hdf5_obj – LEAP

type, public :: hdf5_obj

A utility to read/write files in HDF5 format

Inherits

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Inherited by

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Components

Type	Visibility	Attributes		Name		Initial
character(len=:),	public,	allocatable	::	filename			file to read/write
type(parallel_obj),	public,	pointer	::	parallel	=>	null()	Associated parallel structure
integer(kind=HID_T),	private		::	fid			File identifier
logical,	private		::	is_open	=	.false.	Switch for when file is open/closed
integer(kind=HID_T),	private		::	plistid			Property list identifier
type(hashtbl_obj),	private		::	tbl			Hash table

Type-Bound Procedures

procedure, public :: Close => hdf5_obj_Close

private impure subroutine hdf5_obj_Close(this)

Closes hdf5 file.

Arguments

Type	Intent	Optional	Attributes		Name
class(hdf5_obj),	intent(inout)			::	this	A HDF5 object

procedure, public :: CloseGroup => hdf5_obj_CloseGroup

private impure subroutine hdf5_obj_CloseGroup(this, groupname)

Closes an HDF5 group and removes it from the hashtable.

Arguments

Type	Intent	Optional	Attributes		Name
class(hdf5_obj),	intent(inout)			::	this	A HDF5 object
character(len=*),	intent(in)			::	groupname	Group to close

procedure, public :: CreateGroup => hdf5_obj_CreateGroup

private impure subroutine hdf5_obj_CreateGroup(this, groupname)

Creates a group (analogous to directory) in an HDF5 file and updates hash table.

Arguments

Type	Intent	Optional	Attributes		Name
class(hdf5_obj),	intent(inout)			::	this	A HDF5 object
character(len=*),	intent(in)			::	groupname	Group name

procedure, public :: Finalize => hdf5_obj_Final

private impure subroutine hdf5_obj_Final(this)

Finalizes object and frees memory.

Arguments

Type	Intent	Optional	Attributes		Name
class(hdf5_obj),	intent(inout)			::	this	A HDF5 object

procedure, public :: GetNPoints => hdf5_obj_GetNPoints

private impure function hdf5_obj_GetNPoints(this, groupname, name) result(val)

Returns the number of points in a dataset given by name under group given by name.

Arguments

Type	Intent		Name
class(hdf5_obj),	intent(inout)	::	this	A HDF5 object
character(len=*),	intent(in)	::	groupname	Parent group name
character(len=*),	intent(in)	::	name	Dataset name

Return Value integer

Result

procedure, public :: Initialize => hdf5_obj_Init

private impure subroutine hdf5_obj_Init(this, parallel)

Initializes the hdf5 object.

Arguments

Type	Intent	Optional	Attributes		Name
class(hdf5_obj),	intent(inout)			::	this	A HDF5 object
type(parallel_obj),	intent(in),		target	::	parallel	Parallel structure to point to

procedure, public :: Open => hdf5_obj_Open

private impure subroutine hdf5_obj_Open(this, name, flag)

Opens a hdf5 file given by name with mode stated by flag. This can take one of these values: 'R' for read only 'W' for write only (will delete existing file) 'RW' for read-write

Arguments

Type	Intent		Name
class(hdf5_obj),	intent(inout)	::	this	A HDF5 object
character(len=*),	intent(in)	::	name	Filename
character(len=*),	intent(in)	::	flag	Access mode

procedure, public :: OpenGroup => hdf5_obj_OpenGroup

private impure subroutine hdf5_obj_OpenGroup(this, groupname)

Opens a group (analogous to directory) in an HDF5 file and updates hash table.

Arguments

Type	Intent	Optional	Attributes		Name
class(hdf5_obj),	intent(inout)			::	this	A HDF5 object
character(len=*),	intent(in)			::	groupname	Group name

generic, public :: Read => hdf5_obj_Read3D, hdf5_obj_Read1D

private impure subroutine hdf5_obj_Read3D(this, groupname, name, array, lo, hi)

Reads a 3D dataset located under groupname and given by name.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Parent group containing the dataset
character(len=*),	intent(in)		::	name	Dataset name
class(*),	intent(out),	target	::	array(:,:,:)	Data array
integer,	intent(in)		::	lo(3)	Low bounds
integer,	intent(in)		::	hi(3)	High bounds

private impure subroutine hdf5_obj_Read1D(this, groupname, name, array, offset)

Reads a 1D dataset located under groupname and given by name. If no offset is provided, uses default file view. Otherwise, sets file view manually.

Arguments

Type	Intent	Optional	Attributes		Name
class(hdf5_obj),	intent(inout)			::	this	A HDF5 object
character(len=*),	intent(in)			::	groupname	Parent group containing the dataset
character(len=*),	intent(in)			::	name	Dataset name
class(*),	intent(out),		target	::	array(:)	Data array
integer,	intent(in),	optional		::	offset	Indicates number of elements to skip before reading

generic, public :: ReadAttributes => hdf5_obj_ReadAttributes0D, hdf5_obj_ReadAttributes1D

private impure subroutine hdf5_obj_ReadAttributes0D(this, groupname, label, val)

Read a scalar attribute under a given group.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	label	Attribute label
class(*),	intent(out),	target	::	val	Attribute value

private impure subroutine hdf5_obj_ReadAttributes1D(this, groupname, label, val)

Read a 1-D array of attributes under a given group.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	label	Attribute label
class(*),	intent(out),	target	::	val(:)	Attribute values

procedure, public :: ReadCoord => hdf5_obj_ReadCoord

private impure subroutine hdf5_obj_ReadCoord(this, groupname, name, Coord)

Reads coordinates from HDF5 file. Only the root MPI rank does the reading, and then broadcasts to other MPI ranks.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	name	Variable name
class(*),	intent(out),	target	::	Coord(:)	1-D Coordinates

procedure, public :: ReadDatasetNames => hdf5_obj_ReadDatasetNames

private impure subroutine hdf5_obj_ReadDatasetNames(this, basegroup, names)

Reads the dataset names under a given base group in an HDF5 file.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	basegroup	Base group to explore
character(len=str64),	intent(out),	allocatable	::	names(:)	Dataset names under the base group

procedure, public :: ReadGroupNames => hdf5_obj_ReadGroupNames

private impure subroutine hdf5_obj_ReadGroupNames(this, basegroup, names)

Reads the groups (i.e., directories) under a given base group in an HDF5 file.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	basegroup	Base group to explore
character(len=str64),	intent(out),	allocatable	::	names(:)	Names of groups under the base group

generic, public :: Write => hdf5_obj_Write3D, hdf5_obj_Write1D

private impure subroutine hdf5_obj_Write3D(this, groupname, name, array, lo, hi)

Writes Eulerian/3D data to a HDF5 file.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	name	Variable name
class(*),	intent(in),	target	::	array(:,:,:)	3-D data array
integer,	intent(in)		::	lo(3)	Low bounds
integer,	intent(in)		::	hi(3)	High bounds

private impure subroutine hdf5_obj_Write1D(this, groupname, name, array)

Writes an array/1D data to a HDF5 file.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	name	Variable name
class(*),	intent(in),	target	::	array(:)	1-D data array

generic, public :: WriteAttributes => hdf5_obj_WriteAttributes0D, hdf5_obj_WriteAttributes1D

private impure subroutine hdf5_obj_WriteAttributes0D(this, groupname, label, val)

Writes a scalar attribute.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	label	attribute label
class(*),	intent(in),	target	::	val	Attribute label

private impure subroutine hdf5_obj_WriteAttributes1D(this, groupname, label, val)

Writes an array of attributes.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	label	attribute label
class(*),	intent(in),	target	::	val(:)	Attribute labels

procedure, public :: WriteCoord => hdf5_obj_WriteCoord

private impure subroutine hdf5_obj_WriteCoord(this, groupname, name, Coord)

Writes coordinates to HDF5 file. Only the root MPI rank does the writing.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	name	Variable name
class(*),	intent(in),	target	::	Coord(:)	1-D Coordinates

procedure, private, nopass :: FixGroupName => hdf5_obj_FixGroupName

private pure function hdf5_obj_FixGroupName(groupname) result(val)

Function that will append and prepend '/' if missing.

Arguments

Type	Intent	Optional	Attributes		Name
character(len=*),	intent(in)			::	groupname

Return Value character(len=:), allocatable

procedure, private :: GetGroupObject => hdf5_obj_GetGroupObject

private impure function hdf5_obj_GetGroupObject(this, groupname) result(val)

Returns the HDF5 object id of the group.

Arguments

Type	Intent	Optional	Attributes		Name
class(hdf5_obj),	intent(in)			::	this	A HDF5 object
character(len=*),	intent(in)			::	groupname	Name of region

Return Value integer(kind=HID_T)

procedure, private :: hdf5_obj_Read1D

private impure subroutine hdf5_obj_Read1D(this, groupname, name, array, offset)

Reads a 1D dataset located under groupname and given by name. If no offset is provided, uses default file view. Otherwise, sets file view manually.

Arguments

Type	Intent	Optional	Attributes		Name
class(hdf5_obj),	intent(inout)			::	this	A HDF5 object
character(len=*),	intent(in)			::	groupname	Parent group containing the dataset
character(len=*),	intent(in)			::	name	Dataset name
class(*),	intent(out),		target	::	array(:)	Data array
integer,	intent(in),	optional		::	offset	Indicates number of elements to skip before reading

procedure, private :: hdf5_obj_Read3D

private impure subroutine hdf5_obj_Read3D(this, groupname, name, array, lo, hi)

Reads a 3D dataset located under groupname and given by name.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Parent group containing the dataset
character(len=*),	intent(in)		::	name	Dataset name
class(*),	intent(out),	target	::	array(:,:,:)	Data array
integer,	intent(in)		::	lo(3)	Low bounds
integer,	intent(in)		::	hi(3)	High bounds

procedure, private :: hdf5_obj_ReadAttributes0D

private impure subroutine hdf5_obj_ReadAttributes0D(this, groupname, label, val)

Read a scalar attribute under a given group.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	label	Attribute label
class(*),	intent(out),	target	::	val	Attribute value

procedure, private :: hdf5_obj_ReadAttributes1D

private impure subroutine hdf5_obj_ReadAttributes1D(this, groupname, label, val)

Read a 1-D array of attributes under a given group.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	label	Attribute label
class(*),	intent(out),	target	::	val(:)	Attribute values

procedure, private :: hdf5_obj_Write1D

private impure subroutine hdf5_obj_Write1D(this, groupname, name, array)

Writes an array/1D data to a HDF5 file.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	name	Variable name
class(*),	intent(in),	target	::	array(:)	1-D data array

procedure, private :: hdf5_obj_Write3D

private impure subroutine hdf5_obj_Write3D(this, groupname, name, array, lo, hi)

Writes Eulerian/3D data to a HDF5 file.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	name	Variable name
class(*),	intent(in),	target	::	array(:,:,:)	3-D data array
integer,	intent(in)		::	lo(3)	Low bounds
integer,	intent(in)		::	hi(3)	High bounds

procedure, private :: hdf5_obj_WriteAttributes0D

private impure subroutine hdf5_obj_WriteAttributes0D(this, groupname, label, val)

Writes a scalar attribute.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	label	attribute label
class(*),	intent(in),	target	::	val	Attribute label

procedure, private :: hdf5_obj_WriteAttributes1D

private impure subroutine hdf5_obj_WriteAttributes1D(this, groupname, label, val)

Writes an array of attributes.

Arguments

Type	Intent	Attributes		Name
class(hdf5_obj),	intent(inout)		::	this	A HDF5 object
character(len=*),	intent(in)		::	groupname	Groupname
character(len=*),	intent(in)		::	label	attribute label
class(*),	intent(in),	target	::	val(:)	Attribute labels

hdf5_obj Derived Type

Contents

Variables

Type-Bound Procedures

type, public :: hdf5_obj

Inherits

Inherited by

Components

Type-Bound Procedures

procedure, public :: Close => hdf5_obj_Close

private impure subroutine hdf5_obj_Close(this)

Arguments

procedure, public :: CloseGroup => hdf5_obj_CloseGroup

private impure subroutine hdf5_obj_CloseGroup(this, groupname)

Arguments

procedure, public :: CreateGroup => hdf5_obj_CreateGroup

private impure subroutine hdf5_obj_CreateGroup(this, groupname)

Arguments

procedure, public :: Finalize => hdf5_obj_Final

private impure subroutine hdf5_obj_Final(this)

Arguments

procedure, public :: GetNPoints => hdf5_obj_GetNPoints

private impure function hdf5_obj_GetNPoints(this, groupname, name) result(val)

Arguments

Return Value integer

procedure, public :: Initialize => hdf5_obj_Init

private impure subroutine hdf5_obj_Init(this, parallel)

Arguments

procedure, public :: Open => hdf5_obj_Open

private impure subroutine hdf5_obj_Open(this, name, flag)

Arguments

procedure, public :: OpenGroup => hdf5_obj_OpenGroup

private impure subroutine hdf5_obj_OpenGroup(this, groupname)

Arguments

generic, public :: Read => hdf5_obj_Read3D, hdf5_obj_Read1D

private impure subroutine hdf5_obj_Read3D(this, groupname, name, array, lo, hi)

Arguments

private impure subroutine hdf5_obj_Read1D(this, groupname, name, array, offset)

Arguments

generic, public :: ReadAttributes => hdf5_obj_ReadAttributes0D, hdf5_obj_ReadAttributes1D

private impure subroutine hdf5_obj_ReadAttributes0D(this, groupname, label, val)

Arguments

private impure subroutine hdf5_obj_ReadAttributes1D(this, groupname, label, val)

Arguments

procedure, public :: ReadCoord => hdf5_obj_ReadCoord

private impure subroutine hdf5_obj_ReadCoord(this, groupname, name, Coord)

Arguments

procedure, public :: ReadDatasetNames => hdf5_obj_ReadDatasetNames

private impure subroutine hdf5_obj_ReadDatasetNames(this, basegroup, names)

Arguments

procedure, public :: ReadGroupNames => hdf5_obj_ReadGroupNames

private impure subroutine hdf5_obj_ReadGroupNames(this, basegroup, names)

Arguments

generic, public :: Write => hdf5_obj_Write3D, hdf5_obj_Write1D

private impure subroutine hdf5_obj_Write3D(this, groupname, name, array, lo, hi)

Arguments

private impure subroutine hdf5_obj_Write1D(this, groupname, name, array)

Arguments

generic, public :: WriteAttributes => hdf5_obj_WriteAttributes0D, hdf5_obj_WriteAttributes1D

private impure subroutine hdf5_obj_WriteAttributes0D(this, groupname, label, val)

Arguments

private impure subroutine hdf5_obj_WriteAttributes1D(this, groupname, label, val)

Arguments

procedure, public :: WriteCoord => hdf5_obj_WriteCoord

private impure subroutine hdf5_obj_WriteCoord(this, groupname, name, Coord)

Arguments

procedure, private, nopass :: FixGroupName => hdf5_obj_FixGroupName

private pure function hdf5_obj_FixGroupName(groupname) result(val)

Arguments

Return Value character(len=:), allocatable

procedure, private :: GetGroupObject => hdf5_obj_GetGroupObject

private impure function hdf5_obj_GetGroupObject(this, groupname) result(val)

Arguments

Return Value integer(kind=HID_T)

procedure, private :: hdf5_obj_Read1D

private impure subroutine hdf5_obj_Read1D(this, groupname, name, array, offset)

Arguments

procedure, private :: hdf5_obj_Read3D

private impure subroutine hdf5_obj_Read3D(this, groupname, name, array, lo, hi)

Arguments