escript  Revision_
ripley/src/Brick.h
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1 
2 /*****************************************************************************
3 *
4 * Copyright (c) 2003-2016 by The University of Queensland
5 * http://www.uq.edu.au
6 *
7 * Primary Business: Queensland, Australia
8 * Licensed under the Apache License, version 2.0
9 * http://www.apache.org/licenses/LICENSE-2.0
10 *
11 * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12 * Development 2012-2013 by School of Earth Sciences
13 * Development from 2014 by Centre for Geoscience Computing (GeoComp)
14 *
15 *****************************************************************************/
16 
17 #ifndef __RIPLEY_BRICK_H__
18 #define __RIPLEY_BRICK_H__
19 
20 #include <ripley/RipleyDomain.h>
21 
22 namespace ripley {
23 
29 {
30  template<class Scalar> friend class DefaultAssembler3D;
31  friend class WaveAssembler3D;
32  friend class LameAssembler3D;
33 public:
34 
42  Brick(dim_t n0, dim_t n1, dim_t n2, double x0, double y0, double z0,
43  double x1, double y1, double z1, int d0=-1, int d1=-1, int d2=-1,
44  const std::vector<double>& points = std::vector<double>(),
45  const std::vector<int>& tags = std::vector<int>(),
46  const TagMap& tagnamestonums = TagMap(),
48 
53  ~Brick();
54 
59  virtual std::string getDescription() const;
60 
64  virtual bool operator==(const escript::AbstractDomain& other) const;
65 
71  virtual void write(const std::string& filename) const;
72 
78  void dump(const std::string& filename) const;
79 
82  virtual void readNcGrid(escript::Data& out, std::string filename,
83  std::string varname, const ReaderParameters& params) const;
84 
87  virtual void readBinaryGrid(escript::Data& out, std::string filename,
88  const ReaderParameters& params) const;
89 
90  virtual void readBinaryGridFromZipped(escript::Data& out, std::string filename,
91  const ReaderParameters& params) const;
92 
95  virtual void writeBinaryGrid(const escript::Data& in,
96  std::string filename,
97  int byteOrder, int dataType) const;
98 
104  const dim_t* borrowSampleReferenceIDs(int fsType) const;
105 
110  virtual bool ownSample(int fsType, index_t id) const;
111 
118  virtual void setToNormal(escript::Data& out) const;
119 
125  virtual void setToSize(escript::Data& out) const;
126 
131  virtual dim_t getNumDataPointsGlobal() const;
132 
138  virtual void Print_Mesh_Info(const bool full=false) const;
139 
144  virtual const dim_t* getNumNodesPerDim() const { return m_NN; }
145 
150  virtual const dim_t* getNumElementsPerDim() const { return m_NE; }
151 
157  virtual const dim_t* getNumFacesPerBoundary() const { return m_faceCount; }
158 
163  virtual IndexVector getNodeDistribution() const { return m_nodeDistribution; }
164 
169  virtual const int* getNumSubdivisionsPerDim() const { return m_NX; }
170 
175  virtual double getLocalCoordinate(index_t index, int dim) const;
176 
181  virtual boost::python::tuple getGridParameters() const;
182 
187  virtual escript::Data randomFill(const escript::DataTypes::ShapeType& shape,
188  const escript::FunctionSpace& what,
189  long seed,
190  const boost::python::tuple& filter) const;
191 
192  virtual Assembler_ptr createAssembler(std::string type,
193  const DataMap& options) const;
198  const double *getLength() const { return m_length; }
199 
204  const double *getElementLength() const { return m_dx; }
205 
211  virtual RankVector getOwnerVector(int fsType) const;
212 
213 protected:
214  virtual dim_t getNumNodes() const;
215  virtual dim_t getNumElements() const;
216  virtual dim_t getNumFaceElements() const;
217  virtual dim_t getNumDOF() const;
218  virtual dim_t getNumDOFInAxis(unsigned axis) const;
219  virtual dim_t getFirstInDim(unsigned axis) const;
220 
221  virtual IndexVector getDiagonalIndices(bool upperOnly) const;
222  virtual void assembleCoordinates(escript::Data& arg) const;
223  virtual void assembleGradient(escript::Data& out,
224  const escript::Data& in) const;
225  virtual void assembleIntegrate(DoubleVector& integrals,
226  const escript::Data& arg) const;
227  virtual std::vector<IndexVector> getConnections(bool includeShared=false) const;
228 #ifdef ESYS_HAVE_TRILINOS
229  virtual esys_trilinos::const_TrilinosGraph_ptr getTrilinosGraph() const;
230 #endif
231 
232 #ifdef ESYS_HAVE_PASO
233  virtual paso::SystemMatrixPattern_ptr getPasoMatrixPattern(
234  bool reducedRowOrder, bool reducedColOrder) const;
235 #endif
236  virtual void interpolateNodesOnElements(escript::Data& out,
237  const escript::Data& in, bool reduced) const;
238  virtual void interpolateNodesOnFaces(escript::Data& out,
239  const escript::Data& in,
240  bool reduced) const;
241  virtual void nodesToDOF(escript::Data& out, const escript::Data& in) const;
242  virtual dim_t getDofOfNode(dim_t node) const;
243 
244  void populateSampleIds();
245  void populateDofMap();
246 
247  template<typename Scalar>
248  void addToMatrixAndRHS(escript::AbstractSystemMatrix* S, escript::Data& F,
249  const std::vector<Scalar>& EM_S, const std::vector<Scalar>& EM_F,
250  bool addS, bool addF, index_t firstNode, int nEq=1, int nComp=1) const;
251 
252  template<typename ValueType>
253  void readBinaryGridImpl(escript::Data& out, const std::string& filename,
254  const ReaderParameters& params) const;
255 #ifdef ESYS_HAVE_BOOST_IO
256  template<typename ValueType>
257  void readBinaryGridZippedImpl(escript::Data& out,
258  const std::string& filename,
259  const ReaderParameters& params) const;
260 #endif
261  template<typename ValueType>
262  void writeBinaryGridImpl(const escript::Data& in,
263  const std::string& filename, int byteOrder) const;
264 
265  dim_t findNode(const double *coords) const;
266 
267  virtual escript::Data randomFillWorker(
268  const escript::DataTypes::ShapeType& shape, long seed,
269  const boost::python::tuple& filter) const;
270 
272  dim_t m_gNE[3];
273 
275  double m_origin[3];
276 
278  double m_length[3];
279 
281  double m_dx[3];
282 
284  int m_NX[3];
285 
287  dim_t m_NE[3];
288 
290  dim_t m_ownNE[3];
291 
293  dim_t m_NN[3];
294 
296  dim_t m_offset[3];
297 
299  dim_t m_faceCount[6];
300 
305 
311 
312  // vector with first node id on each rank
314 
315  // vector that maps each node to a DOF index
317 
318 #ifdef ESYS_HAVE_PASO
319  // the Paso System Matrix pattern
320  mutable paso::SystemMatrixPattern_ptr m_pattern;
321 #endif
322 
323 #ifdef ESYS_HAVE_TRILINOS
324  mutable esys_trilinos::const_TrilinosGraph_ptr m_graph;
326 #endif
327 };
328 
330 inline dim_t Brick::getDofOfNode(dim_t node) const
331 {
332  return m_dofMap[node];
333 }
334 
336 {
337  return (m_gNE[0]+1)*(m_gNE[1]+1)*(m_gNE[2]+1);
338 }
339 
340 inline double Brick::getLocalCoordinate(index_t index, int dim) const
341 {
342  ESYS_ASSERT(dim>=0 && dim<3, "'dim' out of bounds");
343  ESYS_ASSERT(index>=0 && index<m_NN[dim], "'index' out of bounds");
344  return m_origin[dim]+m_dx[dim]*(m_offset[dim]+index);
345 }
346 
347 inline boost::python::tuple Brick::getGridParameters() const
348 {
349  return boost::python::make_tuple(
350  boost::python::make_tuple(m_origin[0], m_origin[1], m_origin[2]),
351  boost::python::make_tuple(m_dx[0], m_dx[1], m_dx[2]),
352  boost::python::make_tuple(m_gNE[0], m_gNE[1], m_gNE[2]));
353 }
354 
355 //protected
356 inline dim_t Brick::getNumDOF() const
357 {
358  return (m_gNE[0]+1)/m_NX[0]*(m_gNE[1]+1)/m_NX[1]*(m_gNE[2]+1)/m_NX[2];
359 }
360 
361 //protected
362 inline dim_t Brick::getNumDOFInAxis(unsigned axis) const
363 {
364  ESYS_ASSERT(axis < m_numDim, "Invalid axis");
365  return (m_gNE[axis]+1)/m_NX[axis];
366 }
367 
368 //protected
369 inline dim_t Brick::getNumNodes() const
370 {
371  return m_NN[0]*m_NN[1]*m_NN[2];
372 }
373 
374 //protected
376 {
377  return m_NE[0]*m_NE[1]*m_NE[2];
378 }
379 
380 //protected
382 {
383  return m_faceCount[0] + m_faceCount[1] + m_faceCount[2]
384  + m_faceCount[3] + m_faceCount[4] + m_faceCount[5];
385 }
386 
387 //protected
388 inline index_t Brick::getFirstInDim(unsigned axis) const
389 {
390  return m_offset[axis] == 0 ? 0 : 1;
391 }
392 
393 } // end of namespace ripley
394 
395 #endif // __RIPLEY_BRICK_H__
396 
Definition: FunctionSpace.h:34
std::vector< int > RankVector
Definition: Ripley.h:45
escript::Data readNcGrid(std::string filename, std::string varname, escript::FunctionSpace fs, const object &pyShape, double fill, const object &pyFirst, const object &pyNum, const object &pyMultiplier, const object &pyReverse)
Definition: ripleycpp.cpp:116
virtual const dim_t * getNumFacesPerBoundary() const
returns the number of face elements in the order (left,right,bottom,top,front,back) on current MPI ra...
Definition: ripley/src/Brick.h:157
virtual const dim_t * getNumElementsPerDim() const
returns the number of elements per MPI rank in each dimension
Definition: ripley/src/Brick.h:150
const double * getElementLength() const
returns the lengths of an element
Definition: ripley/src/Brick.h:204
std::vector< int > ShapeType
The shape of a single datapoint.
Definition: DataTypes.h:42
escript::Data readBinaryGrid(std::string filename, escript::FunctionSpace fs, const object &pyShape, double fill, int byteOrder, int dataType, const object &pyFirst, const object &pyNum, const object &pyMultiplier, const object &pyReverse)
Definition: ripleycpp.cpp:62
virtual dim_t getNumDOF() const
returns the number of degrees of freedom per MPI rank
Definition: ripley/src/Brick.h:356
boost::shared_ptr< SystemMatrixPattern > SystemMatrixPattern_ptr
Definition: SystemMatrixPattern.h:39
virtual dim_t getDofOfNode(dim_t node) const
Definition: ripley/src/Brick.h:330
std::map< std::string, int > TagMap
Definition: Ripley.h:46
IndexVector m_nodeDistribution
Definition: ripley/src/Brick.h:313
int index_t
type for array/matrix indices used both globally and on each rank
Definition: DataTypes.h:59
std::vector< index_t > IndexVector
Definition: Ripley.h:43
std::map< std::string, escript::Data > DataMap
Definition: ripley/src/domainhelpers.h:24
virtual dim_t getFirstInDim(unsigned axis) const
Definition: ripley/src/Brick.h:388
boost::shared_ptr< SubWorld > SubWorld_ptr
Definition: SubWorld.h:146
Structure that wraps parameters for the grid reading routines.
Definition: ripley/src/RipleyDomain.h:68
Data represents a collection of datapoints.
Definition: Data.h:63
virtual const int * getNumSubdivisionsPerDim() const
returns the number of spatial subdivisions in each dimension
Definition: ripley/src/Brick.h:169
RipleyDomain extends the AbstractContinuousDomain interface for the Ripley library and is the base cl...
Definition: ripley/src/RipleyDomain.h:101
Definition: ripley/src/WaveAssembler3D.h:24
Definition: LameAssembler3D.h:24
virtual dim_t getNumNodes() const
returns the number of nodes per MPI rank
Definition: ripley/src/Brick.h:369
virtual dim_t getNumDOFInAxis(unsigned axis) const
Definition: ripley/src/Brick.h:362
Brick is the 3-dimensional implementation of a RipleyDomain.
Definition: ripley/src/Brick.h:28
virtual const dim_t * getNumNodesPerDim() const
returns the number of nodes per MPI rank in each dimension
Definition: ripley/src/Brick.h:144
virtual IndexVector getNodeDistribution() const
returns the node distribution vector
Definition: ripley/src/Brick.h:163
Definition: ripley/src/DefaultAssembler3D.h:24
virtual boost::python::tuple getGridParameters() const
returns the tuple (origin, spacing, number_of_elements)
Definition: ripley/src/Brick.h:347
virtual double getLocalCoordinate(index_t index, int dim) const
returns the index&#39;th coordinate value in given dimension for this rank
Definition: ripley/src/Brick.h:340
virtual dim_t getNumFaceElements() const
returns the number of face elements on current MPI rank
Definition: ripley/src/Brick.h:381
const double * getLength() const
returns the lengths of the domain
Definition: ripley/src/Brick.h:198
Base class for escript system matrices.
Definition: AbstractSystemMatrix.h:42
IndexVector m_nodeId
Definition: ripley/src/Brick.h:308
IndexVector m_dofId
vector of sample reference identifiers
Definition: ripley/src/Brick.h:307
Definition: ripley/src/AbstractAssembler.h:25
std::vector< real_t > DoubleVector
Definition: Ripley.h:44
escript::Data readBinaryGridFromZipped(std::string filename, escript::FunctionSpace fs, const object &pyShape, double fill, int byteOrder, int dataType, const object &pyFirst, const object &pyNum, const object &pyMultiplier, const object &pyReverse)
Definition: ripleycpp.cpp:87
Base class for all escript domains.
Definition: AbstractDomain.h:45
#define ESYS_ASSERT(a, b)
EsysAssert is a MACRO that will throw an exception if the boolean condition specified is false...
Definition: Assert.h:78
virtual dim_t getNumElements() const
returns the number of elements per MPI rank
Definition: ripley/src/Brick.h:375
#define RIPLEY_DLL_API
Definition: ripley/src/system_dep.h:20
IndexVector m_faceId
Definition: ripley/src/Brick.h:310
IndexVector m_elementId
Definition: ripley/src/Brick.h:309
#define S(_J_, _I_)
Definition: ShapeFunctions.cpp:121
IndexVector m_dofMap
Definition: ripley/src/Brick.h:316
index_t dim_t
Definition: DataTypes.h:64
virtual dim_t getNumDataPointsGlobal() const
returns the number of data points summed across all MPI processes
Definition: ripley/src/Brick.h:335
IndexVector m_faceOffset
Definition: ripley/src/Brick.h:304