lammps/lmp format

lammps/lmp format#

lmp format#

Class: LAMMPSLmpFormat

Conversions#

Convert from this format to System#

dpdata.System(file_name: 'FileType', type_map=None, atom_style='auto', fmt: Literal['lammps/lmp'] = None) → dpdata.system.System
dpdata.System(file_name: 'FileType', type_map=None, atom_style='auto', fmt: Literal['lmp'] = None) → dpdata.system.System
dpdata.System.from_lammps_lmp(file_name: 'FileType', type_map=None, atom_style='auto') → dpdata.system.System
dpdata.System.from_lmp(file_name: 'FileType', type_map=None, atom_style='auto') → dpdata.system.System

Load LAMMPS data file to system data format.

This method supports multiple LAMMPS atom styles with automatic charge extraction and maintains backward compatibility. The parser can automatically detect the atom style from the LAMMPS data file header when possible.

Parameters:
file_namestr or Path

Path to LAMMPS data file

type_maplist, optional

Mapping from atom types to element names

atom_stylestr, optional

The LAMMPS atom style. Default is “auto” which attempts to detect the style automatically from the file. Can also be explicitly set to: atomic, full, charge, bond, angle, molecular, dipole, sphere

Returns:
System

converted system

Notes

Atom Style Column Layouts: - atomic: atom-ID atom-type x y z (default) - full: atom-ID molecule-ID atom-type charge x y z - charge: atom-ID atom-type charge x y z - bond: atom-ID molecule-ID atom-type x y z - angle: atom-ID molecule-ID atom-type x y z - molecular: atom-ID molecule-ID atom-type x y z - dipole: atom-ID atom-type charge x y z mux muy muz - sphere: atom-ID atom-type diameter density x y z

Examples

Load LAMMPS data with automatic detection:

>>> system = dpdata.System("data.lmp", type_map=["O", "H"])

Load with specific atom styles:

>>> # Full style with charges and molecule IDs
>>> system = dpdata.System("data.lmp", type_map=["O", "H"], atom_style="full")
>>> print(system["charges"])  # Access extracted charges

>>> # Charge style with charges only
>>> system = dpdata.System("data.lmp", type_map=["O", "H"], atom_style="charge")

>>> # Bond/molecular styles with molecule IDs
>>> system = dpdata.System("data.lmp", type_map=["O", "H"], atom_style="bond")

Convert from System to this format#

dpdata.System.to(fmt: Literal['lammps/lmp'], file_name: 'FileType', frame_idx=0)
dpdata.System.to(fmt: Literal['lammps/lmp'], file_name: 'FileType', frame_idx=0)
dpdata.System.to_lammps_lmp(file_name: 'FileType', frame_idx=0)
dpdata.System.to_lmp(file_name: 'FileType', frame_idx=0)

Dump the system in lammps data format.

Parameters:
file_namestr

The output file name

frame_idxint

The index of the frame to dump

Convert from LabeledSystem to this format#

dpdata.LabeledSystem.to(fmt: Literal['lammps/lmp'], file_name: 'FileType', frame_idx=0)
dpdata.LabeledSystem.to(fmt: Literal['lammps/lmp'], file_name: 'FileType', frame_idx=0)
dpdata.LabeledSystem.to_lammps_lmp(file_name: 'FileType', frame_idx=0)
dpdata.LabeledSystem.to_lmp(file_name: 'FileType', frame_idx=0)

Dump the system in lammps data format.

Parameters:
file_namestr

The output file name

frame_idxint

The index of the frame to dump