xyz format#
Aliases#
xyz
Implementation: XYZFormat
Overview#
Plain XYZ molecular structure file.
Plain XYZ stores element symbols and Cartesian coordinates but no cell or labels. dpdata therefore treats it as nonperiodic and assigns a placeholder cell. Use extxyz when energies, forces, virials, or multiple chemical formulas must be preserved.
Examples
>>> import dpdata
>>> system = dpdata.System("POSCAR", fmt="vasp/poscar")
>>> system.to("xyz", "a.xyz")
Quick examples#
The examples use the preferred alias xyz; any alias listed above is equivalent.
import dpdata
# Geometry-only data
system = dpdata.System("input_file", fmt="xyz")
# Write geometry-only data
system.to("xyz", "output_path")
Conversions#
Convert from this format to System#
- dpdata.System(file_name: 'FileType', fmt: Literal['xyz'] = None, **kwargs) dpdata.system.System
- dpdata.System.from_xyz(file_name: 'FileType', **kwargs) dpdata.system.System
Load the first structure from a plain XYZ file.
- Parameters:
- file_namestr or os.PathLike or file-like object
Input XYZ file.
- **kwargsdict
Additional format arguments accepted for API compatibility.
- Returns:
- System
converted system
Convert from System to this format#
- dpdata.System.to(fmt: Literal['xyz'], file_name: 'FileType', **kwargs)
- dpdata.System.to_xyz(file_name: 'FileType', **kwargs)
Write all frames as concatenated plain XYZ records.
- Parameters:
- file_namestr or os.PathLike or file-like object
Destination XYZ file.
- **kwargsdict
Additional format arguments accepted for API compatibility.
Convert from LabeledSystem to this format#
- dpdata.LabeledSystem.to(fmt: Literal['xyz'], file_name: 'FileType', **kwargs)
- dpdata.LabeledSystem.to_xyz(file_name: 'FileType', **kwargs)
Write all frames as concatenated plain XYZ records.
- Parameters:
- file_namestr or os.PathLike or file-like object
Destination XYZ file.
- **kwargsdict
Additional format arguments accepted for API compatibility.