ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
Any argument can be changed after the initial construction of the
calculator, simply by setting it with the method
>>> calc.set( keyword=value )
Volumetric Data Output
The class
class FHI-aims.AimsCube(origin=(0,0,0),edges=[(0.1,0.0,0.0),(0.0,0.1,0.0),(0.0,0.0,0.1)],points=(50,50,50),plots=None)
describes an object that takes care of the volumetric output requests within FHI-aims. An object of this type can
be attached to the main Aims() object as an option.
The possible arguments for AimsCube are:
keyword type
origin list
edges 3x3-array
points list
plots list
The possible values for the entry of plots are discussed in detail in the FHI-aims manual, see below for an example.
Example
As an example, here is a possible setup to obtain the geometry of a water molecule:
from ase import Atoms
from ase.visualize import view
from ase.calculators.aims import Aims, AimsCube
from ase.optimize import QuasiNewton
water = Atoms(’HOH’, [(1,0,0), (0,0,0), (0,1,0)])
water_cube = AimsCube(points=(29,29,29),
plots=(’total_density’,’delta_density’,
’eigenstate 5’,’eigenstate 6’))
calc=Aims(xc=’pbe’,
sc_accuracy_etot=1e-6,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-6,
sc_accuracy_forces=1e-4,
species_dir=’/home/hanke/codes/fhi-aims/fhi-aims.workshop/species_defaults/light/’,
run_command=’aims.workshop.serial.x’,
cubes=water_cube)
water.set_calculator(calc)
dynamics = QuasiNewton(water,trajectory=’square_water.traj’)
dynamics.run(fmax=0.01)
view(water)
LAMMPS
Introduction
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code.
126 Chapter 7. Documentation for modules in ASE