dpdata.formats.xyz package

Submodules

dpdata.formats.xyz.quip_gap_xyz module

class dpdata.formats.xyz.quip_gap_xyz.QuipGapxyzSystems(file_name)

Bases: object

deal with QuipGapxyzFile.

Methods

get_block_generator
handle_single_xyz_frame

get_block_generator()

static handle_single_xyz_frame(lines)

dpdata.formats.xyz.quip_gap_xyz.format_single_frame(data, frame_idx)

Format a single frame of system data into QUIP/GAP XYZ format lines.

Parameters:

datadict

system data

frame_idxint

frame index

Returns:

list[str]

lines for the frame

dpdata.formats.xyz.xyz module

dpdata.formats.xyz.xyz.coord_to_xyz(coord: ndarray, types: list) → str

Convert coordinates and types to xyz format.

Parameters:

coordnp.ndarray

coordinates, Nx3 array

typeslist

list of types

Returns:

str

xyz format string

Examples

>>> coord_to_xyz(np.ones((1,3)), ["C"])
1

C 1.000000 1.000000 1.000000

dpdata.formats.xyz.xyz.xyz_to_coord(xyz: str) → tuple[ndarray, list]

Convert xyz format to coordinates and types.

Parameters:

xyzstr

xyz format string

Returns:

coordsnp.ndarray

coordinates, Nx3 array

typeslist

list of types