escript  Revision_
dudley/src/NodeFile.h
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1 
2 /*****************************************************************************
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
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 2014-2017 by Centre for Geoscience Computing (GeoComp)
14 * Development from 2019 by School of Earth and Environmental Sciences
15 **
16 *****************************************************************************/
17 
18 #ifndef __DUDLEY_NODEFILE_H__
19 #define __DUDLEY_NODEFILE_H__
20 
21 #include "Dudley.h"
22 #include "NodeMapping.h"
23 
24 #include <escript/Distribution.h>
25 
26 #ifdef ESYS_HAVE_PASO
27 #include <paso/Coupler.h>
28 #endif
29 #ifdef ESYS_HAVE_TRILINOS
30 #include <trilinoswrap/types.h>
31 #endif
32 
33 namespace escript {
34  struct IndexList;
35 }
36 
37 namespace dudley {
38 
39 class NodeFile
40 {
41 public:
42 
45  NodeFile(int nDim, escript::JMPI MPIInfo);
46 
48  ~NodeFile();
49 
52 
54  void freeTable();
55 
56  void print() const;
57 
58  inline index_t getFirstNode() const;
59  inline index_t getLastNode() const;
60  inline dim_t getGlobalNumNodes() const;
61  inline const index_t* borrowGlobalNodesIndex() const;
62 
64  inline dim_t getNumNodes() const;
65 
67  inline dim_t getNumDegreesOfFreedom() const;
68 
70  inline dim_t getNumDegreesOfFreedomTargets() const;
71 
73  inline const index_t* borrowNodesTarget() const;
74 
76  inline const index_t* borrowDegreesOfFreedomTarget() const;
77 
79  inline const index_t* borrowTargetDegreesOfFreedom() const;
80 
82  inline const index_t* borrowTargetNodes() const;
83 
84  inline void updateTagList();
85 
89 
92 
94  const IndexVector& nodeDistribution);
95 
96  void assignMPIRankToDOFs(int* mpiRankOfDOF,
97  const IndexVector& distribution);
98 
99  void copyTable(index_t offset, index_t idOffset, index_t dofOffset,
100  const NodeFile* in);
101 
105  void gather(const index_t* index, const NodeFile* in);
106 
107  void gather_global(const index_t* index, const NodeFile* in);
108 
109  void setCoordinates(const escript::Data& newX);
110 
112  void setTags(int newTag, const escript::Data& mask);
113 
114  std::pair<index_t,index_t> getDOFRange() const;
115 
116 #ifdef ESYS_HAVE_TRILINOS
117  void createTrilinosGraph(const escript::IndexList* indexList);
118  esys_trilinos::const_TrilinosGraph_ptr getTrilinosGraph() const {
119  return m_graph;
120  }
121 #endif
122 
123 private:
124  std::pair<index_t,index_t> getGlobalIdRange() const;
125  std::pair<index_t,index_t> getGlobalDOFRange() const;
126  std::pair<index_t,index_t> getGlobalNodeIDIndexRange() const;
127  dim_t prepareLabeling(const std::vector<short>& mask, IndexVector& buffer,
128  IndexVector& distribution, bool useNodes);
130 
133 
136 
137 #ifdef ESYS_HAVE_TRILINOS
139  esys_trilinos::const_TrilinosGraph_ptr m_graph;
140 #endif
141 
142 public:
146  int numDim;
150  int* Tag;
152  std::vector<int> tagsInUse;
153 
159  double* Coordinates;
162 
165 
168 
169 #ifdef ESYS_HAVE_PASO
170  paso::Connector_ptr degreesOfFreedomConnector;
171 #endif
172  // these are the packed versions of Id
174 
177  int status;
178 };
179 
180 //
181 // implementation of inline methods
182 //
183 
185 {
186  return nodesDistribution->getFirstComponent();
187 }
188 
190 {
191  return nodesDistribution->getLastComponent();
192 }
193 
195 {
196  return nodesDistribution->getGlobalNumComponents();
197 }
198 
200 {
201  return globalNodesIndex;
202 }
203 
205 {
206  return numNodes;
207 }
208 
210 {
211  return dofDistribution->getMyNumComponents();
212 }
213 
215 {
217 }
218 
220 {
221  return nodesMapping.map;
222 }
223 
225 {
227 }
228 
230 {
231  return nodesMapping.target;
232 }
233 
235 {
237 }
238 
240 {
242 }
243 
244 
245 } // namespace dudley
246 
247 #endif // __DUDLEY_NODEFILE_H__
248 
Definition: dudley/src/NodeFile.h:40
NodeMapping degreesOfFreedomMapping
Definition: dudley/src/NodeFile.h:132
std::pair< index_t, index_t > getGlobalNodeIDIndexRange() const
Definition: dudley/src/NodeFile.cpp:167
int numDim
number of spatial dimensions
Definition: dudley/src/NodeFile.h:146
~NodeFile()
destructor
Definition: dudley/src/NodeFile.cpp:58
escript::Distribution_ptr dofDistribution
MPI distribution of degrees of freedom.
Definition: dudley/src/NodeFile.h:167
dim_t createDenseNodeLabeling(IndexVector &nodeDistribution, const IndexVector &dofDistribution)
index_t * globalNodesIndex
assigns each local node a global unique ID in a dense labeling
Definition: dudley/src/NodeFile.h:161
index_t * degreesOfFreedomId
Definition: dudley/src/NodeFile.h:173
const index_t * borrowNodesTarget() const
returns the mapping from target to the local nodes
Definition: dudley/src/NodeFile.h:219
void setTags(int newTag, const escript::Data &mask)
set tags to newTag where mask > 0
Definition: dudley/src/NodeFile.cpp:201
dim_t getNumNodes() const
returns the number of FEM nodes (on this rank)
Definition: dudley/src/NodeFile.h:204
dim_t prepareLabeling(const std::vector< short > &mask, IndexVector &buffer, IndexVector &distribution, bool useNodes)
const index_t * borrowTargetDegreesOfFreedom() const
returns the mapping from local degrees of freedom to a target
Definition: dudley/src/NodeFile.h:234
void setCoordinates(const escript::Data &newX)
Definition: dudley/src/NodeFile.cpp:172
void gather(const index_t *index, const NodeFile *in)
Definition: NodeFile_gather.cpp:77
std::pair< index_t, index_t > getGlobalDOFRange() const
Definition: dudley/src/NodeFile.cpp:162
dim_t createDenseDOFLabeling()
Definition: NodeFile_createDenseLabelings.cpp:22
void createNodeMappings(const IndexVector &dofDistribution, const IndexVector &nodeDistribution)
Definition: NodeFile_createMappings.cpp:224
const index_t * borrowGlobalNodesIndex() const
Definition: dudley/src/NodeFile.h:199
std::pair< index_t, index_t > getDOFRange() const
Definition: dudley/src/NodeFile.cpp:146
index_t * globalDegreesOfFreedom
Definition: dudley/src/NodeFile.h:157
dim_t getNumDegreesOfFreedom() const
returns the number of degrees of freedom (on this rank)
Definition: dudley/src/NodeFile.h:209
void print() const
Definition: dudley/src/NodeFile.cpp:108
std::vector< int > tagsInUse
vector of tags which are actually used
Definition: dudley/src/NodeFile.h:152
void assignMPIRankToDOFs(int *mpiRankOfDOF, const IndexVector &distribution)
Definition: dudley/src/NodeFile.cpp:220
dim_t getGlobalNumNodes() const
Definition: dudley/src/NodeFile.h:194
void freeTable()
empties the node table and frees all memory
Definition: dudley/src/NodeFile.cpp:90
const index_t * borrowTargetNodes() const
returns the mapping from local nodes to a target
Definition: dudley/src/NodeFile.h:229
index_t getLastNode() const
Definition: dudley/src/NodeFile.h:189
dim_t numNodes
number of nodes
Definition: dudley/src/NodeFile.h:135
NodeMapping nodesMapping
Definition: dudley/src/NodeFile.h:131
int status
Definition: dudley/src/NodeFile.h:177
void copyTable(index_t offset, index_t idOffset, index_t dofOffset, const NodeFile *in)
Definition: dudley/src/NodeFile.cpp:125
void createDOFMappingAndCoupling()
Definition: NodeFile_createMappings.cpp:29
escript::JMPI MPIInfo
MPI information.
Definition: dudley/src/NodeFile.h:144
index_t getFirstNode() const
Definition: dudley/src/NodeFile.h:184
dim_t getNumDegreesOfFreedomTargets() const
returns the number of degrees of freedom targets (own and shared)
Definition: dudley/src/NodeFile.h:214
void gather_global(const index_t *index, const NodeFile *in)
Definition: NodeFile_gather.cpp:85
NodeFile(int nDim, escript::JMPI MPIInfo)
Definition: dudley/src/NodeFile.cpp:44
const index_t * borrowDegreesOfFreedomTarget() const
returns the mapping from target to the local degrees of freedom
Definition: dudley/src/NodeFile.h:224
void allocTable(dim_t numNodes)
allocates the node table within this node file to hold numNodes nodes.
Definition: dudley/src/NodeFile.cpp:63
std::pair< index_t, index_t > getGlobalIdRange() const
Definition: dudley/src/NodeFile.cpp:157
int * Tag
Tag[i] is the tag of node i.
Definition: dudley/src/NodeFile.h:150
void updateTagList()
Definition: dudley/src/NodeFile.h:239
double * Coordinates
Coordinates[INDEX2(k,i,numDim)] is the k-th coordinate of node i.
Definition: dudley/src/NodeFile.h:159
escript::Distribution_ptr nodesDistribution
MPI distribution of nodes.
Definition: dudley/src/NodeFile.h:164
index_t * Id
Id[i] is the unique ID number of FEM node i.
Definition: dudley/src/NodeFile.h:148
Data represents a collection of datapoints.
Definition: Data.h:64
void setValuesInUse(const int *values, dim_t numValues, std::vector< int > &valuesInUse, escript::JMPI mpiinfo)
Definition: dudley/src/Util.cpp:224
A suite of factory methods for creating 2D and 3D dudley domains.
Definition: dudley/src/Assemble.h:32
std::vector< index_t > IndexVector
Definition: DataTypes.h:64
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
Definition: AbstractContinuousDomain.cpp:23
boost::shared_ptr< Distribution > Distribution_ptr
Definition: Distribution.h:25
boost::shared_ptr< JMPI_ > JMPI
Definition: EsysMPI.h:74
boost::shared_ptr< Connector > Connector_ptr
Definition: Coupler.h:38
Definition: dudley/src/NodeMapping.h:28
index_t * map
maps the target nodes back to the FEM nodes: target[map[i]]=i
Definition: dudley/src/NodeMapping.h:99
dim_t numTargets
size of map (number of target nodes, e.g. DOF, reduced DOF, etc.)
Definition: dudley/src/NodeMapping.h:96
index_t * target
target[i] defines the target of FEM node i=0,...,numNodes
Definition: dudley/src/NodeMapping.h:93
Definition: escriptcore/src/IndexList.h:29