NodeAMRIO.H File Reference

#include "REAL.H"
#include "LevelData.H"
#include "RealVect.H"
#include "Vector.H"
#include "NodeFArrayBox.H"
#include <string>
#include "IntVect.H"
#include "NamespaceHeader.H"
#include "NamespaceFooter.H"

Include dependency graph for NodeAMRIO.H:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Functions

void WriteAMRHierarchyHDF5 (const string &filename, const Vector< DisjointBoxLayout > &a_vectGrids, const Vector< LevelData< NodeFArrayBox > * > &a_vectData, const Vector< string > &a_vectNames, const Box &a_domain, const Real &a_dx, const Real &a_dt, const Real &a_time, const Vector< int > &a_vectRatio, const int &a_numLevels, const RealVect &a_origin=RealVect::Zero, const Interval &a_comps=Interval())
void WriteAMRHierarchyHDF5 (const string &filename, const Vector< DisjointBoxLayout > &a_vectGrids, const Vector< Vector< LevelData< NodeFArrayBox > * > > &a_vectData, const Vector< string > &a_vectNames, const Box &a_domain, const Real &a_dx, const Real &a_dt, const Real &a_time, const Vector< int > &a_vectRatio, const int &a_numLevels)
void WriteAMRHierarchyHDF5 (HDF5Handle &handle, const Vector< DisjointBoxLayout > &a_vectGrids, const Vector< LevelData< NodeFArrayBox > * > &a_vectData, const Vector< string > &a_vectNames, const Box &a_domain, const Real &a_dx, const Real &a_dt, const Real &a_time, const Vector< int > &a_vectRatio, const int &a_numLevels, const RealVect &a_origin=RealVect::Zero, const Interval &a_comps=Interval())
void WriteAMRHierarchyHDF5 (const string &filename, const Vector< DisjointBoxLayout > &a_vectGrids, const Vector< LevelData< NodeFArrayBox > * > &a_vectData, const Box &a_domain, const Vector< int > &a_vectRatio, const int &a_numLevels)
void WriteAMRHierarchyHDF5 (HDF5Handle &handle, const Vector< DisjointBoxLayout > &a_vectGrids, const Vector< LevelData< NodeFArrayBox > * > &a_vectData, const Box &a_domain, const Vector< int > &a_vectRatio, const int &a_numLevels)
int ReadAMRHierarchyHDF5 (const string &filename, Vector< DisjointBoxLayout > &a_vectGrids, Vector< LevelData< NodeFArrayBox > * > &a_vectData, Vector< string > &a_vectNames, Box &a_domain, Real &a_dx, Real &a_dt, Real &a_time, Vector< int > &a_refRatio, int &a_numLevels, bool a_setGhost=false)
int ReadAMRHierarchyHDF5 (HDF5Handle &handle, Vector< DisjointBoxLayout > &a_vectGrids, Vector< LevelData< NodeFArrayBox > * > &a_vectData, Vector< string > &a_vectNames, Box &a_domain, Real &a_dx, Real &a_dt, Real &a_time, Vector< int > &a_refRatio, int &a_numLevels, bool a_setGhost=false)
int ReadAMRHierarchyHDF5 (const string &filename, Vector< DisjointBoxLayout > &a_vectGrids, Vector< LevelData< NodeFArrayBox > * > &a_vectData, Box &a_domain, Vector< int > &a_refRatio, int &a_numLevels, bool a_setGhost=false)
int ReadAMRHierarchyHDF5 (HDF5Handle &handle, Vector< DisjointBoxLayout > &a_vectGrids, Vector< LevelData< NodeFArrayBox > * > &a_vectData, Box &a_domain, Vector< int > &a_refRatio, int &a_numLevels, bool a_setGhost=false)
void writeNFAB (const NodeFArrayBox *a_dataPtr)
void viewNFAB (const NodeFArrayBox *a_dataPtr)
void writeNFABname (const NodeFArrayBox *a_dataPtr, const char *a_filename)
void writeNodeLevel (const LevelData< NodeFArrayBox > *a_dataPtr)
void viewNodeLevel (const LevelData< NodeFArrayBox > *a_dataPtr)
void writeNodeLevelname (const LevelData< NodeFArrayBox > *a_dataPtr, const char *a_filename)
void WritePartialAMRHierarchyHDF5 (const string &filename, const Vector< DisjointBoxLayout > &a_vectGrids, const Vector< LevelData< FArrayBox > * > &a_vectData, const Vector< string > &a_vectNames, const Box &a_baseDomain, const Real &a_baseDx, const Real &a_dt, const Real &a_time, const Vector< int > &a_vectRatio, const Interval &a_levels)
void WritePartialAMRHierarchyHDF5 (const string &filename, const Vector< DisjointBoxLayout > &a_vectGrids, const Vector< Vector< LevelData< NodeFArrayBox > * > > &a_vectData, const Vector< string > &a_vectNames, const Box &a_baseDomain, const Real &a_baseDx, const Real &a_dt, const Real &a_time, const Vector< int > &a_vectRatio, const Interval &a_levels)


Function Documentation

void WriteAMRHierarchyHDF5 ( const string &  filename,
const Vector< DisjointBoxLayout > &  a_vectGrids,
const Vector< LevelData< NodeFArrayBox > * > &  a_vectData,
const Vector< string > &  a_vectNames,
const Box a_domain,
const Real a_dx,
const Real a_dt,
const Real a_time,
const Vector< int > &  a_vectRatio,
const int &  a_numLevels,
const RealVect a_origin = RealVect::Zero,
const Interval a_comps = Interval() 
)

Writes hierarchy of levels in HDF5 format. Only available if the preprocessor macro HDF5 is defined at compilation.

This is blocking.

Parameters:
filename  file to send output to
a_vectGrids  grids at each level
a_vectData  data indexed by level
a_vectNames  names of variables in a_vectData
a_domain  domain at coarsest level
a_dx  grid spacing at coarsest level
a_dt  time step at coarsest level
a_time  time
a_vectRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_numLevels  number of levels to write out
a_origin  physical coordinates of lower corner of cell at IntVect 0
a_comps  Interval of components to be written

void WriteAMRHierarchyHDF5 ( const string &  filename,
const Vector< DisjointBoxLayout > &  a_vectGrids,
const Vector< Vector< LevelData< NodeFArrayBox > * > > &  a_vectData,
const Vector< string > &  a_vectNames,
const Box a_domain,
const Real a_dx,
const Real a_dt,
const Real a_time,
const Vector< int > &  a_vectRatio,
const int &  a_numLevels 
)

Writes hierarchy of levels in HDF5 format. Only available if the preprocessor macro HDF5 is defined at compilation.

This function differs from the previous one in that a_vectData[ind][lev] indexes a LevelData<NodeFArrayBox>* (which may have several components) at level lev.

This is blocking.

Parameters:
filename  file to send output to
a_vectGrids  grids at each level
a_vectData  data indexed by set and then by level
a_vectNames  names of variables in a_vectData: first the names of the components of a_vectData[0], then the names of the components of a_vectData[1], etc.
a_domain  domain at coarsest level
a_dx  grid spacing at coarsest level
a_dt  time step at coarsest level
a_time  time
a_vectRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_numLevels  number of levels to write out

void WriteAMRHierarchyHDF5 ( HDF5Handle handle,
const Vector< DisjointBoxLayout > &  a_vectGrids,
const Vector< LevelData< NodeFArrayBox > * > &  a_vectData,
const Vector< string > &  a_vectNames,
const Box a_domain,
const Real a_dx,
const Real a_dt,
const Real a_time,
const Vector< int > &  a_vectRatio,
const int &  a_numLevels,
const RealVect a_origin = RealVect::Zero,
const Interval a_comps = Interval() 
)

Writes hierarchy of levels in HDF5 format. Only available if the preprocessor macro HDF5 is defined at compilation.

This is not blocking.

Parameters:
handle  handle to send output to
a_vectGrids  grids at each level
a_vectData  data indexed by level
a_vectNames  names of variables in a_vectData
a_domain  domain at coarsest level
a_dx  grid spacing at coarsest level
a_dt  time step at coarsest level
a_time  time
a_vectRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_numLevels  number of levels to write out
a_origin  physical coordinates of lower corner of cell at IntVect 0
a_comps  Interval of components to be written

void WriteAMRHierarchyHDF5 ( const string &  filename,
const Vector< DisjointBoxLayout > &  a_vectGrids,
const Vector< LevelData< NodeFArrayBox > * > &  a_vectData,
const Box a_domain,
const Vector< int > &  a_vectRatio,
const int &  a_numLevels 
)

Writes hierarchy of levels in HDF5 format. Only available if the preprocessor macro HDF5 is defined at compilation.

This is blocking.

Parameters:
filename  file to send output to
a_vectGrids  grids at each level
a_vectData  data indexed by level
a_domain  domain at coarsest level
a_vectRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_numLevels  number of levels to write out

void WriteAMRHierarchyHDF5 ( HDF5Handle handle,
const Vector< DisjointBoxLayout > &  a_vectGrids,
const Vector< LevelData< NodeFArrayBox > * > &  a_vectData,
const Box a_domain,
const Vector< int > &  a_vectRatio,
const int &  a_numLevels 
)

Writes hierarchy of levels in HDF5 format. Only available if the preprocessor macro HDF5 is defined at compilation.

This is not blocking.

Parameters:
handle  handle to send output to
a_vectGrids  grids at each level
a_vectData  data indexed by level
a_domain  domain at coarsest level
a_vectRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_numLevels  number of levels to write out

int ReadAMRHierarchyHDF5 ( const string &  filename,
Vector< DisjointBoxLayout > &  a_vectGrids,
Vector< LevelData< NodeFArrayBox > * > &  a_vectData,
Vector< string > &  a_vectNames,
Box a_domain,
Real a_dx,
Real a_dt,
Real a_time,
Vector< int > &  a_refRatio,
int &  a_numLevels,
bool  a_setGhost = false 
)

Reads hierarchy of levels in HDF5 format. Only available if the preprocessor macro HDF5 is defined at compilation. Returns 0 on success.

Returns status code with values:

  • 0: success
  • -1: bogus number of levels
  • -2: bogus number of components
  • -3: error in readlevel
  • -4: file open failed

This is blocking.

Parameters:
filename  file to read input from
a_vectGrids  grids at each level
a_vectData  data indexed by level
a_vectNames  names of variables in a_vectData
a_domain  domain at coarsest level
a_dx  grid spacing at coarsest level
a_dt  time step at coarsest level
a_time  time
a_refRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_numLevels  number of levels to read in

int ReadAMRHierarchyHDF5 ( HDF5Handle handle,
Vector< DisjointBoxLayout > &  a_vectGrids,
Vector< LevelData< NodeFArrayBox > * > &  a_vectData,
Vector< string > &  a_vectNames,
Box a_domain,
Real a_dx,
Real a_dt,
Real a_time,
Vector< int > &  a_refRatio,
int &  a_numLevels,
bool  a_setGhost = false 
)

Reads hierarchy of levels in HDF5 format. Only available if the preprocessor macro HDF5 is defined at compilation. Returns 0 on success.

Returns status code with values:

  • 0: success
  • -1: bogus number of levels
  • -2: bogus number of components
  • -3: error in readlevel
  • -4: file open failed

This is not blocking.

Parameters:
handle  handle to read input from
a_vectGrids  grids at each level
a_vectData  data indexed by level
a_vectNames  names of variables in a_vectData
a_domain  domain at coarsest level
a_dx  grid spacing at coarsest level
a_dt  time step at coarsest level
a_time  time
a_refRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_numLevels  number of levels to read in

int ReadAMRHierarchyHDF5 ( const string &  filename,
Vector< DisjointBoxLayout > &  a_vectGrids,
Vector< LevelData< NodeFArrayBox > * > &  a_vectData,
Box a_domain,
Vector< int > &  a_refRatio,
int &  a_numLevels,
bool  a_setGhost = false 
)

Reads hierarchy of levels in HDF5 format. Only available if the preprocessor macro HDF5 is defined at compilation. Returns 0 on success.

Returns status code with values:

  • 0: success
  • -1: bogus number of levels
  • -2: bogus number of components
  • -3: error in readlevel
  • -4: file open failed

This is blocking.

Parameters:
filename  file to read input from
a_vectGrids  grids at each level
a_vectData  data indexed by level
a_domain  domain at coarsest level
a_refRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_numLevels  number of levels to read in

int ReadAMRHierarchyHDF5 ( HDF5Handle handle,
Vector< DisjointBoxLayout > &  a_vectGrids,
Vector< LevelData< NodeFArrayBox > * > &  a_vectData,
Box a_domain,
Vector< int > &  a_refRatio,
int &  a_numLevels,
bool  a_setGhost = false 
)

Reads hierarchy of levels in HDF5 format. Only available if the preprocessor macro HDF5 is defined at compilation. Returns 0 on success.

Returns status code with values:

  • 0: success
  • -1: bogus number of levels
  • -2: bogus number of components
  • -3: error in readlevel
  • -4: file open failed

This is not blocking.

Parameters:
handle  handle to input from
a_vectGrids  grids at each level
a_vectData  data indexed by level
a_domain  domain at coarsest level
a_refRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_numLevels  number of levels to read in

void writeNFAB ( const NodeFArrayBox a_dataPtr  ) 

Writes a plotfile using the same format as WriteAMRHierarchyHDF5, but for a NodeFArrayBox. This is useful for debugging. a_dataPtr is written to a file named nfab.hdf5

Referenced by InitWriteFAB().

void viewNFAB ( const NodeFArrayBox a_dataPtr  ) 

View *a_dataPtr by writing it to an HDF5 plotfile (to a temporary file) and then running ChomboVis with a python script which brings up a data browser by default. The file has the same format as WriteAMRHierarchyHDF5, but for a single NodeFArrayBox. This is useful for debugging.

Referenced by InitWriteFAB().

void writeNFABname ( const NodeFArrayBox a_dataPtr,
const char *  a_filename 
)

Writes a plotfile using the same format as WriteAMRHierarchyHDF5, but for a NodeFArrayBox. This is useful for debugging. a_dataPtr is written to the file given by a_filename.

Referenced by InitWriteFAB().

void writeNodeLevel ( const LevelData< NodeFArrayBox > *  a_dataPtr  ) 

Write a plotfile using the same format as WriteAMRHierarchyHDF5, but for a single LevelData<NodeFArrayBox>. Useful for debugging. a_dataPtr is written to a file named LDF.hdf5.

Referenced by InitWriteFAB().

void viewNodeLevel ( const LevelData< NodeFArrayBox > *  a_dataPtr  ) 

View *a_dataPtr by writing it to an HDF5 plotfile (to a temporary file) and then running ChomboVis with a python script which brings up a data browser by default. The file has the same format as WriteAMRHierarchyHDF5, but for a single LevelData<NodeFArrayBox>. This is useful for debugging.

Referenced by InitWriteFAB().

void writeNodeLevelname ( const LevelData< NodeFArrayBox > *  a_dataPtr,
const char *  a_filename 
)

Write a plotfile using the same format as WriteAMRHierarchyHDF5, but for a single LevelData<FArrayBox>. Useful for debugging. a_dataPtr is written to the file given by a_filename.

Referenced by InitWriteFAB().

void WritePartialAMRHierarchyHDF5 ( const string &  filename,
const Vector< DisjointBoxLayout > &  a_vectGrids,
const Vector< LevelData< FArrayBox > * > &  a_vectData,
const Vector< string > &  a_vectNames,
const Box a_baseDomain,
const Real a_baseDx,
const Real a_dt,
const Real a_time,
const Vector< int > &  a_vectRatio,
const Interval a_levels 
)

Write a plotfile with levels that don't necessarily begin with 0 (will translate things so that base level comes out as level 0, etc.). Levels in Vector arguments should correspond with actual levels, and so should be defined for a_levels.begin() through a_levels.end().

This is blocking.

Parameters:
filename  file to send output to
a_vectGrids  grids at each level
a_vectData  data indexed by level
a_vectNames  names of variables in a_vectData
a_baseDomain  domain at base level given by a_levels.begin()
a_baseDx  grid spacing at base level
a_dt  time step at base level
a_time  time
a_vectRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_levels  indices of levels to write out

void WritePartialAMRHierarchyHDF5 ( const string &  filename,
const Vector< DisjointBoxLayout > &  a_vectGrids,
const Vector< Vector< LevelData< NodeFArrayBox > * > > &  a_vectData,
const Vector< string > &  a_vectNames,
const Box a_baseDomain,
const Real a_baseDx,
const Real a_dt,
const Real a_time,
const Vector< int > &  a_vectRatio,
const Interval a_levels 
)

Write a plotfile with levels that don't necessarily begin with 0 (will translate things so that base level comes out as level 0, etc.). Levels in Vector arguments should correspond with actual levels, and so should be defined for a_levels.begin() through a_levels.end().

This function differs from the previous one in that a_vectData[ind][lev] indexes a LevelData<NodeFArrayBox>* (which may have several components) at level lev.

This is blocking.

Parameters:
filename  file to send output to
a_vectGrids  grids at each level
a_vectData  data indexed by set and then by level
a_vectNames  names of variables in a_vectData
a_baseDomain  domain at base level given by a_levels.begin()
a_baseDx  grid spacing at base level
a_dt  time step at base level
a_time  time
a_vectRatio  refinement ratios between adjacent levels, starting with a_refRatio[0], the refinement ratio between levels 0 and 1; Vector length at least a_numLevels-1
a_levels  indices of levels to write out


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