escript  Revision_
ripley/src/Brick.h
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3 *
4 * Copyright (c) 2003-2020 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
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11 * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12 * Development 2012-2013 by School of Earth Sciences
13 * Development from 2014-2017 by Centre for Geoscience Computing (GeoComp)
14 * Development from 2019 by School of Earth and Environmental Sciences
15 **
16 *****************************************************************************/
17 
18 #ifndef __RIPLEY_BRICK_H__
19 #define __RIPLEY_BRICK_H__
20 
21 #ifdef _WIN32 // for M_1_PI
22 #define _USE_MATH_DEFINES
23 #include <math.h>
24 #endif
25 
26 #include <ripley/RipleyDomain.h>
27 
28 namespace ripley {
29 
35 {
36  template<class Scalar> friend class DefaultAssembler3D;
37  friend class WaveAssembler3D;
38  friend class LameAssembler3D;
39 public:
40 
48  Brick(dim_t n0, dim_t n1, dim_t n2, double x0, double y0, double z0,
49  double x1, double y1, double z1, int d0=-1, int d1=-1, int d2=-1,
50  const std::vector<double>& points = std::vector<double>(),
51  const std::vector<int>& tags = std::vector<int>(),
52  const TagMap& tagnamestonums = TagMap(),
54 
59  ~Brick();
60 
65  virtual std::string getDescription() const;
66 
70  virtual bool operator==(const escript::AbstractDomain& other) const;
71 
77  virtual void write(const std::string& filename) const;
78 
84  void dump(const std::string& filename) const;
85 
88  virtual void readNcGrid(escript::Data& out, std::string filename,
89  std::string varname, const ReaderParameters& params) const;
90 
93  virtual void readBinaryGrid(escript::Data& out, std::string filename,
94  const ReaderParameters& params) const;
95 
96  virtual void readBinaryGridFromZipped(escript::Data& out, std::string filename,
97  const ReaderParameters& params) const;
98 
101  virtual void writeBinaryGrid(const escript::Data& in,
102  std::string filename,
103  int byteOrder, int dataType) const;
104 
110  const dim_t* borrowSampleReferenceIDs(int fsType) const;
111 
116  virtual bool ownSample(int fsType, index_t id) const;
117 
124  virtual void setToNormal(escript::Data& out) const;
125 
131  virtual void setToSize(escript::Data& out) const;
132 
137  virtual dim_t getNumDataPointsGlobal() const;
138 
144  virtual void Print_Mesh_Info(const bool full=false) const;
145 
150  virtual const dim_t* getNumNodesPerDim() const { return m_NN; }
151 
156  virtual const dim_t* getNumElementsPerDim() const { return m_NE; }
157 
163  virtual const dim_t* getNumFacesPerBoundary() const { return m_faceCount; }
164 
169  virtual IndexVector getNodeDistribution() const { return m_nodeDistribution; }
170 
175  virtual const int* getNumSubdivisionsPerDim() const { return m_NX; }
176 
181  virtual double getLocalCoordinate(index_t index, int dim) const;
182 
187  virtual boost::python::tuple getGridParameters() const;
188 
194  const escript::FunctionSpace& what,
195  long seed,
196  const boost::python::tuple& filter) const;
197 
198  virtual Assembler_ptr createAssembler(std::string type,
199  const DataMap& options) const;
204  const double *getLength() const { return m_length; }
205 
210  const double *getElementLength() const { return m_dx; }
211 
217  virtual RankVector getOwnerVector(int fsType) const;
218 
219 protected:
220  virtual dim_t getNumNodes() const;
221  virtual dim_t getNumElements() const;
222  virtual dim_t getNumFaceElements() const;
223  virtual dim_t getNumDOF() const;
224  virtual dim_t getNumDOFInAxis(unsigned axis) const;
225  virtual dim_t getFirstInDim(unsigned axis) const;
226 
227  virtual IndexVector getDiagonalIndices(bool upperOnly) const;
228  virtual void assembleCoordinates(escript::Data& arg) const;
229  virtual void assembleGradient(escript::Data& out,
230  const escript::Data& in) const;
231  virtual void assembleIntegrate(std::vector<real_t>& integrals,
232  const escript::Data& arg) const;
233  virtual void assembleIntegrate(std::vector<cplx_t>& integrals,
234  const escript::Data& arg) const;
235  virtual std::vector<IndexVector> getConnections(bool includeShared=false) const;
236 #ifdef ESYS_HAVE_TRILINOS
237  virtual esys_trilinos::const_TrilinosGraph_ptr getTrilinosGraph() const;
238 #endif
239 
240 #ifdef ESYS_HAVE_PASO
241  virtual paso::SystemMatrixPattern_ptr getPasoMatrixPattern(
242  bool reducedRowOrder, bool reducedColOrder) const;
243 #endif
244  virtual void interpolateNodesOnElements(escript::Data& out,
245  const escript::Data& in, bool reduced) const;
246  virtual void interpolateNodesOnFaces(escript::Data& out,
247  const escript::Data& in,
248  bool reduced) const;
249  virtual void nodesToDOF(escript::Data& out, const escript::Data& in) const;
250  virtual dim_t getDofOfNode(dim_t node) const;
251 
252  void populateSampleIds();
253  void populateDofMap();
254 
255  template<typename Scalar>
256  void assembleGradientImpl(escript::Data& out,
257  const escript::Data& in) const;
258 
259  template<typename Scalar>
260  void addToMatrixAndRHS(escript::AbstractSystemMatrix* S, escript::Data& F,
261  const std::vector<Scalar>& EM_S, const std::vector<Scalar>& EM_F,
262  bool addS, bool addF, index_t firstNode, int nEq=1, int nComp=1) const;
263 
264  template<typename ValueType>
265  void readBinaryGridImpl(escript::Data& out, const std::string& filename,
266  const ReaderParameters& params) const;
267 #ifdef ESYS_HAVE_BOOST_IO
268  template<typename ValueType>
269  void readBinaryGridZippedImpl(escript::Data& out,
270  const std::string& filename,
271  const ReaderParameters& params) const;
272 #endif
273  template<typename ValueType>
274  void writeBinaryGridImpl(const escript::Data& in,
275  const std::string& filename, int byteOrder) const;
276 
277  dim_t findNode(const double *coords) const;
278 
280  const escript::DataTypes::ShapeType& shape, long seed,
281  const boost::python::tuple& filter) const;
282 
284  dim_t m_gNE[3];
285 
287  double m_origin[3];
288 
290  double m_length[3];
291 
293  double m_dx[3];
294 
296  int m_NX[3];
297 
299  dim_t m_NE[3];
300 
302  dim_t m_ownNE[3];
303 
305  dim_t m_NN[3];
306 
308  dim_t m_offset[3];
309 
311  dim_t m_faceCount[6];
312 
317 
323 
324  // vector with first node id on each rank
326 
327  // vector that maps each node to a DOF index
329 
330 #ifdef ESYS_HAVE_PASO
331  // the Paso System Matrix pattern
332  mutable paso::SystemMatrixPattern_ptr m_pattern;
333 #endif
334 
335 #ifdef ESYS_HAVE_TRILINOS
337  mutable esys_trilinos::const_TrilinosGraph_ptr m_graph;
338 #endif
339 private:
340  template<typename Scalar>
341  void assembleIntegrateImpl(std::vector<Scalar>& integrals, const escript::Data& arg) const;
342 
343  template <typename S>
344  void interpolateNodesOnElementsWorker(escript::Data& out,
345  const escript::Data& in, bool reduced, S sentinel) const;
346  template <typename S>
347  void interpolateNodesOnFacesWorker(escript::Data& out,
348  const escript::Data& in,
349  bool reduced, S sentinel) const;
350 };
351 
353 inline dim_t Brick::getDofOfNode(dim_t node) const
354 {
355  return m_dofMap[node];
356 }
357 
359 {
360  return (m_gNE[0]+1)*(m_gNE[1]+1)*(m_gNE[2]+1);
361 }
362 
363 inline double Brick::getLocalCoordinate(index_t index, int dim) const
364 {
365  ESYS_ASSERT(dim>=0 && dim<3, "'dim' out of bounds");
366  ESYS_ASSERT(index>=0 && index<m_NN[dim], "'index' out of bounds");
367  return m_origin[dim]+m_dx[dim]*(m_offset[dim]+index);
368 }
369 
370 inline boost::python::tuple Brick::getGridParameters() const
371 {
372  return boost::python::make_tuple(
373  boost::python::make_tuple(m_origin[0], m_origin[1], m_origin[2]),
374  boost::python::make_tuple(m_dx[0], m_dx[1], m_dx[2]),
375  boost::python::make_tuple(m_gNE[0], m_gNE[1], m_gNE[2]));
376 }
377 
378 //protected
379 inline dim_t Brick::getNumDOF() const
380 {
381  return (m_gNE[0]+1)/m_NX[0]*(m_gNE[1]+1)/m_NX[1]*(m_gNE[2]+1)/m_NX[2];
382 }
383 
384 //protected
385 inline dim_t Brick::getNumDOFInAxis(unsigned axis) const
386 {
387  ESYS_ASSERT(axis < m_numDim, "Invalid axis");
388  return (m_gNE[axis]+1)/m_NX[axis];
389 }
390 
391 //protected
392 inline dim_t Brick::getNumNodes() const
393 {
394  return m_NN[0]*m_NN[1]*m_NN[2];
395 }
396 
397 //protected
399 {
400  return m_NE[0]*m_NE[1]*m_NE[2];
401 }
402 
403 //protected
405 {
406  return m_faceCount[0] + m_faceCount[1] + m_faceCount[2]
407  + m_faceCount[3] + m_faceCount[4] + m_faceCount[5];
408 }
409 
410 //protected
411 inline index_t Brick::getFirstInDim(unsigned axis) const
412 {
413  return m_offset[axis] == 0 ? 0 : 1;
414 }
415 
416 } // end of namespace ripley
417 
418 #endif // __RIPLEY_BRICK_H__
419 
#define ESYS_ASSERT(a, b)
EsysAssert is a MACRO that will throw an exception if the boolean condition specified is false.
Definition: Assert.h:79
#define S(_J_, _I_)
Definition: ShapeFunctions.cpp:122
Base class for all escript domains.
Definition: AbstractDomain.h:51
Base class for escript system matrices.
Definition: AbstractSystemMatrix.h:44
Data represents a collection of datapoints.
Definition: Data.h:64
Definition: FunctionSpace.h:36
Brick is the 3-dimensional implementation of a RipleyDomain.
Definition: ripley/src/Brick.h:35
virtual dim_t getNumElements() const
returns the number of elements per MPI rank
Definition: ripley/src/Brick.h:398
const double * getLength() const
returns the lengths of the domain
Definition: ripley/src/Brick.h:204
int m_NX[3]
number of spatial subdivisions
Definition: ripley/src/Brick.h:296
IndexVector m_nodeId
Definition: ripley/src/Brick.h:320
IndexVector m_faceId
Definition: ripley/src/Brick.h:322
IndexVector m_dofId
vector of sample reference identifiers
Definition: ripley/src/Brick.h:319
dim_t m_offset[3]
first node on this rank is at (offset0,offset1,offset2) in global mesh
Definition: ripley/src/Brick.h:308
double m_origin[3]
origin of domain
Definition: ripley/src/Brick.h:287
const double * getElementLength() const
returns the lengths of an element
Definition: ripley/src/Brick.h:210
virtual const dim_t * getNumNodesPerDim() const
returns the number of nodes per MPI rank in each dimension
Definition: ripley/src/Brick.h:150
virtual IndexVector getNodeDistribution() const
returns the node distribution vector
Definition: ripley/src/Brick.h:169
virtual escript::Data randomFillWorker(const escript::DataTypes::ShapeType &shape, long seed, const boost::python::tuple &filter) const
double m_dx[3]
grid spacings / cell sizes of domain
Definition: ripley/src/Brick.h:293
virtual const dim_t * getNumElementsPerDim() const
returns the number of elements per MPI rank in each dimension
Definition: ripley/src/Brick.h:156
virtual escript::Data randomFill(const escript::DataTypes::ShapeType &shape, const escript::FunctionSpace &what, long seed, const boost::python::tuple &filter) const
Returns a Data object filled with random data passed through filter.
virtual dim_t getNumDataPointsGlobal() const
returns the number of data points summed across all MPI processes
Definition: ripley/src/Brick.h:358
IndexVector m_faceOffset
Definition: ripley/src/Brick.h:316
virtual boost::python::tuple getGridParameters() const
returns the tuple (origin, spacing, number_of_elements)
Definition: ripley/src/Brick.h:370
IndexVector m_dofMap
Definition: ripley/src/Brick.h:328
virtual const int * getNumSubdivisionsPerDim() const
returns the number of spatial subdivisions in each dimension
Definition: ripley/src/Brick.h:175
dim_t m_NN[3]
number of nodes for this rank in each dimension
Definition: ripley/src/Brick.h:305
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:163
virtual dim_t getNumNodes() const
returns the number of nodes per MPI rank
Definition: ripley/src/Brick.h:392
virtual dim_t getFirstInDim(unsigned axis) const
Definition: ripley/src/Brick.h:411
dim_t m_gNE[3]
total number of elements in each dimension
Definition: ripley/src/Brick.h:284
dim_t m_NE[3]
number of elements for this rank in each dimension including shared
Definition: ripley/src/Brick.h:299
dim_t m_faceCount[6]
number of face elements per edge (left, right, bottom, top, front, back)
Definition: ripley/src/Brick.h:311
virtual dim_t getNumDOF() const
returns the number of degrees of freedom per MPI rank
Definition: ripley/src/Brick.h:379
IndexVector m_nodeDistribution
Definition: ripley/src/Brick.h:325
IndexVector m_elementId
Definition: ripley/src/Brick.h:321
virtual dim_t getNumFaceElements() const
returns the number of face elements on current MPI rank
Definition: ripley/src/Brick.h:404
virtual double getLocalCoordinate(index_t index, int dim) const
returns the index'th coordinate value in given dimension for this rank
Definition: ripley/src/Brick.h:363
virtual dim_t getDofOfNode(dim_t node) const
Definition: ripley/src/Brick.h:353
virtual dim_t getNumDOFInAxis(unsigned axis) const
Definition: ripley/src/Brick.h:385
Definition: ripley/src/DefaultAssembler3D.h:26
Definition: LameAssembler3D.h:26
RipleyDomain extends the AbstractContinuousDomain interface for the Ripley library and is the base cl...
Definition: ripley/src/RipleyDomain.h:103
int m_numDim
Definition: ripley/src/RipleyDomain.h:771
Definition: ripley/src/WaveAssembler3D.h:26
std::vector< int > ShapeType
The shape of a single datapoint.
Definition: DataTypes.h:44
index_t dim_t
Definition: DataTypes.h:66
int index_t
type for array/matrix indices used both globally and on each rank
Definition: DataTypes.h:61
boost::shared_ptr< SubWorld > SubWorld_ptr
Definition: SubWorld.h:147
boost::shared_ptr< SystemMatrixPattern > SystemMatrixPattern_ptr
Definition: SystemMatrixPattern.h:40
Definition: ripley/src/AbstractAssembler.h:26
std::vector< index_t > IndexVector
Definition: Ripley.h:44
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:63
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:117
std::map< std::string, int > TagMap
Definition: Ripley.h:47
std::vector< int > RankVector
Definition: Ripley.h:46
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:88
std::map< std::string, escript::Data > DataMap
Definition: ripley/src/domainhelpers.h:25
#define RIPLEY_DLL_API
Definition: ripley/src/system_dep.h:21
Structure that wraps parameters for the grid reading routines.
Definition: ripley/src/RipleyDomain.h:70