abacus/stru format

Aliases

abacus/stru, stru

Implementation: AbacusSTRUFormat

Overview

ABACUS structure file.

ABACUS (Atomic-orbital Based Ab-initio Computation at UStc) is an open-source DFT package based on LCAO and plane-wave basis sets.

STRU stores the cell, species, coordinates, pseudopotential/orbital references, and optional movement or magnetic-moment fields for one ABACUS configuration. This format reads and writes unlabeled dpdata.System objects.

Quick examples

The examples use the preferred alias abacus/stru; any alias listed above is equivalent.

import dpdata

# Geometry-only data
system = dpdata.System("input_file", fmt="abacus/stru")

# Write geometry-only data
system.to("abacus/stru", "output_path")

Conversions

Convert from this format to System

dpdata.System(file_name, fmt: Literal['abacus/stru'] = None, **kwargs) → dpdata.system.System

dpdata.System(file_name, fmt: Literal['stru'] = None, **kwargs) → dpdata.system.System

dpdata.System.from_abacus_stru(file_name, **kwargs) → dpdata.system.System

dpdata.System.from_stru(file_name, **kwargs) → dpdata.system.System

Load one ABACUS STRU file.

Parameters:

file_namestr or os.PathLike

Input STRU file.

**kwargsdict

Additional format arguments accepted for API compatibility.

Returns:

System

converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['abacus/stru'], file_name: 'FileType', frame_idx=0, **kwargs)

dpdata.System.to(fmt: Literal['stru'], file_name: 'FileType', frame_idx=0, **kwargs)

dpdata.System.to_abacus_stru(file_name: 'FileType', frame_idx=0, **kwargs)

dpdata.System.to_stru(file_name: 'FileType', frame_idx=0, **kwargs)

Dump the system into ABACUS STRU format file.

Parameters:

file_namestr

The output file name

frame_idxint

The index of the frame to dump

**kwargsdict

Additional STRU fields described below.

Other Parameters:

pp_filelist[str] or dict[str, str], optional

Pseudopotential file for each atom type.

numerical_orbitallist[str] or dict[str, str], optional

Numerical orbital file for each atom type.

numerical_descriptorstr, optional

Numerical descriptor file used by ABACUS.

masslist[float], optional

Atomic mass for each atom type.

movearray-like, optional

Per-frame, per-atom Cartesian movement flags.

velocityarray-like, optional

Initial Cartesian velocity for each atom.

magarray-like, optional

Scalar or vector magnetic moment for each atom.

angle1, angle2array-like, optional

Polar and azimuthal magnetic-moment angles for noncollinear spins.

scarray-like, optional

Spin-constraint flags.

lambda_array-like, optional

Spin-constraint lambda values.

link_filebool, default=False

Write basenames and create symbolic links for referenced files.

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['abacus/stru'], file_name: 'FileType', frame_idx=0, **kwargs)

dpdata.LabeledSystem.to(fmt: Literal['stru'], file_name: 'FileType', frame_idx=0, **kwargs)

dpdata.LabeledSystem.to_abacus_stru(file_name: 'FileType', frame_idx=0, **kwargs)

dpdata.LabeledSystem.to_stru(file_name: 'FileType', frame_idx=0, **kwargs)

Dump the system into ABACUS STRU format file.

Parameters:

file_namestr

The output file name

frame_idxint

The index of the frame to dump

**kwargsdict

Additional STRU fields described below.

Other Parameters:

pp_filelist[str] or dict[str, str], optional

Pseudopotential file for each atom type.

numerical_orbitallist[str] or dict[str, str], optional

Numerical orbital file for each atom type.

numerical_descriptorstr, optional

Numerical descriptor file used by ABACUS.

masslist[float], optional

Atomic mass for each atom type.

movearray-like, optional

Per-frame, per-atom Cartesian movement flags.

velocityarray-like, optional

Initial Cartesian velocity for each atom.

magarray-like, optional

Scalar or vector magnetic moment for each atom.

angle1, angle2array-like, optional

Polar and azimuthal magnetic-moment angles for noncollinear spins.

scarray-like, optional

Spin-constraint flags.

lambda_array-like, optional

Spin-constraint lambda values.

link_filebool, default=False

Write basenames and create symbolic links for referenced files.