pyxtal.interface.LJ module

class pyxtal.interface.LJ.FIRE(struc, model, symmetrize=False, e_tol=1e-05, f_tol=0.01, dt=0.1, maxmove=0.1, dtmax=1.0, Nmin=10, finc=1.1, fdec=0.5, astart=0.1, fa=0.99, a=0.1)

Bases: object

FIRE algorithm for structure optimization

check_convergence()

There should be two options to terminate the optimization before it reaches the maximum number of cycles 1, by energy difference compared to the previous step: self.e_tol 2, by the residual force: self.f_tol Will implement both options later.

initialize()

initilaize the positions, energy, force for the 1st step

run(max_steps=1000)

step()

symmetrized_coords(coords)

symmetrized_force(coords)

symmetrized_stress(stress)

update(freq=50)

pyxtal.interface.LJ.GPa2eV = 0.0062415349182670995

Scripts to compute LJ energy and force

class pyxtal.interface.LJ.LJ(epsilon=1.0, sigma=1.0, rcut=8.0)

Bases: object

LJ model for 3D crystals, maybe extended to 0D, 1D, 2D later

calc(struc, press=0.0001)

pyxtal.interface.LJ.get_neighbors(struc, i, rcut)

script to get the neighbors info for an atom in the struct