/[escript]/trunk/ripley/src/ripleycpp.cpp
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Revision 4357 - (hide annotations)
Thu Apr 11 06:07:14 2013 UTC (6 years ago) by caltinay
File size: 18021 byte(s)
templated writeBinaryGrid and a bit of cleanup.

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

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