Operations on HDF5 and XDMF variables. More...

Interfaces and Types
interface	reset_hdf5_item
	Resets an HDF5 XDMF item. More...

Functions/Subroutines
integer function, public	open_hdf5_file (file_info, file_name, sym_type, descr, ind_plot, cont_plot)
	Opens an HDF5 file and accompanying xmf file and returns the handles. More...

integer function, public	close_hdf5_file (file_info, ind_plot, cont_plot)
	Closes an HDF5 file and writes the accompanying xmf file. More...

integer function, public	add_hdf5_item (file_info, XDMF_item, reset, ind_plot)
	Add an XDMF item to a HDF5 file. More...

integer function, public	print_hdf5_3d_data_item (dataitem_id, file_info, var_name, var, dim_tot, loc_dim, loc_offset, init_val, ind_plot, cont_plot)
	Prints an HDF5 data item. More...

subroutine, public	merge_hdf5_3d_data_items (merged_id, dataitem_ids, var_name, dim_tot, reset, ind_plot, cont_plot)
	Joins dataitems in a vector. More...

subroutine, public	print_hdf5_att (att_id, att_dataitem, att_name, att_center, att_type, reset, ind_plot)
	Prints an HDF5 attribute. More...

subroutine, public	print_hdf5_top (top_id, top_type, top_n_elem, ind_plot)
	Prints an HDF5 topology. More...

subroutine, public	print_hdf5_geom (geom_id, geom_type, geom_dataitems, reset, ind_plot)
	Prints an HDF5 geometry. More...

integer function, public	print_hdf5_grid (grid_id, grid_name, grid_type, grid_time, grid_top, grid_geom, grid_atts, grid_grids, reset, ind_plot)
	Prints an HDF5 grid. More...

integer function, public	create_output_hdf5 (HDF5_name)
	Creates an HDF5 output file. More...

integer function, public	print_hdf5_arrs (vars, PB3D_name, head_name, rich_lvl, disp_info, ind_print, remove_previous_arrs)
	Prints a series of arrays, in the form of an array of pointers, to an HDF5 file. More...

integer function, public	read_hdf5_arr (var, PB3D_name, head_name, var_name, rich_lvl, disp_info, lim_loc)
	Reads a PB3D output file in HDF5 format. More...

Variables
logical, public	debug_hdf5_ops = .false.
	set to true to debug general information More...

logical, public	debug_print_hdf5_arrs = .false.
	set to true to debug print_HDF5_arrs More...

Detailed Description

Operations on HDF5 and XDMF variables.

Note

Notes about XDMF:

Collections can be spatial or temporal. If a variable is to be evolved in time or if its domain is decomposed (e.g. the same physical variable is defined in multiple HDF5 variables), then the attribute name of this variable has to be the same for all the grids in the collection.
If no collection is used, but just multiple grids, the attribute can be different but does not have to be, as the different grid are distinguished by their different grid names, not by the attribute of the variables they contain.
The selection of hyperslabs is used, as described here: http://davis.lbl.gov/Manuals/HDF5-1.8.7/UG/12_Dataspaces.html
Chunking is used for partial I/O, as described here: https://www.hdfgroup.org/HDF5/doc/Advanced/Chunking/ As no chunk cache is reused, the w0 setting should be 1. Furthermore, the number of slots is chosen to be equal to the number of chunks. And Finally, the chunk size is chosen to be the size of the previous dimensions, if it does not exceed 4GB
Individual writes or plots are done now using the standard I/O driver, as using MPI does not allow for more than 2GB. This is important for the HELENA version of PB3D where X_2 variables get larger than that. https://www.hdfgroup.org/HDF5/doc/UG/OldHtmlSource/UG_frame08TheFile.html
Have a look in Documentation/XDMF_HDF5.pdf for an example.

Function/Subroutine Documentation

◆ add_hdf5_item()

integer function, public hdf5_ops::add_hdf5_item	(	type(hdf5_file_type), intent(inout)	file_info,
		type(xml_str_type), intent(inout)	XDMF_item,
		logical, intent(in), optional	reset,
		logical, intent(in), optional	ind_plot
	)

Add an XDMF item to a HDF5 file.

Note: This should only be used with grids (or for topologies and geometries that are used throughout)

Returns: ierr

Parameters

[in,out]	file_info	info about HDF5 file
[in,out]	xdmf_item	XDMF item to add
[in]	reset	if .true., XDMF_item is reset
[in]	ind_plot	whether individual plot

Definition at line 340 of file HDF5_ops.f90.

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◆ close_hdf5_file()

integer function, public hdf5_ops::close_hdf5_file	(	type(hdf5_file_type), intent(inout)	file_info,
		logical, intent(in), optional	ind_plot,
		logical, intent(in), optional	cont_plot
	)

Closes an HDF5 file and writes the accompanying xmf file.

Returns: ierr

Parameters

[in,out]	file_info	info about HDF5 file
[in]	ind_plot	whether individual plot
[in]	cont_plot	continued plot

Definition at line 264 of file HDF5_ops.f90.

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◆ create_output_hdf5()

integer function, public hdf5_ops::create_output_hdf5 ( character(len=*), intent(in) HDF5_name )

Creates an HDF5 output file.

Parameters

[in] hdf5_name name of HDF5 file

Definition at line 1075 of file HDF5_ops.f90.

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◆ merge_hdf5_3d_data_items()

subroutine, public hdf5_ops::merge_hdf5_3d_data_items	(	type(xml_str_type), intent(inout)	merged_id,
		type(xml_str_type), dimension(:), intent(inout)	dataitem_ids,
		character(len=*), intent(in)	var_name,
		integer, dimension(3), intent(in)	dim_tot,
		logical, intent(in), optional	reset,
		logical, intent(in), optional	ind_plot,
		logical, intent(in), optional	cont_plot
	)

Joins dataitems in a vector.

Parameters

[in,out]	merged_id	ID of merged data item
[in,out]	dataitem_ids	ID of data items
[in]	var_name	name of variable
[in]	dim_tot	total dimensions of variable
[in]	reset	whether to reset dataitems
[in]	ind_plot	whether individual plot
[in]	cont_plot	continued plot

Definition at line 603 of file HDF5_ops.f90.

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◆ open_hdf5_file()

integer function, public hdf5_ops::open_hdf5_file	(	type(hdf5_file_type), intent(inout)	file_info,
		character(len=*), intent(in)	file_name,
		integer, intent(inout), optional	sym_type,
		character(len=*), intent(in), optional	descr,
		logical, intent(in), optional	ind_plot,
		logical, intent(in), optional	cont_plot
	)

Opens an HDF5 file and accompanying xmf file and returns the handles.

Optionally, a description of the file can be provided.

Also, the plot can be done for only one process, setting the variable ind_plot.

Furthermore, if the plot is a continuation, using cont_plot, the previous plot is opened and sym_type is returned.

Returns: ierr

Parameters

[in,out]	file_info	info about HDF5 file
[in]	file_name	name of HDF5 file
[in,out]	sym_type	symmetry type
[in]	descr	description of file
[in]	ind_plot	whether individual plot
[in]	cont_plot	continued plot

Definition at line 78 of file HDF5_ops.f90.

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◆ print_hdf5_3d_data_item()

integer function, public hdf5_ops::print_hdf5_3d_data_item	(	type(xml_str_type), intent(inout)	dataitem_id,
		type(hdf5_file_type), intent(in)	file_info,
		character(len=*), intent(in)	var_name,
		real(dp), dimension(:,:,:), intent(in)	var,
		integer, dimension(3), intent(in)	dim_tot,
		integer, dimension(3), intent(in), optional	loc_dim,
		integer, dimension(3), intent(in), optional	loc_offset,
		real(dp), intent(in), optional	init_val,
		logical, intent(in), optional	ind_plot,
		logical, intent(in), optional	cont_plot
	)

Prints an HDF5 data item.

If this is a parallel data item, the group dimension and offset have to be specified as well.

Returns: ierr

Parameters

[in,out]	dataitem_id	ID of data item
[in]	file_info	info about HDF5 file
[in]	var_name	name of variable
[in]	var	variable to write
[in]	dim_tot	total dimensions of variable
[in]	loc_dim	dimensions in this group
[in]	loc_offset	offset in this group
[in]	init_val	initial fill value
[in]	ind_plot	whether individual plot
[in]	cont_plot	continued plot

Definition at line 396 of file HDF5_ops.f90.

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◆ print_hdf5_arrs()

integer function, public hdf5_ops::print_hdf5_arrs	(	type(var_1d_type), dimension(:), intent(in)	vars,
		character(len=*), intent(in)	PB3D_name,
		character(len=*), intent(in)	head_name,
		integer, intent(in), optional	rich_lvl,
		logical, intent(in), optional	disp_info,
		logical, intent(in), optional	ind_print,
		logical, intent(in), optional	remove_previous_arrs
	)

Prints a series of arrays, in the form of an array of pointers, to an HDF5 file.

Optionally, output can be given about the variable being written. Also, if rich_lvl is provided, _R_[rich_lvl] is appended to the head name if it is > 0.

Also optionally, previously encountered arrays can be removed. This is to be used with care, as it may disturb the internal workings of PB3D. Currently (v2.15) it is used only for the specific case of jumping to solutions for X_grid_style 1 or 3, when writing solutions and solution grids.

Note: See https://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html, 7.4.2.3 for an explanation of the selection of the dataspaces.

Returns: ierr

Parameters

[in]	vars	variables to write
[in]	pb3d_name	name of PB3D file
[in]	head_name	head name of variables
[in]	rich_lvl	Richardson level to append to file name
[in]	disp_info	display additional information about variable being read
[in]	ind_print	individual write (possibly partial I/O)
[in]	remove_previous_arrs	remove previous variables if present

Definition at line 1132 of file HDF5_ops.f90.

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◆ print_hdf5_att()

subroutine, public hdf5_ops::print_hdf5_att	(	type(xml_str_type), intent(inout)	att_id,
		type(xml_str_type), intent(inout)	att_dataitem,
		character(len=*), intent(in)	att_name,
		integer, intent(in)	att_center,
		integer, intent(in)	att_type,
		logical, intent(in), optional	reset,
		logical, intent(in), optional	ind_plot
	)

Prints an HDF5 attribute.

Parameters

[in,out]	att_id	ID of attribute
[in,out]	att_dataitem	dataitem of attribute
[in]	att_name	name of attribute
[in]	att_center	center of attribute
[in]	att_type	type of attribute
[in]	reset	whether to reset dataitems
[in]	ind_plot	whether individual plot

Definition at line 696 of file HDF5_ops.f90.

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◆ print_hdf5_geom()

subroutine, public hdf5_ops::print_hdf5_geom	(	type(xml_str_type), intent(inout)	geom_id,
		integer, intent(in)	geom_type,
		type(xml_str_type), dimension(:), intent(inout)	geom_dataitems,
		logical, intent(in), optional	reset,
		logical, intent(in), optional	ind_plot
	)

Prints an HDF5 geometry.

Parameters

[in,out]	geom_id	ID of geometry
[in]	geom_type	type of geometry
[in,out]	geom_dataitems	data items of geometry
[in]	reset	whether to reset dataitems
[in]	ind_plot	whether individual plot

Definition at line 805 of file HDF5_ops.f90.

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◆ print_hdf5_grid()

integer function, public hdf5_ops::print_hdf5_grid	(	type(xml_str_type), intent(inout)	grid_id,
		character(len=*), intent(in)	grid_name,
		integer, intent(in)	grid_type,
		real(dp), intent(in), optional	grid_time,
		type(xml_str_type), optional	grid_top,
		type(xml_str_type), optional	grid_geom,
		type(xml_str_type), dimension(:), optional	grid_atts,
		type(xml_str_type), dimension(:), optional	grid_grids,
		logical, intent(in), optional	reset,
		logical, intent(in), optional	ind_plot
	)

Prints an HDF5 grid.

If this is is a uniform grid, the geometry and topology have to be specified, or else it will be assumed that it is already present in the XDMF domain, and reused.

If the grid is a collection grid, the grids in the collection have to be specified.

Optionally, also a time can be specified (for the grids in a collection grid).

Returns: ierr

Parameters

[in,out]	grid_id	ID of grid
[in]	grid_name	name
[in]	grid_type	type
[in]	grid_time	time of grid
	grid_top	topology
	grid_geom	geometry
	grid_atts	attributes
	grid_grids	grids
[in]	reset	whether top, geom and atts and grids are reset
[in]	ind_plot	whether individual plot

Definition at line 886 of file HDF5_ops.f90.

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◆ print_hdf5_top()

subroutine, public hdf5_ops::print_hdf5_top	(	type(xml_str_type), intent(inout)	top_id,
		integer, intent(in)	top_type,
		integer, dimension(:), intent(in)	top_n_elem,
		logical, intent(in), optional	ind_plot
	)

Prints an HDF5 topology.

Note: Currently only structured grids supported.

Parameters

[in,out]	top_id	ID of topology
[in]	top_type	type
[in]	top_n_elem	nr. of elements
[in]	ind_plot	whether individual plot

Definition at line 755 of file HDF5_ops.f90.

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◆ read_hdf5_arr()

integer function, public hdf5_ops::read_hdf5_arr	(	type(var_1d_type), intent(inout)	var,
		character(len=*), intent(in)	PB3D_name,
		character(len=*), intent(in)	head_name,
		character(len=*), intent(in)	var_name,
		integer, intent(in), optional	rich_lvl,
		logical, intent(in), optional	disp_info,
		integer, dimension(:,:), intent(in), optional	lim_loc
	)

Reads a PB3D output file in HDF5 format.

This happens in a non-parallel way. By default, all variables are read, but an array of strings with acceptable variable names can be passed.

Optionally, output can be given about the variable being read. Also, if rich_lvl is provided, _R_rich_lvl is appended to the head name if it is > 0.

Furthermore, using lim_loc, a hyperslab of the variable can be read.

Note: If a limit of lim_loc is a negative value, the procedure just takes the entire range. This is necessary as sometimes the calling procuderes don't have, and don't need to have, knowledge of the underlying sizes, for example in the case of having multiple parallel jobs.

Returns: ierr

Parameters

[in,out]	var	variable to read
[in]	pb3d_name	name of PB3D file
[in]	head_name	head name of variables
[in]	var_name	name of variable
[in]	rich_lvl	Richardson level to reconstruct
[in]	disp_info	display additional information about variable being read
[in]	lim_loc	local limits

Definition at line 1530 of file HDF5_ops.f90.

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Variable Documentation

◆ debug_hdf5_ops

logical, public hdf5_ops::debug_hdf5_ops = .false.

set to true to debug general information

Note: Debug version only

Definition at line 47 of file HDF5_ops.f90.

◆ debug_print_hdf5_arrs

logical, public hdf5_ops::debug_print_hdf5_arrs = .false.

set to true to debug print_HDF5_arrs

Note: Debug version only

Definition at line 48 of file HDF5_ops.f90.

Interfaces and Types

Functions/Subroutines

Variables

Detailed Description

Function/Subroutine Documentation

◆ add_hdf5_item()

◆ close_hdf5_file()

◆ create_output_hdf5()

◆ merge_hdf5_3d_data_items()

◆ open_hdf5_file()

◆ print_hdf5_3d_data_item()

◆ print_hdf5_arrs()

◆ print_hdf5_att()

◆ print_hdf5_geom()

◆ print_hdf5_grid()

◆ print_hdf5_top()

◆ read_hdf5_arr()

Variable Documentation

◆ debug_hdf5_ops

◆ debug_print_hdf5_arrs