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Abins Data Formats

Code	Data type	File extension	AbInitioProgram	Frozen atoms
CASTEP	.phonon	modes	CASTEP
CASTEP	force constants	.castep_bin	FORCECONSTANTS
CRYSTAL	modes	.out	CRYSTAL	N
DMOL3	modes	.outmol	DMOL3
Euphonic	modes	.json	JSON	N
Euphonic	force constants	.json	JSON	N
Gaussian	modes	.log	GAUSSIAN	Y
Phonopy	force constants	.yaml	FORCECONSTANTS
VASP	modes	.xml	VASP	Y

CASTEP

Writing force constants

To include force constants in a .castep_bin file, set phonon_write_force_constants = True, phonon_fine_method = interpolate and ensure the phonon_mp_grid includes the Gamma point (0, 0, 0). This can be achieved by carefully setting phonon_kpoint_mp_offset to suitable divisions or, in recent CASTEP versions, setting it to INCLUDE_GAMMA.

Further information is available in the castep docs.

Isotopes

CASTEP allows arbitrary labels to be assigned to species with corresponding masses and pseudopotentials. In order to match customised species to on-the-fly-generated pseudopotentials, it is recommended to use the EL:tag syntax, where e.g. deuterium would be specified as H:D or H:2 and a corresponding species put in the SPECIES_MASS block. Abins expects this syntax and uses it to identify appropriate neutron cross-section data.

Some examples are given in the castep docs.

Phonopy

Abins expects to read force constants from a phonopy.yaml file generated with INCLUDE_ALL = .TRUE.. It is also permitted to use a phonopy YAML file which does not contain the force constants, if the force constants are stored in a FORCE_CONSTANTS or force_constants.hdf5 file in the same directory. We recommend using the force_constants.hdf5 file where practical as the read/write performance is significantly better. (With the power and flexibility of .yaml comes a lot of computational overhead to read simple arrays!)

VASP

Abins can read the frequencies and displacements from Gamma-point vibration calculations performed with the IBRION=5,6,7,8 tags. We do not (currently) support the Fourier-interpolated supercell calculations added in VASP 6.4.0 (i.e. using QPOINTS file and PHON_DOS). We recommend that VASP users use Phonopy for such work, which makes it easier for large calculations to be “task farmed”.

From VASP XML inputs, it is permitted to use “selective dynamics” in which some atoms are frozen. In this case, data is only available for the moving atoms and contributions from the other atoms are omitted from the calculated spectrum. This may be a suitable model for systems where the frozen atoms form a rigid substrate (e.g. a noble metal surface) for an adsorbed molecule of lightweight atoms. It is not recommended where there is significant vibrational coupling between frozen and moving atoms, or where substrate modes would occupy a similar frequency range to the adsorbate.

Category: Concepts