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FinleyNodes.h
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17 
18 #ifndef __WEIPA_FINLEYNODES_H__
19 #define __WEIPA_FINLEYNODES_H__
20 
21 #include <weipa/NodeData.h>
22 
23 class DBfile;
24 
25 #ifdef NETCDF4
26 #include <ncFile.h>
27 #define NCFTYPE netCDF::NcFile&
28 
29 #else
30 class NcFile;
31 #define NCFTYPE NcFile*
32 #endif
33 
34 namespace finley {
35  class NodeFile;
36 }
37 namespace dudley {
38  class NodeFile;
39 }
40 
41 namespace weipa {
42 
44 typedef boost::shared_ptr<FinleyNodes> FinleyNodes_ptr;
45 
51 class FinleyNodes : public NodeData
52 {
53 public:
55  FinleyNodes(const std::string& meshName);
56 
57  FinleyNodes(FinleyNodes_ptr fullNodes, IntVec& requiredNodes,
58  const std::string& meshName);
59 
61  FinleyNodes(const FinleyNodes& m);
62 
64  virtual ~FinleyNodes();
65 
67  bool initFromDudley(const dudley::NodeFile* dudleyFile);
68 
70  bool initFromFinley(const finley::NodeFile* finleyFile);
71 
73  bool readFromNc(NCFTYPE ncFile);
74 
76  bool writeToSilo(DBfile* dbfile);
77 
79  virtual void writeCoordinatesVTK(std::ostream& os, int ownIndex);
80 
82  void setSiloPath(const std::string& path) { siloPath = path; }
83 
87  const IntVec& getVarDataByName(const std::string& name) const;
88 
90  virtual StringVec getVarNames() const;
91 
93  virtual std::string getName() const { return name; }
94 
96  std::string getFullSiloName() const;
97 
99  virtual const IntVec& getNodeIDs() const { return nodeID; }
100 
102  virtual const IntVec& getNodeDistribution() const { return nodeDist; }
103 
105  virtual const IntVec& getGlobalNodeIndices() const { return nodeGNI; }
106 
108  virtual const CoordArray& getCoords() const { return coords; }
109 
111  virtual int getNumDims() const { return numDims; }
112 
114  virtual int getNumNodes() const { return numNodes; }
115 
117  virtual int getGlobalNumNodes() const;
118 
119 protected:
121  int numDims;
122  int numNodes;
126  std::string name;
127  std::string siloPath;
128 };
129 
130 
131 inline std::string FinleyNodes::getFullSiloName() const
132 {
133  std::string result(siloPath);
134  if (result.length() == 0 || *result.rbegin() != '/')
135  result += '/';
136  result += name;
137  return result;
138 }
139 
140 } // namespace weipa
141 
142 #undef NCFTYPE
143 #endif // __WEIPA_FINLEYNODES_H__
144 
dudley::NodeFile::globalDegreesOfFreedom
index_t * globalDegreesOfFreedom
Definition: dudley/src/NodeFile.h:157
weipa::FinleyNodes::getNumNodes
virtual int getNumNodes() const
Returns the number of mesh nodes.
Definition: FinleyNodes.h:114
weipa::FinleyNodes::getVarDataByName
const IntVec & getVarDataByName(const std::string &name) const
Returns an array of nodal data by the given name.
Definition: FinleyNodes.cpp:397
finley::NodeFile::globalReducedNodesIndex
index_t * globalReducedNodesIndex
Definition: finley/src/NodeFile.h:181
weipa::FinleyNodes::initFromDudley
bool initFromDudley(const dudley::NodeFile *dudleyFile)
Initialises with dudley node file.
Definition: FinleyNodes.cpp:142
weipa::FinleyNodes::nodeDist
IntVec nodeDist
Definition: FinleyNodes.h:125
dudley::NodeFile::nodesDistribution
escript::Distribution_ptr nodesDistribution
MPI distribution of nodes.
Definition: dudley/src/NodeFile.h:164
dudley::NodeFile::numDim
int numDim
number of spatial dimensions
Definition: dudley/src/NodeFile.h:146
dudley::NodeFile
Definition: dudley/src/NodeFile.h:39
finley::NodeFile::globalDegreesOfFreedom
index_t * globalDegreesOfFreedom
Definition: finley/src/NodeFile.h:173
weipa::FinleyNodes::getName
virtual std::string getName() const
Returns the name of this node mesh.
Definition: FinleyNodes.h:93
finley::NodeFile::Tag
int * Tag
Tag[i] is the tag of node i.
Definition: finley/src/NodeFile.h:166
finley::NodeFile::nodesDistribution
escript::Distribution_ptr nodesDistribution
MPI distribution of nodes.
Definition: finley/src/NodeFile.h:186
dudley::NodeFile::getNumNodes
dim_t getNumNodes() const
returns the number of FEM nodes (on this rank)
Definition: dudley/src/NodeFile.h:204
finley::NodeFile::globalReducedDOFIndex
index_t * globalReducedDOFIndex
Definition: finley/src/NodeFile.h:178
weipa::FinleyNodes::writeCoordinatesVTK
virtual void writeCoordinatesVTK(std::ostream &os, int ownIndex)
Writes coordinates to a stream in VTK text format.
Definition: FinleyNodes.cpp:444
weipa::FinleyNodes::nodeGNI
IntVec nodeGNI
Definition: FinleyNodes.h:124
weipa::FinleyNodes::siloPath
std::string siloPath
the name of this node mesh
Definition: FinleyNodes.h:127
weipa::FinleyNodes::readFromNc
bool readFromNc(NcFile *ncFile)
Reads node data from a NetCDF file.
Definition: FinleyNodes.cpp:320
weipa::FinleyNodes::getGlobalNumNodes
virtual int getGlobalNumNodes() const
Returns the total number of mesh nodes for a distributed mesh.
Definition: FinleyNodes.cpp:433
weipa
Definition: DataVar.cpp:51
finley::NodeFile::getNumNodes
dim_t getNumNodes() const
returns the number of FEM nodes (on this rank)
Definition: finley/src/NodeFile.h:256
paso::util::copy
void copy(dim_t N, double *out, const double *in)
out = in
Definition: PasoUtil.h:116
finley::NodeFile::Coordinates
double * Coordinates
Coordinates[INDEX2(k,i,numDim)] is the k-th coordinate of node i.
Definition: finley/src/NodeFile.h:175
weipa::NodeData
Definition: NodeData.h:41
dudley
A suite of factory methods for creating 2D and 3D dudley domains.
Definition: dudley/src/Assemble.h:32
weipa::FinleyNodes::nodeGDOF
IntVec nodeGDOF
Definition: FinleyNodes.h:124
weipa::FinleyNodes::nodeTag
IntVec nodeTag
node IDs
Definition: FinleyNodes.h:124
weipa::IndexMap
std::map< int, size_t > IndexMap
Definition: weipa.h:63
weipa::CoordArray
std::vector< float * > CoordArray
Definition: weipa.h:62
weipa::FinleyNodes::getGlobalNodeIndices
virtual const IntVec & getGlobalNodeIndices() const
Returns the global node index array.
Definition: FinleyNodes.h:105
weipa::FinleyNodes::initFromFinley
bool initFromFinley(const finley::NodeFile *finleyFile)
Initialises with finley node file.
Definition: FinleyNodes.cpp:189
finley::NodeFile::Id
index_t * Id
Id[i] is the unique ID number of FEM node i.
Definition: finley/src/NodeFile.h:164
weipa::FinleyNodes::~FinleyNodes
virtual ~FinleyNodes()
Virtual destructor.
Definition: FinleyNodes.cpp:132
weipa::FinleyNodes::nodeID
IntVec nodeID
number of nodes
Definition: FinleyNodes.h:123
weipa::FinleyNodes::getFullSiloName
std::string getFullSiloName() const
Returns full Silo mesh name, e.g. "/block0000/Nodes".
Definition: FinleyNodes.h:131
weipa::FinleyNodes::getNumDims
virtual int getNumDims() const
Returns the dimensionality of this mesh (2 or 3).
Definition: FinleyNodes.h:111
weipa::FinleyNodes::numNodes
int numNodes
dimensionality (2 or 3)
Definition: FinleyNodes.h:122
weipa::FinleyNodes::writeToSilo
bool writeToSilo(DBfile *dbfile)
Writes node data to a Silo file.
Definition: FinleyNodes.cpp:465
weipa::FinleyNodes::setSiloPath
void setSiloPath(const std::string &path)
Sets the silo path to be used when saving.
Definition: FinleyNodes.h:82
weipa::FinleyNodes::getCoords
virtual const CoordArray & getCoords() const
Returns the coordinates of the mesh nodes.
Definition: FinleyNodes.h:108
weipa::FinleyNodes::numDims
int numDims
x, y[, z] coordinates of nodes
Definition: FinleyNodes.h:121
NCFTYPE
#define NCFTYPE
Definition: FinleyNodes.h:31
escript::DataTypes::index_t
int index_t
type for array/matrix indices used both globally and on each rank
Definition: DataTypes.h:88
weipa::FinleyNodes::getNodeIDs
virtual const IntVec & getNodeIDs() const
Returns the node ID array.
Definition: FinleyNodes.h:99
weipa::FinleyNodes::coords
CoordArray coords
Definition: FinleyNodes.h:120
finley::NodeFile
Definition: finley/src/NodeFile.h:41
weipa::FinleyNodes::nodeGRDFI
IntVec nodeGRDFI
Definition: FinleyNodes.h:124
weipa::FinleyNodes::name
std::string name
node distribution
Definition: FinleyNodes.h:126
weipa::FinleyNodes::FinleyNodes
FinleyNodes(const std::string &meshName)
Constructor with mesh name.
Definition: FinleyNodes.cpp:55
weipa::StringVec
std::vector< std::string > StringVec
Definition: weipa.h:61
finley::NodeFile::globalNodesIndex
index_t * globalNodesIndex
assigns each local node a global unique ID in a dense labeling
Definition: finley/src/NodeFile.h:183
dudley::NodeFile::Id
index_t * Id
Id[i] is the unique ID number of FEM node i.
Definition: dudley/src/NodeFile.h:148
dudley::NodeFile::Tag
int * Tag
Tag[i] is the tag of node i.
Definition: dudley/src/NodeFile.h:150
weipa::FinleyNodes
Stores and manipulates finley mesh nodes.
Definition: FinleyNodes.h:51
weipa::FinleyNodes_ptr
boost::shared_ptr< FinleyNodes > FinleyNodes_ptr
Definition: FinleyNodes.h:43
weipa::FinleyNodes::getNodeDistribution
virtual const IntVec & getNodeDistribution() const
Returns the node distribution array.
Definition: FinleyNodes.h:102
weipa::FinleyNodes::getVarNames
virtual StringVec getVarNames() const
Returns a vector with the mesh variable names.
Definition: FinleyNodes.cpp:418
weipa::IntVec
std::vector< int > IntVec
Definition: weipa.h:60
finley
A suite of factory methods for creating various finley domains.
Definition: finley/src/Assemble.h:32
finley::NodeFile::numDim
int numDim
number of spatial dimensions
Definition: finley/src/NodeFile.h:162
dudley::NodeFile::Coordinates
double * Coordinates
Coordinates[INDEX2(k,i,numDim)] is the k-th coordinate of node i.
Definition: dudley/src/NodeFile.h:159
weipa::FinleyNodes::nodeGRNI
IntVec nodeGRNI
Definition: FinleyNodes.h:124
dudley::NodeFile::globalNodesIndex
index_t * globalNodesIndex
assigns each local node a global unique ID in a dense labeling
Definition: dudley/src/NodeFile.h:161