/[escript]/trunk/ripley/src/ripleycpp.cpp
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Revision 4615 - (hide annotations)
Mon Jan 13 05:05:33 2014 UTC (5 years, 8 months ago) by caltinay
File size: 18472 byte(s)
Step 1 for #31: wrap parameters in an object.

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 4615 GridParameters params;
36     std::vector<int> shape;
37 caltinay 3971
38     if (extract<tuple>(pyFirst).check() || extract<list>(pyFirst).check()) {
39     if (len(pyFirst)==dim) {
40     for (int i=0; i<dim; i++) {
41 caltinay 4615 params.first.push_back(extract<int>(pyFirst[i]));
42 caltinay 3971 }
43     } else
44     throw RipleyException("Argument 'first' has wrong length");
45     } else
46     throw RipleyException("Argument 'first' must be a tuple or list");
47    
48     if (extract<tuple>(pyNum).check() || extract<list>(pyNum).check()) {
49     if (len(pyNum)==dim) {
50     for (int i=0; i<dim; i++) {
51 caltinay 4615 params.numValues.push_back(extract<int>(pyNum[i]));
52 caltinay 3971 }
53     } else
54     throw RipleyException("Argument 'numValues' has wrong length");
55     } else
56     throw RipleyException("Argument 'numValues' must be a tuple or list");
57    
58     if (extract<tuple>(pyShape).check() || extract<list>(pyShape).check()) {
59     for (int i=0; i<len(pyShape); i++) {
60     shape.push_back(extract<int>(pyShape[i]));
61     }
62     } else
63     throw RipleyException("Argument 'shape' must be a tuple or list");
64    
65 caltinay 4277 if (extract<tuple>(pyMultiplier).check() || extract<list>(pyMultiplier).check()) {
66     if (len(pyMultiplier)==dim) {
67     for (int i=0; i<dim; i++) {
68 caltinay 4615 params.multiplier.push_back(extract<int>(pyMultiplier[i]));
69 caltinay 4277 }
70     } else
71     throw RipleyException("Argument 'multiplier' has wrong length");
72     } else
73     throw RipleyException("Argument 'multiplier' must be a tuple or list");
74    
75 caltinay 3971 const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
76     if (!dom)
77     throw RipleyException("Function space must be on a ripley domain");
78    
79    
80     escript::Data res(fill, shape, fs, true);
81    
82 caltinay 4615 dom->readBinaryGrid(res, filename, params);
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 4615 GridParameters params;
92     std::vector<int> shape;
93 caltinay 4013
94     if (extract<tuple>(pyFirst).check() || extract<list>(pyFirst).check()) {
95     if (len(pyFirst)==dim) {
96     for (int i=0; i<dim; i++) {
97 caltinay 4615 params.first.push_back(extract<int>(pyFirst[i]));
98 caltinay 4013 }
99     } else
100     throw RipleyException("Argument 'first' has wrong length");
101     } else
102     throw RipleyException("Argument 'first' must be a tuple or list");
103    
104     if (extract<tuple>(pyNum).check() || extract<list>(pyNum).check()) {
105     if (len(pyNum)==dim) {
106     for (int i=0; i<dim; i++) {
107 caltinay 4615 params.numValues.push_back(extract<int>(pyNum[i]));
108 caltinay 4013 }
109     } else
110     throw RipleyException("Argument 'numValues' has wrong length");
111     } else
112     throw RipleyException("Argument 'numValues' must be a tuple or list");
113    
114 caltinay 4277 if (extract<tuple>(pyMultiplier).check() || extract<list>(pyMultiplier).check()) {
115     if (len(pyMultiplier)==dim) {
116     for (int i=0; i<dim; i++) {
117 caltinay 4615 params.multiplier.push_back(extract<int>(pyMultiplier[i]));
118 caltinay 4277 }
119     } else
120     throw RipleyException("Argument 'multiplier' has wrong length");
121     } else
122     throw RipleyException("Argument 'multiplier' must be a tuple or list");
123    
124 caltinay 4013 if (extract<tuple>(pyShape).check() || extract<list>(pyShape).check()) {
125     for (int i=0; i<len(pyShape); i++) {
126     shape.push_back(extract<int>(pyShape[i]));
127     }
128     } else
129     throw RipleyException("Argument 'shape' must be a tuple or list");
130    
131     const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
132     if (!dom)
133     throw RipleyException("Function space must be on a ripley domain");
134    
135    
136     escript::Data res(fill, shape, fs, true);
137    
138 caltinay 4615 dom->readNcGrid(res, filename, varname, params);
139 caltinay 4013 return res;
140     }
141    
142 caltinay 3691 // These wrappers are required to make the shared pointers work through the
143     // Python wrapper
144 caltinay 3670
145 jfenwick 3892 // The double for n? is just to keep python happy when people need to deal with
146 caltinay 3971 // truediv
147 jfenwick 3892 escript::Domain_ptr _brick(double _n0, double _n1, double _n2, const object& l0,
148 caltinay 3781 const object& l1, const object& l2, int d0, int d1, int d2)
149 caltinay 3691 {
150 jfenwick 3892 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1), n2=static_cast<int>(_n2);
151 caltinay 3781 double x0=0., x1=1., y0=0., y1=1., z0=0., z1=1.;
152     if (extract<tuple>(l0).check()) {
153     tuple x=extract<tuple>(l0);
154     if (len(x)==2) {
155     x0=extract<double>(x[0]);
156     x1=extract<double>(x[1]);
157     } else
158     throw RipleyException("Argument l0 must be a float or 2-tuple");
159     } else if (extract<double>(l0).check()) {
160     x1=extract<double>(l0);
161     } else
162     throw RipleyException("Argument l0 must be a float or 2-tuple");
163    
164     if (extract<tuple>(l1).check()) {
165     tuple y=extract<tuple>(l1);
166     if (len(y)==2) {
167     y0=extract<double>(y[0]);
168     y1=extract<double>(y[1]);
169     } else
170     throw RipleyException("Argument l1 must be a float or 2-tuple");
171     } else if (extract<double>(l1).check()) {
172     y1=extract<double>(l1);
173     } else
174     throw RipleyException("Argument l1 must be a float or 2-tuple");
175    
176     if (extract<tuple>(l2).check()) {
177     tuple z=extract<tuple>(l2);
178     if (len(z)==2) {
179     z0=extract<double>(z[0]);
180     z1=extract<double>(z[1]);
181     } else
182     throw RipleyException("Argument l2 must be a float or 2-tuple");
183     } else if (extract<double>(l2).check()) {
184     z1=extract<double>(l2);
185     } else
186     throw RipleyException("Argument l2 must be a float or 2-tuple");
187    
188 caltinay 3791 return escript::Domain_ptr(new Brick(n0,n1,n2, x0,y0,z0, x1,y1,z1, d0,d1,d2));
189 caltinay 3691 }
190 caltinay 3670
191 caltinay 3791 const int _q[]={0x61686969,0x746c4144,0x79616e43};
192 jfenwick 3892 escript::Domain_ptr _rectangle(double _n0, double _n1, const object& l0,
193 caltinay 3781 const object& l1, int d0, int d1)
194 caltinay 3691 {
195 jfenwick 3892 int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1);
196 caltinay 3781 double x0=0., x1=1., y0=0., y1=1.;
197     if (extract<tuple>(l0).check()) {
198     tuple x=extract<tuple>(l0);
199     if (len(x)==2) {
200     x0=extract<double>(x[0]);
201     x1=extract<double>(x[1]);
202     } else
203     throw RipleyException("Argument l0 must be a float or 2-tuple");
204     } else if (extract<double>(l0).check()) {
205     x1=extract<double>(l0);
206     } else
207     throw RipleyException("Argument l0 must be a float or 2-tuple");
208    
209     if (extract<tuple>(l1).check()) {
210     tuple y=extract<tuple>(l1);
211     if (len(y)==2) {
212     y0=extract<double>(y[0]);
213     y1=extract<double>(y[1]);
214     } else
215     throw RipleyException("Argument l1 must be a float or 2-tuple");
216     } else if (extract<double>(l1).check()) {
217     y1=extract<double>(l1);
218     } else
219     throw RipleyException("Argument l1 must be a float or 2-tuple");
220    
221 caltinay 3791 return escript::Domain_ptr(new Rectangle(n0,n1, x0,y0, x1,y1, d0,d1));
222 caltinay 3691 }
223 caltinay 3791 std::string _who(){int a[]={_q[0]^42,_q[1]^42,_q[2]^42,0};return (char*)&a[0];}
224 caltinay 3670
225 caltinay 4357 } // end of namespace ripley
226 caltinay 3670
227    
228     BOOST_PYTHON_MODULE(ripleycpp)
229     {
230     // This feature was added in boost v1.34
231     #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
232 caltinay 3691 // params are: bool show_user_defined, bool show_py_signatures, bool show_cpp_signatures
233     docstring_options docopt(true, true, false);
234 caltinay 3670 #endif
235    
236 caltinay 3691 register_exception_translator<ripley::RipleyException>(&(esysUtils::esysExceptionTranslator));
237 caltinay 3670
238 caltinay 4174 scope().attr("__doc__") = "To use this module, please import esys.ripley";
239 caltinay 4357 scope().attr("BYTEORDER_NATIVE") = (int)ripley::BYTEORDER_NATIVE;
240     scope().attr("BYTEORDER_LITTLE_ENDIAN") = (int)ripley::BYTEORDER_LITTLE_ENDIAN;
241     scope().attr("BYTEORDER_BIG_ENDIAN") = (int)ripley::BYTEORDER_BIG_ENDIAN;
242     scope().attr("DATATYPE_INT32") = (int)ripley::DATATYPE_INT32;
243     scope().attr("DATATYPE_FLOAT32") = (int)ripley::DATATYPE_FLOAT32;
244     scope().attr("DATATYPE_FLOAT64") = (int)ripley::DATATYPE_FLOAT64;
245 caltinay 4174
246 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),
247 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"
248     ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
249     ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
250     ":param n2: number of elements in direction 2\n:type n2: ``int``\n"
251 caltinay 3781 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
252     ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
253     ":param l2: length of side 2 or coordinate range of side 2\n:type l2: ``float`` or ``tuple``\n"
254 caltinay 3691 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
255     ":param d1: number of subdivisions in direction 1\n:type d1: ``int``\n"
256     ":param d2: number of subdivisions in direction 2\n:type d2: ``int``");
257 caltinay 3670
258 caltinay 3943 def("Rectangle", ripley::_rectangle, (arg("n0"),arg("n1"),arg("l0")=1.0,arg("l1")=1.0,arg("d0")=-1,arg("d1")=-1),
259 caltinay 3691 "Creates a rectangular mesh with n0 x n1 elements over the rectangle [0,l0] x [0,l1].\n\n"
260     ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
261     ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
262 caltinay 3781 ":param l0: length of side 0 or coordinate range of side 0\n:type l0: ``float`` or ``tuple``\n"
263     ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
264 caltinay 3691 ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
265     ":param d1: number of subdivisions in direction 1\n:type d1: ``int``");
266 caltinay 3971 def("_theculprit_", ripley::_who);
267 caltinay 3670
268 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")));
269 caltinay 3971
270 caltinay 4277 def("_readNcGrid", &ripley::readNcGrid, (arg("filename"), arg("varname"), arg("functionspace"), arg("first"), arg("numValues"), arg("multiplier"), arg("shape"), arg("fill")=0.));
271 caltinay 4013
272 jfenwick 4242 class_<ripley::RipleyDomain, bases<escript::AbstractContinuousDomain>, boost::noncopyable >
273 caltinay 3691 ("RipleyDomain", "", no_init)
274     .def("print_mesh_info", &ripley::RipleyDomain::Print_Mesh_Info, (arg("full")=false),
275     "Prints out a summary about the mesh.\n"
276     ":param full: whether to output additional data\n:type full: ``bool``")
277 caltinay 4357 .def("writeBinaryGrid", &ripley::RipleyDomain::writeBinaryGrid)
278    
279 caltinay 3691 .def("dump", &ripley::RipleyDomain::dump, args("filename"),
280     "Dumps the mesh to a file with the given name.")
281 caltinay 4340 .def("getGridParameters", &ripley::RipleyDomain::getGridParameters,
282     "Returns the tuple (origin, spacing, elements) where the entries are tuples:\n"
283     "``origin``=the coordinates of the domain's global origin,\n"
284     "``spacing``=the element size (=node spacing) of the domain,\n"
285     "``elements``=the global number of elements in all dimensions\n\n"
286     ":rtype: ``tuple``")
287 caltinay 3691 .def("getDescription", &ripley::RipleyDomain::getDescription,
288 caltinay 3670 ":return: a description for this domain\n:rtype: ``string``")
289 caltinay 3691 .def("getDim", &ripley::RipleyDomain::getDim, ":rtype: ``int``")
290     .def("getDataShape", &ripley::RipleyDomain::getDataShape, args("functionSpaceCode"),
291 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``")
292 caltinay 3691 .def("getNumDataPointsGlobal", &ripley::RipleyDomain::getNumDataPointsGlobal,
293 caltinay 3670 ":return: the number of data points summed across all MPI processes\n"
294     ":rtype: ``int``")
295 caltinay 3691 .def("addPDEToSystem",&ripley::RipleyDomain::addPDEToSystem,
296     args("mat", "rhs", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
297 caltinay 3670 "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
298     ":param mat:\n:type mat: `OperatorAdapter`\n:param rhs:\n:type rhs: `Data`\n"
299     ":param A:\n:type A: `Data`\n"
300     ":param B:\n:type B: `Data`\n"
301     ":param C:\n:type C: `Data`\n"
302     ":param D:\n:type D: `Data`\n"
303     ":param X:\n:type X: `Data`\n"
304     ":param Y:\n:type Y: `Data`\n"
305     ":param d:\n:type d: `Data`\n"
306     ":param d_contact:\n:type d_contact: `Data`\n"
307 caltinay 3791 ":param y_contact:\n:type y_contact: `Data`"
308 caltinay 3670 )
309 caltinay 3691 .def("addPDEToRHS",&ripley::RipleyDomain::addPDEToRHS,
310 caltinay 3670 args("rhs", "X", "Y", "y", "y_contact"),
311     "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
312     ":param rhs:\n:type rhs: `Data`\n"
313     ":param X:\n:type X: `Data`\n"
314     ":param Y:\n:type Y: `Data`\n"
315     ":param y:\n:type y: `Data`\n"
316     ":param y_contact:\n:type y_contact: `Data`"
317     )
318 caltinay 3691 .def("addPDEToTransportProblem",&ripley::RipleyDomain::addPDEToTransportProblem,
319 caltinay 3670 args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
320     ":param tp:\n:type tp: `TransportProblemAdapter`\n"
321     ":param source:\n:type source: `Data`\n"
322     ":param M:\n:type M: `Data`\n"
323     ":param A:\n:type A: `Data`\n"
324     ":param B:\n:type B: `Data`\n"
325     ":param C:\n:type C: `Data`\n"
326     ":param D:\n:type D: `Data`\n"
327     ":param X:\n:type X: `Data`\n"
328     ":param Y:\n:type Y: `Data`\n"
329     ":param d:\n:type d: `Data`\n"
330     ":param y:\n:type y: `Data`\n"
331     ":param d_contact:\n:type d_contact: `Data`\n"
332 caltinay 3791 ":param y_contact:\n:type y_contact: `Data`"
333 caltinay 3670 )
334 caltinay 3691 .def("newOperator",&ripley::RipleyDomain::newSystemMatrix,
335 caltinay 3670 args("row_blocksize", "row_functionspace", "column_blocksize", "column_functionspace", "type"),
336     "creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros\n\n"
337     ":param row_blocksize:\n:type row_blocksize: ``int``\n"
338     ":param row_functionspace:\n:type row_functionspace: `FunctionSpace`\n"
339     ":param column_blocksize:\n:type column_blocksize: ``int``\n"
340     ":param column_functionspace:\n:type column_functionspace: `FunctionSpace`\n"
341 caltinay 3791 ":param type:\n:type type: ``int``"
342 caltinay 3670 )
343 caltinay 3691 .def("newTransportProblem",&ripley::RipleyDomain::newTransportProblem,
344 caltinay 3670 args("theta", "blocksize", "functionspace", "type"),
345     "creates a TransportProblemAdapter\n\n"
346     ":param theta:\n:type theta: ``float``\n"
347     ":param blocksize:\n:type blocksize: ``int``\n"
348     ":param functionspace:\n:type functionspace: `FunctionSpace`\n"
349 caltinay 3791 ":param type:\n:type type: ``int``"
350 caltinay 3670 )
351 caltinay 3691 .def("getSystemMatrixTypeId",&ripley::RipleyDomain::getSystemMatrixTypeId,
352 caltinay 3670 args("solver", "preconditioner", "package", "symmetry"),
353 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"
354 caltinay 3670 ":rtype: ``int``\n"
355     ":param solver:\n:type solver: ``int``\n"
356     ":param preconditioner:\n:type preconditioner: ``int``\n"
357     ":param package:\n:type package: ``int``\n"
358 caltinay 3791 ":param symmetry:\n:type symmetry: ``int``"
359 caltinay 3670 )
360 caltinay 3691 .def("getTransportTypeId",&ripley::RipleyDomain::getTransportTypeId,
361 caltinay 3670 args("solver", "preconditioner", "package", "symmetry"),
362 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"
363 caltinay 3670 ":rtype: ``int``\n"
364     ":param solver:\n:type solver: ``int``\n"
365     ":param preconditioner:\n:type preconditioner: ``int``\n"
366     ":param package:\n:type package: ``int``\n"
367 caltinay 3791 ":param symmetry:\n:type symmetry: ``int``"
368 caltinay 3670 )
369 caltinay 3691 .def("getX",&ripley::RipleyDomain::getX, ":return: locations in the FEM nodes\n\n"
370 caltinay 3670 ":rtype: `Data`")
371 caltinay 3691 .def("getNormal",&ripley::RipleyDomain::getNormal,
372 caltinay 3670 ":return: boundary normals at the quadrature point on the face elements\n"
373     ":rtype: `Data`")
374 caltinay 3691 .def("getSize",&ripley::RipleyDomain::getSize,":return: the element size\n"
375 caltinay 3670 ":rtype: `Data`")
376 caltinay 3691 .def("setTagMap",&ripley::RipleyDomain::setTagMap,args("name","tag"),
377 caltinay 3670 "Give a tag number a name.\n\n:param name: Name for the tag\n:type name: ``string``\n"
378     ":param tag: numeric id\n:type tag: ``int``\n:note: Tag names must be unique within a domain")
379 caltinay 3691 .def("getTag",&ripley::RipleyDomain::getTag,args("name"),":return: tag id for "
380 caltinay 3670 "``name``\n:rtype: ``string``")
381 caltinay 3691 .def("isValidTagName",&ripley::RipleyDomain::isValidTagName,args("name"),
382     ":return: True if ``name`` corresponds to a tag, otherwise False\n:rtype: ``bool``")
383     .def("showTagNames",&ripley::RipleyDomain::showTagNames,":return: A space separated list of tag names\n:rtype: ``string``")
384     .def("getMPISize",&ripley::RipleyDomain::getMPISize,":return: the number of processes used for this `Domain`\n:rtype: ``int``")
385     .def("getMPIRank",&ripley::RipleyDomain::getMPIRank,":return: the rank of this process\n:rtype: ``int``")
386     .def("MPIBarrier",&ripley::RipleyDomain::MPIBarrier,"Wait until all processes have reached this point")
387     .def("onMasterProcessor",&ripley::RipleyDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
388 caltinay 3670
389 caltinay 3691 class_<ripley::Brick, bases<ripley::RipleyDomain> >("RipleyBrick", "", no_init);
390 jfenwick 4526 class_<ripley::Rectangle, bases<ripley::RipleyDomain> >("RipleyRectangle", "", no_init)
391 jfenwick 4586 .def("randomFill", &ripley::Rectangle::randomFill,":return: random data\n:rtype: `Data`\n:param seed: pass zero to use system generated seed\n:type seed: `int`\n"
392     ":param details: more info about the type of randomness\nCurrently, the only acceptable value for this tuple is ('gaussian', r, s) where r is the radius of the"
393     "guassian blur and s is the sigma parameter."
394     );
395 caltinay 3670 }
396    

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