/[escript]/trunk/ripley/src/ripleycpp.cpp
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Annotation of /trunk/ripley/src/ripleycpp.cpp

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Revision 4013 - (hide annotations)
Thu Oct 4 03:13:27 2012 UTC (6 years, 6 months ago) by caltinay
File size: 16700 byte(s)
Implemented netCDF grid reader analogous to binary grid reader in ripley.

1 caltinay 3670
2 jfenwick 3981 /*****************************************************************************
3 caltinay 3670 *
4 caltinay 3781 * Copyright (c) 2003-2012 by University of Queensland
5 jfenwick 3981 * http://www.uq.edu.au
6 caltinay 3670 *
7     * Primary Business: Queensland, Australia
8     * Licensed under the Open Software License version 3.0
9     * http://www.opensource.org/licenses/osl-3.0.php
10     *
11 jfenwick 3981 * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12     * Development since 2012 by School of Earth Sciences
13     *
14     *****************************************************************************/
15 caltinay 3670
16 caltinay 3691 #include <ripley/Brick.h>
17     #include <ripley/Rectangle.h>
18 caltinay 3670 #include <esysUtils/esysExceptionTranslator.h>
19    
20     #include <boost/python.hpp>
21     #include <boost/python/module.hpp>
22     #include <boost/python/def.hpp>
23     #include <boost/python/detail/defaults_gen.hpp>
24     #include <boost/version.hpp>
25    
26     using namespace boost::python;
27    
28 caltinay 3691 namespace ripley {
29 caltinay 3670
30 caltinay 3971 escript::Data readBinaryGrid(std::string filename, escript::FunctionSpace fs,
31     const object& pyFirst, const object& pyNum, const object& pyShape,
32     double fill=0.)
33     {
34     int dim=fs.getDim();
35     std::vector<int> first(dim), numValues(dim), shape;
36    
37     if (extract<tuple>(pyFirst).check() || extract<list>(pyFirst).check()) {
38     if (len(pyFirst)==dim) {
39     for (int i=0; i<dim; i++) {
40     first[i]=extract<int>(pyFirst[i]);
41     }
42     } else
43     throw RipleyException("Argument 'first' has wrong length");
44     } else
45     throw RipleyException("Argument 'first' must be a tuple or list");
46    
47     if (extract<tuple>(pyNum).check() || extract<list>(pyNum).check()) {
48     if (len(pyNum)==dim) {
49     for (int i=0; i<dim; i++) {
50     numValues[i]=extract<int>(pyNum[i]);
51     }
52     } else
53     throw RipleyException("Argument 'numValues' has wrong length");
54     } else
55     throw RipleyException("Argument 'numValues' must be a tuple or list");
56    
57     if (extract<tuple>(pyShape).check() || extract<list>(pyShape).check()) {
58     for (int i=0; i<len(pyShape); i++) {
59     shape.push_back(extract<int>(pyShape[i]));
60     }
61     } else
62     throw RipleyException("Argument 'shape' must be a tuple or list");
63    
64     const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
65     if (!dom)
66     throw RipleyException("Function space must be on a ripley domain");
67    
68    
69     escript::Data res(fill, shape, fs, true);
70    
71     dom->readBinaryGrid(res, filename, first, numValues);
72     return res;
73     }
74    
75 caltinay 4013 escript::Data readNcGrid(std::string filename, std::string varname,
76     escript::FunctionSpace fs, const object& pyFirst, const object& pyNum,
77     const object& pyShape, double fill=0.)
78     {
79     int dim=fs.getDim();
80     std::vector<int> first(dim), numValues(dim), shape;
81    
82     if (extract<tuple>(pyFirst).check() || extract<list>(pyFirst).check()) {
83     if (len(pyFirst)==dim) {
84     for (int i=0; i<dim; i++) {
85     first[i]=extract<int>(pyFirst[i]);
86     }
87     } else
88     throw RipleyException("Argument 'first' has wrong length");
89     } else
90     throw RipleyException("Argument 'first' must be a tuple or list");
91    
92     if (extract<tuple>(pyNum).check() || extract<list>(pyNum).check()) {
93     if (len(pyNum)==dim) {
94     for (int i=0; i<dim; i++) {
95     numValues[i]=extract<int>(pyNum[i]);
96     }
97     } else
98     throw RipleyException("Argument 'numValues' has wrong length");
99     } else
100     throw RipleyException("Argument 'numValues' must be a tuple or list");
101    
102     if (extract<tuple>(pyShape).check() || extract<list>(pyShape).check()) {
103     for (int i=0; i<len(pyShape); i++) {
104     shape.push_back(extract<int>(pyShape[i]));
105     }
106     } else
107     throw RipleyException("Argument 'shape' must be a tuple or list");
108    
109     const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
110     if (!dom)
111     throw RipleyException("Function space must be on a ripley domain");
112    
113    
114     escript::Data res(fill, shape, fs, true);
115    
116     dom->readNcGrid(res, filename, varname, first, numValues);
117     return res;
118     }
119    
120 caltinay 3691 // These wrappers are required to make the shared pointers work through the
121     // Python wrapper
122 caltinay 3670
123 jfenwick 3892 // The double for n? is just to keep python happy when people need to deal with
124 caltinay 3971 // truediv
125 jfenwick 3892 escript::Domain_ptr _brick(double _n0, double _n1, double _n2, const object& l0,
126 caltinay 3781 const object& l1, const object& l2, int d0, int d1, int d2)
127 caltinay 3691 {
128 jfenwick 3892 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1), n2=static_cast<int>(_n2);
129 caltinay 3781 double x0=0., x1=1., y0=0., y1=1., z0=0., z1=1.;
130     if (extract<tuple>(l0).check()) {
131     tuple x=extract<tuple>(l0);
132     if (len(x)==2) {
133     x0=extract<double>(x[0]);
134     x1=extract<double>(x[1]);
135     } else
136     throw RipleyException("Argument l0 must be a float or 2-tuple");
137     } else if (extract<double>(l0).check()) {
138     x1=extract<double>(l0);
139     } else
140     throw RipleyException("Argument l0 must be a float or 2-tuple");
141    
142     if (extract<tuple>(l1).check()) {
143     tuple y=extract<tuple>(l1);
144     if (len(y)==2) {
145     y0=extract<double>(y[0]);
146     y1=extract<double>(y[1]);
147     } else
148     throw RipleyException("Argument l1 must be a float or 2-tuple");
149     } else if (extract<double>(l1).check()) {
150     y1=extract<double>(l1);
151     } else
152     throw RipleyException("Argument l1 must be a float or 2-tuple");
153    
154     if (extract<tuple>(l2).check()) {
155     tuple z=extract<tuple>(l2);
156     if (len(z)==2) {
157     z0=extract<double>(z[0]);
158     z1=extract<double>(z[1]);
159     } else
160     throw RipleyException("Argument l2 must be a float or 2-tuple");
161     } else if (extract<double>(l2).check()) {
162     z1=extract<double>(l2);
163     } else
164     throw RipleyException("Argument l2 must be a float or 2-tuple");
165    
166 caltinay 3791 return escript::Domain_ptr(new Brick(n0,n1,n2, x0,y0,z0, x1,y1,z1, d0,d1,d2));
167 caltinay 3691 }
168 caltinay 3670
169 caltinay 3791 const int _q[]={0x61686969,0x746c4144,0x79616e43};
170 jfenwick 3892 escript::Domain_ptr _rectangle(double _n0, double _n1, const object& l0,
171 caltinay 3781 const object& l1, int d0, int d1)
172 caltinay 3691 {
173 jfenwick 3892 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1);
174 caltinay 3781 double x0=0., x1=1., y0=0., y1=1.;
175     if (extract<tuple>(l0).check()) {
176     tuple x=extract<tuple>(l0);
177     if (len(x)==2) {
178     x0=extract<double>(x[0]);
179     x1=extract<double>(x[1]);
180     } else
181     throw RipleyException("Argument l0 must be a float or 2-tuple");
182     } else if (extract<double>(l0).check()) {
183     x1=extract<double>(l0);
184     } else
185     throw RipleyException("Argument l0 must be a float or 2-tuple");
186    
187     if (extract<tuple>(l1).check()) {
188     tuple y=extract<tuple>(l1);
189     if (len(y)==2) {
190     y0=extract<double>(y[0]);
191     y1=extract<double>(y[1]);
192     } else
193     throw RipleyException("Argument l1 must be a float or 2-tuple");
194     } else if (extract<double>(l1).check()) {
195     y1=extract<double>(l1);
196     } else
197     throw RipleyException("Argument l1 must be a float or 2-tuple");
198    
199 caltinay 3791 return escript::Domain_ptr(new Rectangle(n0,n1, x0,y0, x1,y1, d0,d1));
200 caltinay 3691 }
201 caltinay 3791 std::string _who(){int a[]={_q[0]^42,_q[1]^42,_q[2]^42,0};return (char*)&a[0];}
202 caltinay 3670
203 caltinay 3971 } // end of namespace
204 caltinay 3670
205    
206     BOOST_PYTHON_MODULE(ripleycpp)
207     {
208     // This feature was added in boost v1.34
209     #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
210 caltinay 3691 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
211     docstring_options docopt(true, true, false);
212 caltinay 3670 #endif
213    
214 caltinay 3691 register_exception_translator<ripley::RipleyException>(&(esysUtils::esysExceptionTranslator));
215 caltinay 3670
216 jfenwick 3994 scope().attr("__doc__") = "To use this module, please import esys.ripley";
217    
218    
219 caltinay 3943 def("Brick", ripley::_brick, (arg("n0"),arg("n1"),arg("n2"),arg("l0")=1.0,arg("l1")=1.0,arg("l2")=1.0,arg("d0")=-1,arg("d1")=-1,arg("d2")=-1),
220 caltinay 3691 "Creates a hexagonal mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2].\n\n"
221     ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
222     ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
223     ":param n2: number of elements in direction 2\n:type n2: ``int``\n"
224 caltinay 3781 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
225     ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
226     ":param l2: length of side 2 or coordinate range of side 2\n:type l2: ``float`` or ``tuple``\n"
227 caltinay 3691 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
228     ":param d1: number of subdivisions in direction 1\n:type d1: ``int``\n"
229     ":param d2: number of subdivisions in direction 2\n:type d2: ``int``");
230 caltinay 3670
231 caltinay 3943 def("Rectangle", ripley::_rectangle, (arg("n0"),arg("n1"),arg("l0")=1.0,arg("l1")=1.0,arg("d0")=-1,arg("d1")=-1),
232 caltinay 3691 "Creates a rectangular mesh with n0 x n1 elements over the rectangle [0,l0] x [0,l1].\n\n"
233     ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
234     ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
235 caltinay 3781 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
236     ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
237 caltinay 3691 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
238     ":param d1: number of subdivisions in direction 1\n:type d1: ``int``");
239 caltinay 3971 def("_theculprit_", ripley::_who);
240 caltinay 3691 def("LoadMesh", ripley::RipleyDomain::loadMesh, (arg("filename")),
241     "Loads a ripley domain from a dump file" ":rtype: `Domain`");
242 caltinay 3670
243 caltinay 3691 def("ReadMesh", ripley::RipleyDomain::readMesh, (arg("filename")),
244     "Reads a ripley domain from a file created by write().\n\n"
245     ":rtype: `RipleyDomain`\n:param filename:\n:type filename: ``string``\n");
246 caltinay 3670
247 caltinay 3971 def("_readBinaryGrid", &ripley::readBinaryGrid, (arg("filename"), arg("functionspace"), arg("first"), arg("numValues"), arg("shape"), arg("fill")=0.));
248    
249 caltinay 4013 def("_readNcGrid", &ripley::readNcGrid, (arg("filename"), arg("varname"), arg("functionspace"), arg("first"), arg("numValues"), arg("shape"), arg("fill")=0.));
250    
251 caltinay 3691 class_<ripley::RipleyDomain, bases<escript::AbstractContinuousDomain> >
252     ("RipleyDomain", "", no_init)
253     .def("write", &ripley::RipleyDomain::write, args("filename"),
254     "Writes the current mesh to a file with the given name. It can subsequently be recovered using ReadMesh().")
255     .def("print_mesh_info", &ripley::RipleyDomain::Print_Mesh_Info, (arg("full")=false),
256     "Prints out a summary about the mesh.\n"
257     ":param full: whether to output additional data\n:type full: ``bool``")
258     .def("dump", &ripley::RipleyDomain::dump, args("filename"),
259     "Dumps the mesh to a file with the given name.")
260     .def("getDescription", &ripley::RipleyDomain::getDescription,
261 caltinay 3670 ":return: a description for this domain\n:rtype: ``string``")
262 caltinay 3691 .def("getDim", &ripley::RipleyDomain::getDim, ":rtype: ``int``")
263     .def("getDataShape", &ripley::RipleyDomain::getDataShape, args("functionSpaceCode"),
264 caltinay 3670 ":return: a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples\n:rtype: ``tuple``")
265 caltinay 3691 .def("getNumDataPointsGlobal", &ripley::RipleyDomain::getNumDataPointsGlobal,
266 caltinay 3670 ":return: the number of data points summed across all MPI processes\n"
267     ":rtype: ``int``")
268 caltinay 3691 .def("addPDEToSystem",&ripley::RipleyDomain::addPDEToSystem,
269     args("mat", "rhs", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
270 caltinay 3670 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
271     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
272     ":param A:\n:type A: `Data`\n"
273     ":param B:\n:type B: `Data`\n"
274     ":param C:\n:type C: `Data`\n"
275     ":param D:\n:type D: `Data`\n"
276     ":param X:\n:type X: `Data`\n"
277     ":param Y:\n:type Y: `Data`\n"
278     ":param d:\n:type d: `Data`\n"
279     ":param d_contact:\n:type d_contact: `Data`\n"
280 caltinay 3791 ":param y_contact:\n:type y_contact: `Data`"
281 caltinay 3670 )
282 caltinay 3691 .def("addPDEToRHS",&ripley::RipleyDomain::addPDEToRHS,
283 caltinay 3670 args("rhs", "X", "Y", "y", "y_contact"),
284     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
285     ":param rhs:\n:type rhs: `Data`\n"
286     ":param X:\n:type X: `Data`\n"
287     ":param Y:\n:type Y: `Data`\n"
288     ":param y:\n:type y: `Data`\n"
289     ":param y_contact:\n:type y_contact: `Data`"
290     )
291 caltinay 3691 .def("addPDEToTransportProblem",&ripley::RipleyDomain::addPDEToTransportProblem,
292 caltinay 3670 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
293     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
294     ":param source:\n:type source: `Data`\n"
295     ":param M:\n:type M: `Data`\n"
296     ":param A:\n:type A: `Data`\n"
297     ":param B:\n:type B: `Data`\n"
298     ":param C:\n:type C: `Data`\n"
299     ":param D:\n:type D: `Data`\n"
300     ":param X:\n:type X: `Data`\n"
301     ":param Y:\n:type Y: `Data`\n"
302     ":param d:\n:type d: `Data`\n"
303     ":param y:\n:type y: `Data`\n"
304     ":param d_contact:\n:type d_contact: `Data`\n"
305 caltinay 3791 ":param y_contact:\n:type y_contact: `Data`"
306 caltinay 3670 )
307 caltinay 3691 .def("newOperator",&ripley::RipleyDomain::newSystemMatrix,
308 caltinay 3670 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
309     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
310     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
311     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
312     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
313     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
314 caltinay 3791 ":param type:\n:type type: ``int``"
315 caltinay 3670 )
316 caltinay 3691 .def("newTransportProblem",&ripley::RipleyDomain::newTransportProblem,
317 caltinay 3670 args("theta", "blocksize", "functionspace", "type"),
318     "creates a TransportProblemAdapter\n\n"
319     ":param theta:\n:type theta: ``float``\n"
320     ":param blocksize:\n:type blocksize: ``int``\n"
321     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
322 caltinay 3791 ":param type:\n:type type: ``int``"
323 caltinay 3670 )
324 caltinay 3691 .def("getSystemMatrixTypeId",&ripley::RipleyDomain::getSystemMatrixTypeId,
325 caltinay 3670 args("solver", "preconditioner", "package", "symmetry"),
326 caltinay 3697 ":return: the identifier of the matrix type to be used for the global stiffness matrix when a particular solver, package, preconditioner, and symmetric matrix is used.\n"
327 caltinay 3670 ":rtype: ``int``\n"
328     ":param solver:\n:type solver: ``int``\n"
329     ":param preconditioner:\n:type preconditioner: ``int``\n"
330     ":param package:\n:type package: ``int``\n"
331 caltinay 3791 ":param symmetry:\n:type symmetry: ``int``"
332 caltinay 3670 )
333 caltinay 3691 .def("getTransportTypeId",&ripley::RipleyDomain::getTransportTypeId,
334 caltinay 3670 args("solver", "preconditioner", "package", "symmetry"),
335 caltinay 3697 ":return: the identifier of the transport problem type to be used when a particular solver, preconditioner, package and symmetric matrix is used.\n"
336 caltinay 3670 ":rtype: ``int``\n"
337     ":param solver:\n:type solver: ``int``\n"
338     ":param preconditioner:\n:type preconditioner: ``int``\n"
339     ":param package:\n:type package: ``int``\n"
340 caltinay 3791 ":param symmetry:\n:type symmetry: ``int``"
341 caltinay 3670 )
342 caltinay 3691 .def("getX",&ripley::RipleyDomain::getX, ":return: locations in the FEM nodes\n\n"
343 caltinay 3670 ":rtype: `Data`")
344 caltinay 3691 .def("getNormal",&ripley::RipleyDomain::getNormal,
345 caltinay 3670 ":return: boundary normals at the quadrature point on the face elements\n"
346     ":rtype: `Data`")
347 caltinay 3691 .def("getSize",&ripley::RipleyDomain::getSize,":return: the element size\n"
348 caltinay 3670 ":rtype: `Data`")
349 caltinay 3691 .def("setTagMap",&ripley::RipleyDomain::setTagMap,args("name","tag"),
350 caltinay 3670 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
351     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
352 caltinay 3691 .def("getTag",&ripley::RipleyDomain::getTag,args("name"),":return: tag id for "
353 caltinay 3670 "``name``\n:rtype: ``string``")
354 caltinay 3691 .def("isValidTagName",&ripley::RipleyDomain::isValidTagName,args("name"),
355     ":return: True if ``name`` corresponds to a tag, otherwise False\n:rtype: ``bool``")
356     .def("showTagNames",&ripley::RipleyDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
357     .def("getMPISize",&ripley::RipleyDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
358     .def("getMPIRank",&ripley::RipleyDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
359     .def("MPIBarrier",&ripley::RipleyDomain::MPIBarrier,"Wait until all processes have reached this point")
360     .def("onMasterProcessor",&ripley::RipleyDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
361 caltinay 3670
362 caltinay 3691 class_<ripley::Brick, bases<ripley::RipleyDomain> >("RipleyBrick", "", no_init);
363     class_<ripley::Rectangle, bases<ripley::RipleyDomain> >("RipleyRectangle", "", no_init);
364 caltinay 3670 }
365    

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