/[escript]/trunk/ripley/src/ripleycpp.cpp
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branches/ripleygmg_from_3668/ripley/src/ripleycpp.cpp revision 3791 by caltinay, Wed Feb 1 05:10:22 2012 UTC trunk/ripley/src/ripleycpp.cpp revision 4650 by jfenwick, Wed Feb 5 04:16:01 2014 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*****************************************************************************
3  *  *
4  * Copyright (c) 2003-2012 by University of Queensland  * Copyright (c) 2003-2013 by University of Queensland
5  * Earth Systems Science Computational Center (ESSCC)  * http://www.uq.edu.au
 * http://www.uq.edu.au/esscc  
6  *  *
7  * Primary Business: Queensland, Australia  * Primary Business: Queensland, Australia
8  * Licensed under the Open Software License version 3.0  * Licensed under the Open Software License version 3.0
9  * http://www.opensource.org/licenses/osl-3.0.php  * http://www.opensource.org/licenses/osl-3.0.php
10  *  *
11  *******************************************************/  * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12    * Development since 2012 by School of Earth Sciences
13    *
14    *****************************************************************************/
15    
16  #include <ripley/Brick.h>  #include <ripley/Brick.h>
17  #include <ripley/Rectangle.h>  #include <ripley/Rectangle.h>
# Line 25  using namespace boost::python; Line 27  using namespace boost::python;
27    
28  namespace ripley {  namespace ripley {
29    
30    template<typename T>
31    std::vector<T> extractPyArray(const object& obj, const std::string& name,
32                                  int expectedLength=0)
33    {
34        std::vector<T> result;
35        if (extract<tuple>(obj).check() || extract<list>(obj).check()) {
36            if (expectedLength==0 || len(obj)==expectedLength) {
37                for (int i=0; i<len(obj); i++) {
38                    result.push_back(extract<T>(obj[i]));
39                }
40            } else {
41                std::stringstream ssError;
42                ssError << "argument '" << name << "' has wrong length";
43                std::string error(ssError.str());
44                throw RipleyException(error.c_str());
45            }
46        } else {
47            std::stringstream ssError;
48            ssError << "argument '" << name << "' must be a tuple or list";
49            std::string error(ssError.str());
50            throw RipleyException(error.c_str());
51        }
52    
53        return result;
54    }
55    
56    escript::Data readBinaryGrid(std::string filename, escript::FunctionSpace fs,
57            const object& pyShape, double fill, int byteOrder, int dataType,
58            const object& pyFirst, const object& pyNum, const object& pyMultiplier,
59            const object& pyReverse)
60    {
61        int dim=fs.getDim();
62        ReaderParameters params;
63    
64        params.first = extractPyArray<int>(pyFirst, "first", dim);
65        params.numValues = extractPyArray<int>(pyNum, "numValues", dim);
66        params.multiplier = extractPyArray<int>(pyMultiplier, "multiplier", dim);
67        params.reverse = extractPyArray<int>(pyReverse, "reverse", dim);
68        params.byteOrder = byteOrder;
69        params.dataType = dataType;
70        std::vector<int> shape(extractPyArray<int>(pyShape, "shape"));
71    
72        const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
73        if (!dom)
74            throw RipleyException("Function space must be on a ripley domain");
75    
76        escript::Data res(fill, shape, fs, true);
77        dom->readBinaryGrid(res, filename, params);
78        return res;
79    }
80    
81    escript::Data readNcGrid(std::string filename, std::string varname,
82            escript::FunctionSpace fs, const object& pyShape, double fill,
83            const object& pyFirst, const object& pyNum, const object& pyMultiplier,
84            const object& pyReverse)
85    {
86        int dim=fs.getDim();
87        ReaderParameters params;
88    
89        params.first = extractPyArray<int>(pyFirst, "first", dim);
90        params.numValues = extractPyArray<int>(pyNum, "numValues", dim);
91        params.multiplier = extractPyArray<int>(pyMultiplier, "multiplier", dim);
92        params.reverse = extractPyArray<int>(pyReverse, "reverse", dim);
93        std::vector<int> shape(extractPyArray<int>(pyShape, "shape"));
94    
95        const RipleyDomain* dom=dynamic_cast<const RipleyDomain*>(fs.getDomain().get());
96        if (!dom)
97            throw RipleyException("Function space must be on a ripley domain");
98    
99        escript::Data res(fill, shape, fs, true);
100        dom->readNcGrid(res, filename, varname, params);
101        return res;
102    }
103    
104  // These wrappers are required to make the shared pointers work through the  // These wrappers are required to make the shared pointers work through the
105  // Python wrapper  // Python wrapper
106    
107  escript::Domain_ptr _brick(int n0, int n1, int n2, const object& l0,  // The double for n? is just to keep python happy when people need to deal with
108                   const object& l1, const object& l2, int d0, int d1, int d2)  // truediv
109    escript::Domain_ptr _brick(double _n0, double _n1, double _n2, const object& l0,
110                     const object& l1, const object& l2, int d0, int d1, int d2,
111                     const object& objpoints, const object& objtags)
112  {  {
113        int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1), n2=static_cast<int>(_n2);
114      double x0=0., x1=1., y0=0., y1=1., z0=0., z1=1.;      double x0=0., x1=1., y0=0., y1=1., z0=0., z1=1.;
115      if (extract<tuple>(l0).check()) {      if (extract<tuple>(l0).check()) {
116          tuple x=extract<tuple>(l0);          tuple x=extract<tuple>(l0);
# Line 68  escript::Domain_ptr _brick(int n0, int n Line 148  escript::Domain_ptr _brick(int n0, int n
148      } else      } else
149          throw RipleyException("Argument l2 must be a float or 2-tuple");          throw RipleyException("Argument l2 must be a float or 2-tuple");
150    
151      return escript::Domain_ptr(new Brick(n0,n1,n2, x0,y0,z0, x1,y1,z1, d0,d1,d2));      boost::python::list pypoints=extract<boost::python::list>(objpoints);
152        boost::python::list pytags=extract<boost::python::list>(objtags);
153        int numpts=extract<int>(pypoints.attr("__len__")());
154        int numtags=extract<int>(pytags.attr("__len__")());
155        std::vector<double> points;
156        std::vector<int> tags;
157        tags.resize(numtags, -1);
158        for (int i=0;i<numpts;++i) {
159            boost::python::object temp=pypoints[i];
160            int l=extract<int>(temp.attr("__len__")());
161            for (int k=0;k<l;++k) {
162                points.push_back(extract<double>(temp[k]));
163            }
164        }
165        std::map<std::string, int> tagstonames;
166        int curmax=40;
167        // but which order to assign tags to names?????
168        for (int i=0;i<numtags;++i) {
169            extract<int> ex_int(pytags[i]);
170            extract<std::string> ex_str(pytags[i]);
171            if (ex_int.check()) {
172                tags[i]=ex_int();
173                if (tags[i]>= curmax) {
174                    curmax=tags[i]+1;
175                }
176            } else if (ex_str.check()) {
177                std::string s=ex_str();
178                std::map<std::string, int>::iterator it=tagstonames.find(s);
179                if (it!=tagstonames.end()) {
180                    // we have the tag already so look it up
181                    tags[i]=it->second;
182                } else {
183                    tagstonames[s]=curmax;
184                    tags[i]=curmax;
185                    curmax++;
186                }
187            } else {
188                throw RipleyException("Error - Unable to extract tag value.");
189            }
190        }
191        return escript::Domain_ptr(new Brick(n0,n1,n2, x0,y0,z0, x1,y1,z1, d0,d1,d2,
192                                                points, tags, tagstonames));
193  }  }
194    
195  const int _q[]={0x61686969,0x746c4144,0x79616e43};  const int _q[]={0x61686969,0x746c4144,0x79616e43};
196  escript::Domain_ptr _rectangle(int n0, int n1, const object& l0,  escript::Domain_ptr _rectangle(double _n0, double _n1, const object& l0,
197                                 const object& l1, int d0, int d1)                                 const object& l1, int d0, int d1,
198                                   const object& objpoints, const object& objtags)
199  {  {
200        int n0=static_cast<int>(_n0), n1=static_cast<int>(_n1);
201      double x0=0., x1=1., y0=0., y1=1.;      double x0=0., x1=1., y0=0., y1=1.;
202      if (extract<tuple>(l0).check()) {      if (extract<tuple>(l0).check()) {
203          tuple x=extract<tuple>(l0);          tuple x=extract<tuple>(l0);
# Line 99  escript::Domain_ptr _rectangle(int n0, i Line 222  escript::Domain_ptr _rectangle(int n0, i
222          y1=extract<double>(l1);          y1=extract<double>(l1);
223      } else      } else
224          throw RipleyException("Argument l1 must be a float or 2-tuple");          throw RipleyException("Argument l1 must be a float or 2-tuple");
225            
226      return escript::Domain_ptr(new Rectangle(n0,n1, x0,y0, x1,y1, d0,d1));      boost::python::list pypoints=extract<boost::python::list>(objpoints);
227        boost::python::list pytags=extract<boost::python::list>(objtags);
228        int numpts=extract<int>(pypoints.attr("__len__")());
229        int numtags=extract<int>(pytags.attr("__len__")());
230        std::vector<double> points;
231        std::vector<int> tags;
232        tags.resize(numtags, -1);
233        for (int i=0;i<numpts;++i) {
234            boost::python::object temp=pypoints[i];
235            int l=extract<int>(temp.attr("__len__")());
236            for (int k=0;k<l;++k) {
237                points.push_back(extract<double>(temp[k]));
238            }
239        }
240        std::map<std::string, int> tagstonames;
241        int curmax=40;
242        // but which order to assign tags to names?????
243        for (int i=0;i<numtags;++i) {
244            extract<int> ex_int(pytags[i]);
245            extract<std::string> ex_str(pytags[i]);
246            if (ex_int.check()) {
247                tags[i]=ex_int();
248                if (tags[i]>= curmax) {
249                    curmax=tags[i]+1;
250                }
251            } else if (ex_str.check()) {
252                std::string s=ex_str();
253                std::map<std::string, int>::iterator it=tagstonames.find(s);
254                if (it!=tagstonames.end()) {
255                    // we have the tag already so look it up
256                    tags[i]=it->second;
257                } else {
258                    tagstonames[s]=curmax;
259                    tags[i]=curmax;
260                    curmax++;
261                }
262            } else {
263                throw RipleyException("Error - Unable to extract tag value.");
264            }
265        }
266        return escript::Domain_ptr(new Rectangle(n0,n1, x0,y0, x1,y1, d0,d1,
267                                                 points, tags, tagstonames));
268  }  }
269  std::string _who(){int a[]={_q[0]^42,_q[1]^42,_q[2]^42,0};return (char*)&a[0];}  std::string _who(){int a[]={_q[0]^42,_q[1]^42,_q[2]^42,0};return (char*)&a[0];}
270    
271  }  } // end of namespace ripley
272    
 /**  
     \page ripley Ripley  
     ripleycpp is the python module name that contains the interfaces  
     to the C++ wrapper to ripley.  
 */  
273    
274  BOOST_PYTHON_MODULE(ripleycpp)  BOOST_PYTHON_MODULE(ripleycpp)
275  {  {
# Line 122  BOOST_PYTHON_MODULE(ripleycpp) Line 281  BOOST_PYTHON_MODULE(ripleycpp)
281    
282      register_exception_translator<ripley::RipleyException>(&(esysUtils::esysExceptionTranslator));      register_exception_translator<ripley::RipleyException>(&(esysUtils::esysExceptionTranslator));
283    
284      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),      scope().attr("__doc__") = "To use this module, please import esys.ripley";
285        scope().attr("BYTEORDER_NATIVE") = (int)ripley::BYTEORDER_NATIVE;
286        scope().attr("BYTEORDER_LITTLE_ENDIAN") = (int)ripley::BYTEORDER_LITTLE_ENDIAN;
287        scope().attr("BYTEORDER_BIG_ENDIAN") = (int)ripley::BYTEORDER_BIG_ENDIAN;
288        scope().attr("DATATYPE_INT32") = (int)ripley::DATATYPE_INT32;
289        scope().attr("DATATYPE_FLOAT32") = (int)ripley::DATATYPE_FLOAT32;
290        scope().attr("DATATYPE_FLOAT64") = (int)ripley::DATATYPE_FLOAT64;
291    
292        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,arg("diracPoints")=list(),arg("diracTags")=list()),
293  "Creates a hexagonal mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2].\n\n"  "Creates a hexagonal mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2].\n\n"
294  ":param n0: number of elements in direction 0\n:type n0: ``int``\n"  ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
295  ":param n1: number of elements in direction 1\n:type n1: ``int``\n"  ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
# Line 134  BOOST_PYTHON_MODULE(ripleycpp) Line 301  BOOST_PYTHON_MODULE(ripleycpp)
301  ":param d1: number of subdivisions in direction 1\n:type d1: ``int``\n"  ":param d1: number of subdivisions in direction 1\n:type d1: ``int``\n"
302  ":param d2: number of subdivisions in direction 2\n:type d2: ``int``");  ":param d2: number of subdivisions in direction 2\n:type d2: ``int``");
303    
304      def("Rectangle", ripley::_rectangle, (arg("n0"),arg("n1"),arg("l0")=1.0,arg("l1")=1.0,arg("d0")=1,arg("d1")=1),      def("Rectangle", ripley::_rectangle, (arg("n0"),arg("n1"),arg("l0")=1.0,arg("l1")=1.0,arg("d0")=-1,arg("d1")=-1,arg("diracPoints")=list(),arg("diracTags")=list()),
305  "Creates a rectangular mesh with n0 x n1 elements over the rectangle [0,l0] x [0,l1].\n\n"  "Creates a rectangular mesh with n0 x n1 elements over the rectangle [0,l0] x [0,l1].\n\n"
306  ":param n0: number of elements in direction 0\n:type n0: ``int``\n"  ":param n0: number of elements in direction 0\n:type n0: ``int``\n"
307  ":param n1: number of elements in direction 1\n:type n1: ``int``\n"  ":param n1: number of elements in direction 1\n:type n1: ``int``\n"
# Line 142  BOOST_PYTHON_MODULE(ripleycpp) Line 309  BOOST_PYTHON_MODULE(ripleycpp)
309  ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"  ":param l1: length of side 1 or coordinate range of side 1\n:type l1: ``float`` or ``tuple``\n"
310  ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"  ":param d0: number of subdivisions in direction 0\n:type d0: ``int``\n"
311  ":param d1: number of subdivisions in direction 1\n:type d1: ``int``");  ":param d1: number of subdivisions in direction 1\n:type d1: ``int``");
312      def("_theculprit_", ripley::_who),      def("_theculprit_", ripley::_who);
313      def("LoadMesh", ripley::RipleyDomain::loadMesh, (arg("filename")),  
314             "Loads a ripley domain from a dump file" ":rtype: `Domain`");      def("_readBinaryGrid", &ripley::readBinaryGrid, (arg("filename"),
315                    arg("functionspace"), arg("shape"), arg("fill")=0.,
316      def("ReadMesh", ripley::RipleyDomain::readMesh, (arg("filename")),                  arg("byteOrder"), arg("dataType"), arg("first"),
317              "Reads a ripley domain from a file created by write().\n\n"                  arg("numValues"), arg("multiplier"), arg("reverse")),
318              ":rtype: `RipleyDomain`\n:param filename:\n:type filename: ``string``\n");  "Reads a binary Grid");
319    
320        def("_readNcGrid", &ripley::readNcGrid, (arg("filename"), arg("varname"),
321                    arg("functionspace"), arg("shape"), arg("fill"), arg("first"),
322                    arg("numValues"), arg("multiplier"), arg("reverse")),
323    "Reads a grid from a netCDF file");
324    
325      class_<ripley::RipleyDomain, bases<escript::AbstractContinuousDomain> >      class_<ripley::RipleyDomain, bases<escript::AbstractContinuousDomain>, boost::noncopyable >
326          ("RipleyDomain", "", no_init)          ("RipleyDomain", "", no_init)
         .def("write", &ripley::RipleyDomain::write, args("filename"),  
                 "Writes the current mesh to a file with the given name. It can subsequently be recovered using ReadMesh().")  
327          .def("print_mesh_info", &ripley::RipleyDomain::Print_Mesh_Info, (arg("full")=false),          .def("print_mesh_info", &ripley::RipleyDomain::Print_Mesh_Info, (arg("full")=false),
328                  "Prints out a summary about the mesh.\n"                  "Prints out a summary about the mesh.\n"
329                  ":param full: whether to output additional data\n:type full: ``bool``")                  ":param full: whether to output additional data\n:type full: ``bool``")
330            .def("writeBinaryGrid", &ripley::RipleyDomain::writeBinaryGrid)
331    
332          .def("dump", &ripley::RipleyDomain::dump, args("filename"),          .def("dump", &ripley::RipleyDomain::dump, args("filename"),
333                  "Dumps the mesh to a file with the given name.")                  "Dumps the mesh to a file with the given name.")
334            .def("getGridParameters", &ripley::RipleyDomain::getGridParameters,
335    "Returns the tuple (origin, spacing, elements) where the entries are tuples:\n"
336    "``origin``=the coordinates of the domain's global origin,\n"
337    "``spacing``=the element size (=node spacing) of the domain,\n"
338    "``elements``=the global number of elements in all dimensions\n\n"
339    ":rtype: ``tuple``")
340          .def("getDescription", &ripley::RipleyDomain::getDescription,          .def("getDescription", &ripley::RipleyDomain::getDescription,
341  ":return: a description for this domain\n:rtype: ``string``")  ":return: a description for this domain\n:rtype: ``string``")
342          .def("getDim", &ripley::RipleyDomain::getDim, ":rtype: ``int``")          .def("getDim", &ripley::RipleyDomain::getDim, ":rtype: ``int``")
# Line 167  BOOST_PYTHON_MODULE(ripleycpp) Line 345  BOOST_PYTHON_MODULE(ripleycpp)
345          .def("getNumDataPointsGlobal", &ripley::RipleyDomain::getNumDataPointsGlobal,          .def("getNumDataPointsGlobal", &ripley::RipleyDomain::getNumDataPointsGlobal,
346  ":return: the number of data points summed across all MPI processes\n"  ":return: the number of data points summed across all MPI processes\n"
347  ":rtype: ``int``")  ":rtype: ``int``")
348            .def("addToSystem",&ripley::RipleyDomain::addToSystemFromPython,
349                args("mat", "rhs", "data"),
350                "adds a PDE to the system, results depend on domain\n\n"
351                ":param mat:\n:type mat: `OperatorAdapter`\n"
352                ":param rhs:\n:type rhs: `Data`\n"
353                ":param data:\ntype data: `list`")
354          .def("addPDEToSystem",&ripley::RipleyDomain::addPDEToSystem,          .def("addPDEToSystem",&ripley::RipleyDomain::addPDEToSystem,
355  args("mat", "rhs", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),  args("mat", "rhs", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
356  "adds a PDE onto the stiffness matrix mat and a rhs\n\n"  "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
# Line 181  args("mat", "rhs", "A", "B", "C", "D", " Line 365  args("mat", "rhs", "A", "B", "C", "D", "
365  ":param d_contact:\n:type d_contact: `Data`\n"  ":param d_contact:\n:type d_contact: `Data`\n"
366  ":param y_contact:\n:type y_contact: `Data`"  ":param y_contact:\n:type y_contact: `Data`"
367  )  )
368    
369          .def("addPDEToRHS",&ripley::RipleyDomain::addPDEToRHS,          .def("addPDEToRHS",&ripley::RipleyDomain::addPDEToRHS,
370  args("rhs", "X", "Y", "y", "y_contact"),  args("rhs", "X", "Y", "y", "y_contact"),
371  "adds a PDE onto the stiffness matrix mat and a rhs\n\n"  "adds a PDE onto the stiffness matrix mat and a rhs\n\n"
# Line 190  args("rhs", "X", "Y", "y", "y_contact"), Line 375  args("rhs", "X", "Y", "y", "y_contact"),
375  ":param y:\n:type y: `Data`\n"  ":param y:\n:type y: `Data`\n"
376  ":param y_contact:\n:type y_contact: `Data`"  ":param y_contact:\n:type y_contact: `Data`"
377  )  )
378            .def("addToRHS",&ripley::RipleyDomain::addToRHSFromPython,
379                args("rhs", "data"),
380                "adds a PDE onto the stiffness matrix mat and a rhs, "
381                "results depends on domain\n\n"
382                ":param rhs:\n:type rhs: `Data`\n"
383                ":param data:\ntype data: `list`")
384            .def("setAssembler", &ripley::RipleyDomain::setAssemblerFromPython,
385                args("typename", "options"),
386                "sets the domain to use the named assembler, if supported, using"
387                "the options if provided"
388                ":param typename:\n:type typename: `string`\n"
389                ":param options:\n:type options: `list`\n")
390          .def("addPDEToTransportProblem",&ripley::RipleyDomain::addPDEToTransportProblem,          .def("addPDEToTransportProblem",&ripley::RipleyDomain::addPDEToTransportProblem,
391  args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),  args( "tp", "source", "M", "A", "B", "C", "D", "X", "Y", "d", "y", "d_contact", "y_contact"),
392  ":param tp:\n:type tp: `TransportProblemAdapter`\n"  ":param tp:\n:type tp: `TransportProblemAdapter`\n"
# Line 261  args("solver", "preconditioner", "packag Line 458  args("solver", "preconditioner", "packag
458          .def("MPIBarrier",&ripley::RipleyDomain::MPIBarrier,"Wait until all processes have reached this point")          .def("MPIBarrier",&ripley::RipleyDomain::MPIBarrier,"Wait until all processes have reached this point")
459          .def("onMasterProcessor",&ripley::RipleyDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");          .def("onMasterProcessor",&ripley::RipleyDomain::onMasterProcessor,":return: True if this code is executing on the master process\n:rtype: `bool`");
460    
461      class_<ripley::Brick, bases<ripley::RipleyDomain> >("RipleyBrick", "", no_init);      class_<ripley::Brick, bases<ripley::RipleyDomain> >("RipleyBrick", "", no_init)
462      class_<ripley::Rectangle, bases<ripley::RipleyDomain> >("RipleyRectangle", "", no_init);      .def("randomFill", &ripley::Brick::randomFill,":return: random data\n:rtype: `Data`\n:param seed: pass zero to use system generated seed\n:type seed: `int`\n"
463    ":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"
464    "guassian blur and s is the sigma parameter."
465        );
466        class_<ripley::Rectangle, bases<ripley::RipleyDomain> >("RipleyRectangle", "", no_init)
467        .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"
468    ":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"
469    "guassian blur and s is the sigma parameter."
470        );
471  }  }
472    

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