Schlipf at 10:09, 10 June 2024

2024-06-10T10:09:44Z

← Older revision		Revision as of 10:09, 10 June 2024
Line 21:		Line 21:

	As of VASP 6.2.0 we only support reading/writing of hdf5 files in serial mode.		As of VASP 6.2.0 we only support reading/writing of hdf5 files in serial mode.
	For extracting data from the {{FILE\|vaspout.h5}} file we strongly recommend using the ~~[https://www.vasp.at/~~py4vasp~~/latest/ py4vasp]~~ package.		For extracting data from the {{FILE\|vaspout.h5}} file we strongly recommend using the {{py4vasp}} package.

	== Command line tools ==		== Command line tools ==

Miranda.henrique: Created page with "Since VASP 6.2.0 we started supporting the feature of reading and writing hdf5 files. The HDF5 file format {{cite|hdf5format:web}} is a hierarchical data file designed to stor..."

2023-10-20T14:53:54Z

Created page with "Since VASP 6.2.0 we started supporting the feature of reading and writing hdf5 files. The HDF5 file format {{cite|hdf5format:web}} is a hierarchical data file designed to stor..."

New page

Since VASP 6.2.0 we started supporting the feature of reading and writing hdf5 files.
The HDF5 file format {{cite|hdf5format:web}} is a hierarchical data file designed to store large amounts of numeric data.
This file format combines the flexibility and hierarchy of an XML file with the speed and size economy of binary files.
The writing and reading of hdf5 files are handled by the HDF5 library which is written in C but wrappers for Fortran, python, and C++ are available.

Currently, VASP accepts the following HDF5 files:

:{|cellpadding="5" cellspacing="0" border="1"
! style="padding:5px; border-style: solid" | Filename || Usage
|-
|{{FILE|vaspin.h5}} || Contains the necessary inputs to start the calculation instead of {{FILE|INCAR}}, {{FILE|POSCAR}}, {{FILE|POTCAR}} and {{FILE|KPOINTS}}
|-
|{{FILE|vaspout.h5}} || Contains the outputs of the VASP calculation
|-
|{{FILE|vaspwave.h5}} || Contains the wavefunctions when {{TAG|LWAVEH5}}=.TRUE. and charge density {{TAG|LCHARGH5}}=.TRUE.
|-
|}

To enable the reading and writing of these files, VASP should be compiled with HDF5 support active.
This is done by modifying the [[Makefile.include#HDF5_support_.28strongly_recommended.29|makefile.include]] accordingly.

As of VASP 6.2.0 we only support reading/writing of hdf5 files in serial mode.
For extracting data from the {{FILE|vaspout.h5}} file we strongly recommend using the [https://www.vasp.at/py4vasp/latest/ py4vasp] package.

== Command line tools ==
The HDF5 library ships with a series of command-line tools that can be used to quickly inspect the contents of any HDF5 file.

In particular <tt>h5ls</tt> outputs the hierarchy of groups and datasets. It is useful to check which data is present in the file.
For example:

$ h5ls vaspout.h5
input Group
intermediate Group
original Group
results Group
version Group

Adding the <tt>-r</tt> modifier lists the contents of the groups recursively, giving an overview of the data contained in the file.

Another very useful tool is the <tt>h5dump</tt> command that with the <tt>-d variable_name</tt> argument outputs the contents of the variable to the screen.
For example:
$ h5dump -d /intermediate/ion_dynamics/energies vaspout.h5
HDF5 "vaspout.h5" {
DATASET "/intermediate/ion_dynamics/energies" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 1, 3 ) / ( H5S_UNLIMITED, 3 ) }
DATA {
(0,0): -11.8515, -11.8515, -11.8515
}
}
}
The meaning of each of the energy values can be printed by replacing <tt>energies</tt> by <tt>energies_tags</tt> in the command above.
For a complete list of HDF5 tools, the user is referred to the official HDF5 documentation {{cite|hdf5tools:web}}.

== References ==
<references/>

[[Category:VASP]][[Category:Files]]

Category:HDF5 support - Revision history

Schlipf at 10:09, 10 June 2024

Miranda.henrique: Created page with "Since VASP 6.2.0 we started supporting the feature of reading and writing hdf5 files. The HDF5 file format {{cite|hdf5format:web}} is a hierarchical data file designed to stor..."