pyxtal.interface.gulp module

class pyxtal.interface.gulp.GULP(struc, label='_', path='tmp', ff='reaxff', pstress=None, opt='conp', steps=1000, exe='gulp', input='gulp.in', output='gulp.log', dump=None, symmetry=False, labels=None, timeout=3600)

Bases: object

A calculator to perform atomic structure optimization in GULP

Args:

struc: structure object generated by Pyxtal ff: path of forcefield lib opt: conv, conp, single pstress (float): external pressure steps (int): relaxation steps symm (bool): whether or not impose the symmetry

clean()

execute()

read()

run(clean=True)

Always go to the directory to run one gulp at once

set_catlow()

set the atomic label for catlow potentials O_O2- general O2- species O_OH oxygen in hydroxyl group H_OH hydrogen in hydroxyl group

to_ase()

to_pymatgen()

to_pyxtal()

write()

class pyxtal.interface.gulp.GULP_OC(struc, label='_', ff='gaff2', bond_type=False, opt='conp', steps=1000, stepmx=0.001, exe='gulp', atom_info=None, input='gulp.in', output='gulp.log', dump=None, folder='.')

Bases: object

A calculator to perform oragnic crystal structure optimization in GULP

Parameters:

• struc – structure object generated by Pyxtal

• ff – path of forcefield lib, e.g., gaff

• bond_type – specify the bond type or not (GULP can detect it automatically)

• opt – e.g., conv, conp, single

• steps – number of steps, int, e.g., 1000

• exe – int, the way to call gulp executable

• atom_info – atomic labels/charges

• input – gulp input file name

• output – gulp output file name

• dump – dumped gulp file name

clean()

execute()

read()

run(clean=True, pause=False)

write()

pyxtal.interface.gulp.optimize(struc, ff, optimizations=None, exe='gulp', pstress=None, path='tmp', label='_', clean=True, adjust=False)

Multiple calls

pyxtal.interface.gulp.single_optimize(struc, ff, steps=1000, pstress=None, opt='conp', exe='gulp', path='tmp', label='_', clean=True, symmetry=False, labels=None)