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/*******************************************************
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* Copyright (c) 2003-2010 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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* 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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#include "esysUtils/Esys_MPI.h"
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#include "../Dudley.h"
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#include "MeshAdapter.h"
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#include "MeshAdapterFactory.h"
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#include "SystemMatrixAdapter.h"
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#include "TransportProblemAdapter.h"
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#include "DudleyAdapterException.h"
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// #include "esysUtils/EsysException.h"
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#include "esysUtils/esysExceptionTranslator.h"
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#include "escript/AbstractContinuousDomain.h"
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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/detail/defaults_gen.hpp>
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#include <boost/version.hpp>
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using namespace boost::python;
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Dudley is the python module name that contains the interfaces
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to the C++ wrapper to dudley.
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\section class_desc Class Description:
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\section class_limits Class Limitations:
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\section class_conds Class Conditions of Use:
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\section throws Throws:
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BOOST_PYTHON_MODULE(dudleycpp)
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// This feature was added in boost v1.34
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#if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
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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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// NOTE: The return_value_policy is necessary for functions that
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register_exception_translator<dudley::DudleyAdapterException>(&(esysUtils::esysExceptionTranslator));
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def("LoadMesh",dudley::loadMesh,
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(arg("fileName")="file.nc"),":rtype: `Domain`"
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/* ,return_value_policy<manage_new_object>());*/
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def("ReadMesh",dudley::readMesh,
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(arg("fileName")="file.fly",arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1, arg("optimize")=true)
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/* ,return_value_policy<manage_new_object>());*/
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,"Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.\n\n"
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":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
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":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
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":type integrationOrder: ``int``\n"
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":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
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":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``");
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def("ReadGmsh",dudley::readGmsh,
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(arg("fileName")="file.msh",
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arg("integrationOrder")=-1,
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arg("reducedIntegrationOrder")=-1,
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arg("useMacroElements")=false)
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// ,return_value_policy<manage_new_object>());
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,"Read a gmsh mesh file\n\n"
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":rtype: `Domain`\n:param fileName:\n:type fileName: ``string``\n"
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":param integrationOrder: order of the quadrature scheme. If *integrationOrder<0* the integration order is selected independently.\n"
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":type integrationOrder: ``int``\n"
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":param reducedIntegrationOrder: order of the quadrature scheme. If *reducedIntegrationOrder<0* the integration order is selected independently.\n"
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":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``\n"
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":param useMacroElements: Enable the usage of macro elements instead of second order elements.\n:type useMacroElements: ``bool``"
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def ("Brick",dudley::brick,
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(arg("n0")=1,arg("n1")=1,arg("n2")=1,
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arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,
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arg("periodic0")=false,arg("periodic1")=false,arg("periodic2")=false,
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arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
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arg("useElementsOnFace")=false,
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arg("useFullElementOrder")=false,
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arg("optimize")=false)
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,"Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2]."
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"\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n:param n2:\n:type n2:\n"
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":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
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":param l0: length of side 0\n:param l1:\n:param l2:\n"
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":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
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":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
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":param useElementsOnFace: whether or not to use elements on face\n"
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":type useElementsOnFace: ``int``"
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":param periodic0: whether or not boundary conditions are periodic\n"
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":param periodic1:\n:param periodic2:\n"
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":param useFullElementOrder:\n:param optimize:\n"
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":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
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def ("Rectangle",dudley::rectangle,
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(arg("n0")=1,arg("n1")=1,arg("order")=1,
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arg("l0")=1.0,arg("l1")=1.0,
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arg("periodic0")=false,arg("periodic1")=false,
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arg("integrationOrder")=-1, arg("reducedIntegrationOrder")=-1,
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arg("useElementsOnFace")=false,
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arg("useFullElementOrder")=false,
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arg("optimize")=false)
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,"Creates a rectangular mesh with n0 x n1 elements over the brick [0,l0] x [0,l1]."
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"\n\n:param n0:\n:type n0:\n:param n1:\n:type n1:\n"
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":param order: =1, =-1 or =2 gives the order of shape function. If -1 macro elements of order 1 are used.\n"
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":param l0: length of side 0\n:param l1:\n"
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":param integrationOrder: order of the quadrature scheme. If integrationOrder<0 the integration order is selected independently.\n"
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":param reducedIntegrationOrder: order of the quadrature scheme. If reducedIntegrationOrder<0 the integration order is selected independently.\n"
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":param useElementsOnFace: whether or not to use elements on face\n"
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":type useElementsOnFace: ``int``"
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":param periodic0: whether or not boundary conditions are periodic\n"
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":param periodic1:\n"
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":param useFullElementOrder:\n:param optimize:\n"
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":param useMacroElements: Enable the usage of first order macro elements.\n:type useMacroElements: ``bool``\n"
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":param optimize: Enable optimisation of node labels\n:type optimize: ``bool``"
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class_<dudley::MeshAdapter, bases<escript::AbstractContinuousDomain> >
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("MeshAdapter","A concrete class representing a domain. For more details, please consult the c++ documentation.",init<optional <Dudley_Mesh*> >())
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.def(init<const dudley::MeshAdapter&>())
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.def("write",&dudley::MeshAdapter::write,args("filename"),
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"Write the current mesh to a file with the given name.")
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.def("print_mesh_info",&dudley::MeshAdapter::Print_Mesh_Info,(arg("full")=false),
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":param full:\n:type full: ``bool``")
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.def("dump",&dudley::MeshAdapter::dump,args("fileName")
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,"dumps the mesh to a file with the given name.")
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.def("getDescription",&dudley::MeshAdapter::getDescription,
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":return: a description for this domain\n:rtype: ``string``")
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.def("getDim",&dudley::MeshAdapter::getDim,":rtype: ``int``")
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.def("getDataShape",&dudley::MeshAdapter::getDataShape, args("functionSpaceCode"),
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":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
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.def("getNumDataPointsGlobal",&dudley::MeshAdapter::getNumDataPointsGlobal,
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":return: the number of data points summed across all MPI processes\n"
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.def("addPDEToSystem",&dudley::MeshAdapter::addPDEToSystem,
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args("mat", "rhs","A", "B", "C", "D", "X", "Y", "d", "y"),
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"adds a PDE onto the stiffness matrix mat and a rhs\n\n"
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":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
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":param A:\n:type A: `Data`\n"
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":param B:\n:type B: `Data`\n"
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":param C:\n:type C: `Data`\n"
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":param D:\n:type D: `Data`\n"
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":param X:\n:type X: `Data`\n"
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":param Y:\n:type Y: `Data`\n"
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":param d:\n:type d: `Data`\n"
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.def("addPDEToLumpedSystem",&dudley::MeshAdapter::addPDEToLumpedSystem,
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args("mat", "D", "d"),
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"adds a PDE onto the lumped stiffness matrix\n\n"
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":param mat:\n:type mat: `Data`\n"
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":param D:\n:type D: `Data`\n"
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":param d:\n:type d: `Data`\n")
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.def("addPDEToRHS",&dudley::MeshAdapter::addPDEToRHS,
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args("rhs", "X", "Y", "y", "y_contact"),
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"adds a PDE onto the stiffness matrix mat and a rhs\n\n"
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":param rhs:\n:type rhs: `Data`\n"
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":param X:\n:type X: `Data`\n"
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":param Y:\n:type Y: `Data`\n"
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":param y:\n:type y: `Data`\n"
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.def("addPDEToTransportProblem",&dudley::MeshAdapter::addPDEToTransportProblem,
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args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
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":param tp:\n:type tp: `TransportProblemAdapter`\n"
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":param source:\n:type source: `Data`\n"
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":param M:\n:type M: `Data`\n"
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":param A:\n:type A: `Data`\n"
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":param B:\n:type B: `Data`\n"
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":param C:\n:type C: `Data`\n"
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":param D:\n:type D: `Data`\n"
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":param X:\n:type X: `Data`\n"
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":param Y:\n:type Y: `Data`\n"
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":param d:\n:type d: `Data`\n"
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":param y:\n:type y: `Data`\n"
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":param d_contact:\n:type d_contact: `Data`\n"
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":param y_contact:\n:type y_contact: `Data`\n"
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.def("newOperator",&dudley::MeshAdapter::newSystemMatrix,
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args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
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"creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
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":param row_blocksize:\n:type row_blocksize: ``int``\n"
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":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
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":param column_blocksize:\n:type column_blocksize: ``int``\n"
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":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
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":param type:\n:type type: ``int``\n"
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.def("newTransportProblem",&dudley::MeshAdapter::newTransportProblem,
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args("theta", "blocksize", "functionspace", "type"),
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"creates a TransportProblemAdapter\n\n"
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":param theta:\n:type theta: ``float``\n"
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":param blocksize:\n:type blocksize: ``int``\n"
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":param functionspace:\n:type functionspace: `FunctionSpace`\n"
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":param type:\n:type type: ``int``\n"
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.def("getSystemMatrixTypeId",&dudley::MeshAdapter::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 when a particular solver, package, perconditioner, and symmetric matrix is used.\n"
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":param solver:\n:type solver: ``int``\n"
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":param preconditioner:\n:type preconditioner: ``int``\n"
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":param package:\n:type package: ``int``\n"
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":param symmetry:\n:type symmetry: ``int``\n"
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.def("getTransportTypeId",&dudley::MeshAdapter::getTransportTypeId,
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args("solver", "preconditioner", "package", "symmetry"),
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":return: the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.\n"
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":param solver:\n:type solver: ``int``\n"
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":param preconditioner:\n:type preconditioner: ``int``\n"
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":param package:\n:type package: ``int``\n"
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":param symmetry:\n:type symmetry: ``int``\n"
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.def("setX",&dudley::MeshAdapter::setNewX,
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args("arg"), "assigns new location to the domain\n\n:param arg:\n:type arg: `Data`")
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.def("getX",&dudley::MeshAdapter::getX, ":return: locations in the FEM nodes\n\n"
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.def("getNormal",&dudley::MeshAdapter::getNormal,
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":return: boundary normals at the quadrature point on the face elements\n"
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.def("getSize",&dudley::MeshAdapter::getSize,":return: the element size\n"
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.def("saveDX",&dudley::MeshAdapter::saveDX,args("filename" ,"arg"),
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"Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier"
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"\n\n:param filename: \n:type filename: ``string``\n"
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"\n:param arg: \n:type arg: ``dict``\n")
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.def("saveVTK",&dudley::MeshAdapter::saveVTK,
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args("filename" ,"arg", "metadata", "metadata_schema"),
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"Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier"
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"\n\n:param filename:\n:type filename: ``string``\n"
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":param arg:\n:type arg: ``dict``\n"
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":param metadata:\n:type metadata: ``string``\n"
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":param metadata_schema:\n:type metadata_schema: ``string``\n"
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.def("setTagMap",&dudley::MeshAdapter::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",&dudley::MeshAdapter::getTag,args("name"),":return: tag id for "
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"``name``\n:rtype: ``string``")
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.def("isValidTagName",&dudley::MeshAdapter::isValidTagName,args("name"),
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":return: True is ``name`` corresponds to a tag\n:rtype: ``bool``")
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.def("showTagNames",&dudley::MeshAdapter::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
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.def("getMPISize",&dudley::MeshAdapter::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
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.def("getMPIRank",&dudley::MeshAdapter::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
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.def("MPIBarrier",&dudley::MeshAdapter::MPIBarrier,"Wait until all processes have reached this point")
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.def("onMasterProcessor",&dudley::MeshAdapter::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
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class_<dudley::SystemMatrixAdapter, bases<escript::AbstractSystemMatrix> >
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("OperatorAdapter","A concrete class representing an operator. For more details, please see the c++ documentation.", no_init)
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.def("print_matrix_info",&dudley::SystemMatrixAdapter::Print_Matrix_Info,(arg("full")=false),"prints information about a system matrix")
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.def("nullifyRowsAndCols",&dudley::SystemMatrixAdapter::nullifyRowsAndCols)
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.def("resetValues",&dudley::SystemMatrixAdapter::resetValues, "resets the matrix entries")
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.def("saveMM",&dudley::SystemMatrixAdapter::saveMM,args("fileName"),
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"writes the matrix to a file using the Matrix Market file format")
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.def("saveHB",&dudley::SystemMatrixAdapter::saveHB, args("filename"),
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"writes the matrix to a file using the Harwell-Boeing file format");
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class_<dudley::TransportProblemAdapter, bases<escript::AbstractTransportProblem> >
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("TransportProblemAdapter","",no_init)
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.def("getSafeTimeStepSize",&dudley::TransportProblemAdapter::getSafeTimeStepSize)
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.def("getUnlimitedTimeStepSize",&dudley::TransportProblemAdapter::getUnlimitedTimeStepSize)
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.def("resetTransport",&dudley::TransportProblemAdapter::resetTransport,
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"resets the transport operator typically as they have been updated");
added
removed
dudley/src/CPPAdapter/dudleycpp.cpp
