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	WriteAnisotropicAMRHierarchyHDF5 (const string &filename, const Vector< DisjointBoxLayout > &a_vectGrids, const Vector< LevelData< NodeFArrayBox > * > &a_vectData, const Vector< string > &a_vectNames, const Box &a_domain, const RealVect &a_dx, const Real &a_dt, const Real &a_time, const Vector< IntVect > &a_vectRatios, 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	WriteAnisotropicAMRHierarchyHDF5 (HDF5Handle &handle, const Vector< DisjointBoxLayout > &a_vectGrids, const Vector< LevelData< NodeFArrayBox > * > &a_vectData, const Vector< string > &a_vectNames, const Box &a_domain, const RealVect &a_dx, const Real &a_dt, const Real &a_time, const Vector< IntVect > &a_vectRatios, 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 WriteAnisotropicAMRHierarchyHDF5	(	const string &	filename,
		const Vector< DisjointBoxLayout > &	a_vectGrids,
		const Vector< LevelData< NodeFArrayBox > * > &	a_vectData,
		const Vector< string > &	a_vectNames,
		const Box &	a_domain,
		const RealVect &	a_dx,
		const Real &	a_dt,
		const Real &	a_time,
		const Vector< IntVect > &	a_vectRatios,
		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 in each direction at coarsest level
a_dt	time step at coarsest level
a_time	time
a_vectRatios	refinement ratios in each direction 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 WriteAnisotropicAMRHierarchyHDF5	(	HDF5Handle &	handle,
		const Vector< DisjointBoxLayout > &	a_vectGrids,
		const Vector< LevelData< NodeFArrayBox > * > &	a_vectData,
		const Vector< string > &	a_vectNames,
		const Box &	a_domain,
		const RealVect &	a_dx,
		const Real &	a_dt,
		const Real &	a_time,
		const Vector< IntVect > &	a_vectRatios,
		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_vectRatios	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