" |
| 475 |
|
|
":param arg1:\n:param axis_offset:\n:type axis_offset: ``int``\n" |
| 476 |
|
|
":param transpose: 0: transpose neither, 1: transpose arg0, 2: transpose arg1\n" |
| 477 |
|
|
":type transpose: int"); |
| 478 |
ksteube |
813 |
|
| 479 |
|
|
// |
| 480 |
jgs |
102 |
// Interface for AbstractSystemMatrix |
| 481 |
|
|
// |
| 482 |
jfenwick |
2061 |
class_<escript::AbstractSystemMatrix>("Operator","",init<>()) // Doco goes in the empty string param |
| 483 |
jfenwick |
2625 |
.def("isEmpty",&escript::AbstractSystemMatrix::isEmpty,":rtype: ``bool``\n" |
| 484 |
|
|
":return: True if matrix is empty") |
| 485 |
|
|
.def("solve",&escript::AbstractSystemMatrix::solve, args("in","options"), |
| 486 |
|
|
":return: the solution *u* of the linear system *this*u=in*\n\n:param in:\n:type in: `Data`") |
| 487 |
|
|
.def("of",&escript::AbstractSystemMatrix::vectorMultiply,args("right"), |
| 488 |
|
|
"matrix*vector multiplication") |
| 489 |
|
|
.def("saveMM",&escript::AbstractSystemMatrix::saveMM, args("fileName"), |
| 490 |
|
|
"writes the matrix to a file using the Matrix Market file format") |
| 491 |
|
|
.def("saveHB",&escript::AbstractSystemMatrix::saveHB, args("filename"), |
| 492 |
|
|
"writes the matrix to a file using the Harwell-Boeing file format") |
| 493 |
|
|
.def("resetValues",&escript::AbstractSystemMatrix::resetValues, "resets the matrix entries") |
| 494 |
jgs |
102 |
.def(self*other<escript::Data>()); |
| 495 |
gross |
1364 |
// |
| 496 |
|
|
// Interface for AbstractTransportProblem |
| 497 |
|
|
// |
| 498 |
jfenwick |
2061 |
class_<escript::AbstractTransportProblem>("TransportProblem","",init<>()) // Doco goes in the empty string param |
| 499 |
jfenwick |
2625 |
.def("isEmpty",&escript::AbstractTransportProblem::isEmpty,":rtype: ``int``") |
| 500 |
|
|
.def("solve",&escript::AbstractTransportProblem::solve, args("source","dt", "options"), |
| 501 |
|
|
"returns the solution *u* for a time step *dt>0*\n\n:rtype: `Data`\n" |
| 502 |
|
|
":param source:\n:type source: `Data`") |
| 503 |
|
|
.def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue, args("u"), |
| 504 |
|
|
"sets the value for *u* at time *t=0*.") |
| 505 |
|
|
.def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint, |
| 506 |
|
|
args("source", "q", "r","factor"), |
| 507 |
|
|
"inserts constraint *u_{,t}=r* where *q>0* into the problem using a weighting factor") |
| 508 |
|
|
.def("reset",&escript::AbstractTransportProblem::resetTransport, |
| 509 |
|
|
"resets the transport operator typically as they have been updated.") |
| 510 |
gross |
1841 |
.def("resetValues",&escript::AbstractTransportProblem::resetTransport) |
| 511 |
gross |
1859 |
.def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize) |
| 512 |
|
|
.def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize); |
| 513 |
jgs |
102 |
|
| 514 |
jfenwick |
1897 |
// Functions to modify global parameters |
| 515 |
|
|
def("setEscriptParamInt",escript::setEscriptParamInt, |
| 516 |
jfenwick |
2625 |
(arg("name"), arg("value")=0), "Modify the value of an escript tuning parameter\n\n" |
| 517 |
|
|
":param name:\n:type name: ``string``\n:param value:\n:type value: ``int``"); |
| 518 |
jfenwick |
1897 |
def("getEscriptParamInt",escript::getEscriptParamInt, |
| 519 |
jfenwick |
2625 |
(arg("name"),arg("sentinel")=0), "Read the value of an escript tuning paramter\n\n" |
| 520 |
|
|
":param name: parameter to lookup\n:type name: ``string``\n:param sentinel: Value to be returned if ``name`` is not a known parameter\n" |
| 521 |
|
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":type sentinel: ``int``"); |
| 522 |
|
|
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."); |
| 523 |
jfenwick |
1897 |
|
| 524 |
jgs |
102 |
// |
| 525 |
|
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// Register esysExceptionTranslator |
| 526 |
|
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// |
| 527 |
|
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register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator); |
| 528 |
|
|
} |
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