ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
# Define DZP basis set for Pt
calc.set_fdf(’PAO.Basis’,
["""\
Pt 2 split 0.00 # Species label, number of l-shells
n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
0.00 0.00 # 0.0 => default [6.982 5.935 \n 1.000 1.000]
n=5 2 2 # n, l, zeta
0.00 0.00"""]) # 0.0 => default [5.172 3.060 \n 1.000 1.000]
You can also reuse the basis set of a previous calculation, by copying the .ion files to the new location, and set the
User.Basis tag to True:
# Load basis from previous calc (*.ion files)
calc.set_fdf(’User.Basis’, True)
Warning: Specifying a basis set manually in any way will, for some obscure reason, make Siesta crash if you have
ghost atoms!
Pseudopotentials
Pseudopotential files in the .psf or .vps formats are needed. Pseudopotentials generated from the ABINIT
code and converted to the SIESTA format are available in the SIESTA website . A database of user contributed
pseudopotentials is also available there.
You can also find an on-line pseudopotential generator from the OCTOPUS code.
Example
Here is an example of how to calculate the total energy for bulk Silicon, using a double-zeta basis generated by
specifying a given energy-shift:
#!/usr/bin/env python
from ase import *
a0 = 5.43
bulk = Atoms(’Si2’, [(0, 0, 0),
(0.25, 0.25, 0.25)],
pbc=True)
b = a0 / 2
bulk.set_cell([(0, b, b),
(b, 0, b),
(b, b, 0)], scale_atoms=True)
calc = Siesta(label=’Si’,
xc=’PBE’,
meshcutoff=200 * Ry,
basis=’dz’,
mix=0.01,
kpts=[10, 10, 10])
calc.set_fdf(’PAO.EnergyShift’, 0.01 * Ry)
bulk.set_calculator(calc)
e = bulk.get_potential_energy()
Here, the only input information on the basis set is, that it should be double-zeta (basis=’dz’) and that the confinement
potential should result in an energy shift of 0.01 Rydberg (the PAO.EnergyShift fdf tag). Sometimes
it can be necessary to specify more information on the basis set. For example, the default basis set generation fails
for Pt for some versions of Siesta. To fix this, you must specify the basis set manually. Manual basis set specifications
are described in Customized basis-set.
116 Chapter 7. Documentation for modules in ASE