ai2_kit.tool.lammps module

class ai2_kit.tool.lammps.LammpsTool

Bases: object

A tool for LAMMPS related operations.

analysis_density_convergence(in_file: str, out_file: Optional[str] = None, debug=False, err=0.0005, col_name: str = 'density')

Select a frame by density from a property file.

Parameters:

• in_file – input properties file, e.g. properties.out

• out_file – output file to save the selected frame, if None, return the result

• col_name – column name to select by, default is ‘density’

• debug – if True, return the average density for each frame

• err – error threshold for convergence, default is 0.0005

Returns:

a dictionary with converged density and frames, or save to out_file

gen_mass_map(atom_types: tuple, out_file=None)

Generate a mass map for LAMMPS. :param atom_types: tuple of atom types, e.g. (‘C’, ‘H’, ‘O’) :return: LAMMPS mass map string :param out_file: output file to save the mass map, if None, return the string

Returns:

mass map string, e.g.:

` mass 1 12.011 # C mass 2 1.008 # H mass 3 15.999 # O `