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

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Revision 4495 - (hide annotations)
Fri Jul 5 02:19:47 2013 UTC (6 years, 2 months ago) by caltinay
File size: 18127 byte(s)
Added support for more input data types in ER Mapper files.
Tests will follow soon.

1 caltinay 3670
2 jfenwick 3981 /*****************************************************************************
3 caltinay 3670 *
4 jfenwick 4154 * Copyright (c) 2003-2013 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 caltinay 4277 const object& pyFirst, const object& pyNum, const object& pyMultiplier,
32 caltinay 4495 const object& pyShape, double fill, int byteOrder, int dataType)
33 caltinay 3971 {
34     int dim=fs.getDim();
35 caltinay 4277 std::vector<int> first(dim), numValues(dim), multiplier(dim), shape;
36 caltinay 3971
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 caltinay 4277 if (extract<tuple>(pyMultiplier).check() || extract<list>(pyMultiplier).check()) {
65     if (len(pyMultiplier)==dim) {
66     for (int i=0; i<dim; i++) {
67     multiplier[i]=extract<int>(pyMultiplier[i]);
68     }
69     } else
70     throw RipleyException("Argument 'multiplier' has wrong length");
71     } else
72     throw RipleyException("Argument 'multiplier' must be a tuple or list");
73    
74 caltinay 3971 const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
75     if (!dom)
76     throw RipleyException("Function space must be on a ripley domain");
77    
78    
79     escript::Data res(fill, shape, fs, true);
80    
81 caltinay 4495 dom->readBinaryGrid(res, filename, first, numValues, multiplier,
82     byteOrder, dataType);
83 caltinay 3971 return res;
84     }
85    
86 caltinay 4013 escript::Data readNcGrid(std::string filename, std::string varname,
87     escript::FunctionSpace fs, const object& pyFirst, const object& pyNum,
88 caltinay 4277 const object& pyMultiplier, const object& pyShape, double fill=0.)
89 caltinay 4013 {
90     int dim=fs.getDim();
91 caltinay 4277 std::vector<int> first(dim), numValues(dim), multiplier(dim), shape;
92 caltinay 4013
93     if (extract<tuple>(pyFirst).check() || extract<list>(pyFirst).check()) {
94     if (len(pyFirst)==dim) {
95     for (int i=0; i<dim; i++) {
96     first[i]=extract<int>(pyFirst[i]);
97     }
98     } else
99     throw RipleyException("Argument 'first' has wrong length");
100     } else
101     throw RipleyException("Argument 'first' must be a tuple or list");
102    
103     if (extract<tuple>(pyNum).check() || extract<list>(pyNum).check()) {
104     if (len(pyNum)==dim) {
105     for (int i=0; i<dim; i++) {
106     numValues[i]=extract<int>(pyNum[i]);
107     }
108     } else
109     throw RipleyException("Argument 'numValues' has wrong length");
110     } else
111     throw RipleyException("Argument 'numValues' must be a tuple or list");
112    
113 caltinay 4277 if (extract<tuple>(pyMultiplier).check() || extract<list>(pyMultiplier).check()) {
114     if (len(pyMultiplier)==dim) {
115     for (int i=0; i<dim; i++) {
116     multiplier[i]=extract<int>(pyMultiplier[i]);
117     }
118     } else
119     throw RipleyException("Argument 'multiplier' has wrong length");
120     } else
121     throw RipleyException("Argument 'multiplier' must be a tuple or list");
122    
123 caltinay 4013 if (extract<tuple>(pyShape).check() || extract<list>(pyShape).check()) {
124     for (int i=0; i<len(pyShape); i++) {
125     shape.push_back(extract<int>(pyShape[i]));
126     }
127     } else
128     throw RipleyException("Argument 'shape' must be a tuple or list");
129    
130     const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
131     if (!dom)
132     throw RipleyException("Function space must be on a ripley domain");
133    
134    
135     escript::Data res(fill, shape, fs, true);
136    
137 caltinay 4277 dom->readNcGrid(res, filename, varname, first, numValues, multiplier);
138 caltinay 4013 return res;
139     }
140    
141 caltinay 3691 // These wrappers are required to make the shared pointers work through the
142     // Python wrapper
143 caltinay 3670
144 jfenwick 3892 // The double for n? is just to keep python happy when people need to deal with
145 caltinay 3971 // truediv
146 jfenwick 3892 escript::Domain_ptr _brick(double _n0, double _n1, double _n2, const object& l0,
147 caltinay 3781 const object& l1, const object& l2, int d0, int d1, int d2)
148 caltinay 3691 {
149 jfenwick 3892 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1), n2=static_cast<int>(_n2);
150 caltinay 3781 double x0=0., x1=1., y0=0., y1=1., z0=0., z1=1.;
151     if (extract<tuple>(l0).check()) {
152     tuple x=extract<tuple>(l0);
153     if (len(x)==2) {
154     x0=extract<double>(x[0]);
155     x1=extract<double>(x[1]);
156     } else
157     throw RipleyException("Argument l0 must be a float or 2-tuple");
158     } else if (extract<double>(l0).check()) {
159     x1=extract<double>(l0);
160     } else
161     throw RipleyException("Argument l0 must be a float or 2-tuple");
162    
163     if (extract<tuple>(l1).check()) {
164     tuple y=extract<tuple>(l1);
165     if (len(y)==2) {
166     y0=extract<double>(y[0]);
167     y1=extract<double>(y[1]);
168     } else
169     throw RipleyException("Argument l1 must be a float or 2-tuple");
170     } else if (extract<double>(l1).check()) {
171     y1=extract<double>(l1);
172     } else
173     throw RipleyException("Argument l1 must be a float or 2-tuple");
174    
175     if (extract<tuple>(l2).check()) {
176     tuple z=extract<tuple>(l2);
177     if (len(z)==2) {
178     z0=extract<double>(z[0]);
179     z1=extract<double>(z[1]);
180     } else
181     throw RipleyException("Argument l2 must be a float or 2-tuple");
182     } else if (extract<double>(l2).check()) {
183     z1=extract<double>(l2);
184     } else
185     throw RipleyException("Argument l2 must be a float or 2-tuple");
186    
187 caltinay 3791 return escript::Domain_ptr(new Brick(n0,n1,n2, x0,y0,z0, x1,y1,z1, d0,d1,d2));
188 caltinay 3691 }
189 caltinay 3670
190 caltinay 3791 const int _q[]={0x61686969,0x746c4144,0x79616e43};
191 jfenwick 3892 escript::Domain_ptr _rectangle(double _n0, double _n1, const object& l0,
192 caltinay 3781 const object& l1, int d0, int d1)
193 caltinay 3691 {
194 jfenwick 3892 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1);
195 caltinay 3781 double x0=0., x1=1., y0=0., y1=1.;
196     if (extract<tuple>(l0).check()) {
197     tuple x=extract<tuple>(l0);
198     if (len(x)==2) {
199     x0=extract<double>(x[0]);
200     x1=extract<double>(x[1]);
201     } else
202     throw RipleyException("Argument l0 must be a float or 2-tuple");
203     } else if (extract<double>(l0).check()) {
204     x1=extract<double>(l0);
205     } else
206     throw RipleyException("Argument l0 must be a float or 2-tuple");
207    
208     if (extract<tuple>(l1).check()) {
209     tuple y=extract<tuple>(l1);
210     if (len(y)==2) {
211     y0=extract<double>(y[0]);
212     y1=extract<double>(y[1]);
213     } else
214     throw RipleyException("Argument l1 must be a float or 2-tuple");
215     } else if (extract<double>(l1).check()) {
216     y1=extract<double>(l1);
217     } else
218     throw RipleyException("Argument l1 must be a float or 2-tuple");
219    
220 caltinay 3791 return escript::Domain_ptr(new Rectangle(n0,n1, x0,y0, x1,y1, d0,d1));
221 caltinay 3691 }
222 caltinay 3791 std::string _who(){int a[]={_q[0]^42,_q[1]^42,_q[2]^42,0};return (char*)&a[0];}
223 caltinay 3670
224 caltinay 4357 } // end of namespace ripley
225 caltinay 3670
226    
227     BOOST_PYTHON_MODULE(ripleycpp)
228     {
229     // This feature was added in boost v1.34
230     #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
231 caltinay 3691 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
232     docstring_options docopt(true, true, false);
233 caltinay 3670 #endif
234    
235 caltinay 3691 register_exception_translator<ripley::RipleyException>(&(esysUtils::esysExceptionTranslator));
236 caltinay 3670
237 caltinay 4174 scope().attr("__doc__") = "To use this module, please import esys.ripley";
238 caltinay 4357 scope().attr("BYTEORDER_NATIVE") = (int)ripley::BYTEORDER_NATIVE;
239     scope().attr("BYTEORDER_LITTLE_ENDIAN") = (int)ripley::BYTEORDER_LITTLE_ENDIAN;
240     scope().attr("BYTEORDER_BIG_ENDIAN") = (int)ripley::BYTEORDER_BIG_ENDIAN;
241     scope().attr("DATATYPE_INT32") = (int)ripley::DATATYPE_INT32;
242     scope().attr("DATATYPE_FLOAT32") = (int)ripley::DATATYPE_FLOAT32;
243     scope().attr("DATATYPE_FLOAT64") = (int)ripley::DATATYPE_FLOAT64;
244 caltinay 4174
245 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),
246 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"
247     ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
248     ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
249     ":param n2: number of elements in direction 2\n:type n2: ``int``\n"
250 caltinay 3781 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
251     ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
252     ":param l2: length of side 2 or coordinate range of side 2\n:type l2: ``float`` or ``tuple``\n"
253 caltinay 3691 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
254     ":param d1: number of subdivisions in direction 1\n:type d1: ``int``\n"
255     ":param d2: number of subdivisions in direction 2\n:type d2: ``int``");
256 caltinay 3670
257 caltinay 3943 def("Rectangle", ripley::_rectangle, (arg("n0"),arg("n1"),arg("l0")=1.0,arg("l1")=1.0,arg("d0")=-1,arg("d1")=-1),
258 caltinay 3691 "Creates a rectangular mesh with n0 x n1 elements over the rectangle [0,l0] x [0,l1].\n\n"
259     ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
260     ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
261 caltinay 3781 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
262     ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
263 caltinay 3691 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
264     ":param d1: number of subdivisions in direction 1\n:type d1: ``int``");
265 caltinay 3971 def("_theculprit_", ripley::_who);
266 caltinay 3670
267 caltinay 4495 def("_readBinaryGrid", &ripley::readBinaryGrid, (arg("filename"), arg("functionspace"), arg("first"), arg("numValues"), arg("multiplier"), arg("shape"), arg("fill")=0., arg("byteOrder"), arg("dataType")));
268 caltinay 3971
269 caltinay 4277 def("_readNcGrid", &ripley::readNcGrid, (arg("filename"), arg("varname"), arg("functionspace"), arg("first"), arg("numValues"), arg("multiplier"), arg("shape"), arg("fill")=0.));
270 caltinay 4013
271 jfenwick 4242 class_<ripley::RipleyDomain, bases<escript::AbstractContinuousDomain>, boost::noncopyable >
272 caltinay 3691 ("RipleyDomain", "", no_init)
273     .def("print_mesh_info", &ripley::RipleyDomain::Print_Mesh_Info, (arg("full")=false),
274     "Prints out a summary about the mesh.\n"
275     ":param full: whether to output additional data\n:type full: ``bool``")
276 caltinay 4357 .def("writeBinaryGrid", &ripley::RipleyDomain::writeBinaryGrid)
277    
278 caltinay 3691 .def("dump", &ripley::RipleyDomain::dump, args("filename"),
279     "Dumps the mesh to a file with the given name.")
280 caltinay 4340 .def("getGridParameters", &ripley::RipleyDomain::getGridParameters,
281     "Returns the tuple (origin, spacing, elements) where the entries are tuples:\n"
282     "``origin``=the coordinates of the domain's global origin,\n"
283     "``spacing``=the element size (=node spacing) of the domain,\n"
284     "``elements``=the global number of elements in all dimensions\n\n"
285     ":rtype: ``tuple``")
286 caltinay 3691 .def("getDescription", &ripley::RipleyDomain::getDescription,
287 caltinay 3670 ":return: a description for this domain\n:rtype: ``string``")
288 caltinay 3691 .def("getDim", &ripley::RipleyDomain::getDim, ":rtype: ``int``")
289     .def("getDataShape", &ripley::RipleyDomain::getDataShape, args("functionSpaceCode"),
290 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``")
291 caltinay 3691 .def("getNumDataPointsGlobal", &ripley::RipleyDomain::getNumDataPointsGlobal,
292 caltinay 3670 ":return: the number of data points summed across all MPI processes\n"
293     ":rtype: ``int``")
294 caltinay 3691 .def("addPDEToSystem",&ripley::RipleyDomain::addPDEToSystem,
295     args("mat", "rhs", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
296 caltinay 3670 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
297     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
298     ":param A:\n:type A: `Data`\n"
299     ":param B:\n:type B: `Data`\n"
300     ":param C:\n:type C: `Data`\n"
301     ":param D:\n:type D: `Data`\n"
302     ":param X:\n:type X: `Data`\n"
303     ":param Y:\n:type Y: `Data`\n"
304     ":param d:\n:type d: `Data`\n"
305     ":param d_contact:\n:type d_contact: `Data`\n"
306 caltinay 3791 ":param y_contact:\n:type y_contact: `Data`"
307 caltinay 3670 )
308 caltinay 3691 .def("addPDEToRHS",&ripley::RipleyDomain::addPDEToRHS,
309 caltinay 3670 args("rhs", "X", "Y", "y", "y_contact"),
310     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
311     ":param rhs:\n:type rhs: `Data`\n"
312     ":param X:\n:type X: `Data`\n"
313     ":param Y:\n:type Y: `Data`\n"
314     ":param y:\n:type y: `Data`\n"
315     ":param y_contact:\n:type y_contact: `Data`"
316     )
317 caltinay 3691 .def("addPDEToTransportProblem",&ripley::RipleyDomain::addPDEToTransportProblem,
318 caltinay 3670 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
319     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
320     ":param source:\n:type source: `Data`\n"
321     ":param M:\n:type M: `Data`\n"
322     ":param A:\n:type A: `Data`\n"
323     ":param B:\n:type B: `Data`\n"
324     ":param C:\n:type C: `Data`\n"
325     ":param D:\n:type D: `Data`\n"
326     ":param X:\n:type X: `Data`\n"
327     ":param Y:\n:type Y: `Data`\n"
328     ":param d:\n:type d: `Data`\n"
329     ":param y:\n:type y: `Data`\n"
330     ":param d_contact:\n:type d_contact: `Data`\n"
331 caltinay 3791 ":param y_contact:\n:type y_contact: `Data`"
332 caltinay 3670 )
333 caltinay 3691 .def("newOperator",&ripley::RipleyDomain::newSystemMatrix,
334 caltinay 3670 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
335     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
336     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
337     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
338     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
339     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
340 caltinay 3791 ":param type:\n:type type: ``int``"
341 caltinay 3670 )
342 caltinay 3691 .def("newTransportProblem",&ripley::RipleyDomain::newTransportProblem,
343 caltinay 3670 args("theta", "blocksize", "functionspace", "type"),
344     "creates a TransportProblemAdapter\n\n"
345     ":param theta:\n:type theta: ``float``\n"
346     ":param blocksize:\n:type blocksize: ``int``\n"
347     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
348 caltinay 3791 ":param type:\n:type type: ``int``"
349 caltinay 3670 )
350 caltinay 3691 .def("getSystemMatrixTypeId",&ripley::RipleyDomain::getSystemMatrixTypeId,
351 caltinay 3670 args("solver", "preconditioner", "package", "symmetry"),
352 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"
353 caltinay 3670 ":rtype: ``int``\n"
354     ":param solver:\n:type solver: ``int``\n"
355     ":param preconditioner:\n:type preconditioner: ``int``\n"
356     ":param package:\n:type package: ``int``\n"
357 caltinay 3791 ":param symmetry:\n:type symmetry: ``int``"
358 caltinay 3670 )
359 caltinay 3691 .def("getTransportTypeId",&ripley::RipleyDomain::getTransportTypeId,
360 caltinay 3670 args("solver", "preconditioner", "package", "symmetry"),
361 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"
362 caltinay 3670 ":rtype: ``int``\n"
363     ":param solver:\n:type solver: ``int``\n"
364     ":param preconditioner:\n:type preconditioner: ``int``\n"
365     ":param package:\n:type package: ``int``\n"
366 caltinay 3791 ":param symmetry:\n:type symmetry: ``int``"
367 caltinay 3670 )
368 caltinay 3691 .def("getX",&ripley::RipleyDomain::getX, ":return: locations in the FEM nodes\n\n"
369 caltinay 3670 ":rtype: `Data`")
370 caltinay 3691 .def("getNormal",&ripley::RipleyDomain::getNormal,
371 caltinay 3670 ":return: boundary normals at the quadrature point on the face elements\n"
372     ":rtype: `Data`")
373 caltinay 3691 .def("getSize",&ripley::RipleyDomain::getSize,":return: the element size\n"
374 caltinay 3670 ":rtype: `Data`")
375 caltinay 3691 .def("setTagMap",&ripley::RipleyDomain::setTagMap,args("name","tag"),
376 caltinay 3670 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
377     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
378 caltinay 3691 .def("getTag",&ripley::RipleyDomain::getTag,args("name"),":return: tag id for "
379 caltinay 3670 "``name``\n:rtype: ``string``")
380 caltinay 3691 .def("isValidTagName",&ripley::RipleyDomain::isValidTagName,args("name"),
381     ":return: True if ``name`` corresponds to a tag, otherwise False\n:rtype: ``bool``")
382     .def("showTagNames",&ripley::RipleyDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
383     .def("getMPISize",&ripley::RipleyDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
384     .def("getMPIRank",&ripley::RipleyDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
385     .def("MPIBarrier",&ripley::RipleyDomain::MPIBarrier,"Wait until all processes have reached this point")
386     .def("onMasterProcessor",&ripley::RipleyDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
387 caltinay 3670
388 caltinay 3691 class_<ripley::Brick, bases<ripley::RipleyDomain> >("RipleyBrick", "", no_init);
389     class_<ripley::Rectangle, bases<ripley::RipleyDomain> >("RipleyRectangle", "", no_init);
390 caltinay 3670 }
391    

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