escript  Revision_
ripley/src/Brick.h
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1 
2 /*****************************************************************************
3 *
4 * Copyright (c) 2003-2017 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(std::vector<real_t>& integrals,
226  const escript::Data& arg) const;
227  virtual void assembleIntegrate(std::vector<cplx_t>& integrals,
228  const escript::Data& arg) const;
229  virtual std::vector<IndexVector> getConnections(bool includeShared=false) const;
230 #ifdef ESYS_HAVE_TRILINOS
231  virtual esys_trilinos::const_TrilinosGraph_ptr getTrilinosGraph() const;
232 #endif
233 
234 #ifdef ESYS_HAVE_PASO
235  virtual paso::SystemMatrixPattern_ptr getPasoMatrixPattern(
236  bool reducedRowOrder, bool reducedColOrder) const;
237 #endif
238  virtual void interpolateNodesOnElements(escript::Data& out,
239  const escript::Data& in, bool reduced) const;
240  virtual void interpolateNodesOnFaces(escript::Data& out,
241  const escript::Data& in,
242  bool reduced) const;
243  virtual void nodesToDOF(escript::Data& out, const escript::Data& in) const;
244  virtual dim_t getDofOfNode(dim_t node) const;
245 
246  void populateSampleIds();
247  void populateDofMap();
248 
249  template<typename Scalar>
250  void assembleGradientImpl(escript::Data& out,
251  const escript::Data& in) const;
252 
253  template<typename Scalar>
254  void addToMatrixAndRHS(escript::AbstractSystemMatrix* S, escript::Data& F,
255  const std::vector<Scalar>& EM_S, const std::vector<Scalar>& EM_F,
256  bool addS, bool addF, index_t firstNode, int nEq=1, int nComp=1) const;
257 
258  template<typename ValueType>
259  void readBinaryGridImpl(escript::Data& out, const std::string& filename,
260  const ReaderParameters& params) const;
261 #ifdef ESYS_HAVE_BOOST_IO
262  template<typename ValueType>
263  void readBinaryGridZippedImpl(escript::Data& out,
264  const std::string& filename,
265  const ReaderParameters& params) const;
266 #endif
267  template<typename ValueType>
268  void writeBinaryGridImpl(const escript::Data& in,
269  const std::string& filename, int byteOrder) const;
270 
271  dim_t findNode(const double *coords) const;
272 
273  virtual escript::Data randomFillWorker(
274  const escript::DataTypes::ShapeType& shape, long seed,
275  const boost::python::tuple& filter) const;
276 
278  dim_t m_gNE[3];
279 
281  double m_origin[3];
282 
284  double m_length[3];
285 
287  double m_dx[3];
288 
290  int m_NX[3];
291 
293  dim_t m_NE[3];
294 
296  dim_t m_ownNE[3];
297 
299  dim_t m_NN[3];
300 
302  dim_t m_offset[3];
303 
305  dim_t m_faceCount[6];
306 
311 
317 
318  // vector with first node id on each rank
320 
321  // vector that maps each node to a DOF index
323 
324 #ifdef ESYS_HAVE_PASO
325  // the Paso System Matrix pattern
326  mutable paso::SystemMatrixPattern_ptr m_pattern;
327 #endif
328 
329 #ifdef ESYS_HAVE_TRILINOS
330  mutable esys_trilinos::const_TrilinosGraph_ptr m_graph;
332 #endif
333 private:
334  template<typename Scalar>
335  void assembleIntegrateImpl(std::vector<Scalar>& integrals, const escript::Data& arg) const;
336 
337  template <typename S>
338  void interpolateNodesOnElementsWorker(escript::Data& out,
339  const escript::Data& in, bool reduced, S sentinel) const;
340  template <typename S>
341  void interpolateNodesOnFacesWorker(escript::Data& out,
342  const escript::Data& in,
343  bool reduced, S sentinel) const;
344 };
345 
347 inline dim_t Brick::getDofOfNode(dim_t node) const
348 {
349  return m_dofMap[node];
350 }
351 
353 {
354  return (m_gNE[0]+1)*(m_gNE[1]+1)*(m_gNE[2]+1);
355 }
356 
357 inline double Brick::getLocalCoordinate(index_t index, int dim) const
358 {
359  ESYS_ASSERT(dim>=0 && dim<3, "'dim' out of bounds");
360  ESYS_ASSERT(index>=0 && index<m_NN[dim], "'index' out of bounds");
361  return m_origin[dim]+m_dx[dim]*(m_offset[dim]+index);
362 }
363 
364 inline boost::python::tuple Brick::getGridParameters() const
365 {
366  return boost::python::make_tuple(
367  boost::python::make_tuple(m_origin[0], m_origin[1], m_origin[2]),
368  boost::python::make_tuple(m_dx[0], m_dx[1], m_dx[2]),
369  boost::python::make_tuple(m_gNE[0], m_gNE[1], m_gNE[2]));
370 }
371 
372 //protected
373 inline dim_t Brick::getNumDOF() const
374 {
375  return (m_gNE[0]+1)/m_NX[0]*(m_gNE[1]+1)/m_NX[1]*(m_gNE[2]+1)/m_NX[2];
376 }
377 
378 //protected
379 inline dim_t Brick::getNumDOFInAxis(unsigned axis) const
380 {
381  ESYS_ASSERT(axis < m_numDim, "Invalid axis");
382  return (m_gNE[axis]+1)/m_NX[axis];
383 }
384 
385 //protected
386 inline dim_t Brick::getNumNodes() const
387 {
388  return m_NN[0]*m_NN[1]*m_NN[2];
389 }
390 
391 //protected
393 {
394  return m_NE[0]*m_NE[1]*m_NE[2];
395 }
396 
397 //protected
399 {
400  return m_faceCount[0] + m_faceCount[1] + m_faceCount[2]
401  + m_faceCount[3] + m_faceCount[4] + m_faceCount[5];
402 }
403 
404 //protected
405 inline index_t Brick::getFirstInDim(unsigned axis) const
406 {
407  return m_offset[axis] == 0 ? 0 : 1;
408 }
409 
410 } // end of namespace ripley
411 
412 #endif // __RIPLEY_BRICK_H__
413 
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:373
boost::shared_ptr< SystemMatrixPattern > SystemMatrixPattern_ptr
Definition: SystemMatrixPattern.h:39
virtual dim_t getDofOfNode(dim_t node) const
Definition: ripley/src/Brick.h:347
std::map< std::string, int > TagMap
Definition: Ripley.h:46
IndexVector m_nodeDistribution
Definition: ripley/src/Brick.h:319
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:405
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:386
virtual dim_t getNumDOFInAxis(unsigned axis) const
Definition: ripley/src/Brick.h:379
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:364
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:357
virtual dim_t getNumFaceElements() const
returns the number of face elements on current MPI rank
Definition: ripley/src/Brick.h:398
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:314
IndexVector m_dofId
vector of sample reference identifiers
Definition: ripley/src/Brick.h:313
Definition: ripley/src/AbstractAssembler.h:25
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:392
#define RIPLEY_DLL_API
Definition: ripley/src/system_dep.h:20
IndexVector m_faceId
Definition: ripley/src/Brick.h:316
IndexVector m_elementId
Definition: ripley/src/Brick.h:315
#define S(_J_, _I_)
Definition: ShapeFunctions.cpp:121
IndexVector m_dofMap
Definition: ripley/src/Brick.h:322
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:352
IndexVector m_faceOffset
Definition: ripley/src/Brick.h:310