ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
In Berendsen NPT simulations the velocities are scaled to achieve the desired temperature. The speed of the
scaling is determined by the parameter taut.
The atom positions and the simulation cell are scaled in order to achieve the desired pressure.
This method does not result proper NPT sampling but it usually is sufficiently good in practise (with large taut and
taup). For discussion see the gromacs manual at www.gromacs.org. or amber at ambermd.org
atoms: The list of atoms.
timestep: The time step.
temperature: The desired temperature, in Kelvin.
taut: Time constant for Berendsen temperature coupling.
fixcm: If True, the position and momentum of the center of mass is kept unperturbed. Default: True.
pressure: The desired pressure, in bar (1 bar = 1e5 Pa).
taup: Time constant for Berendsen pressure coupling.
compressibility: The compressibility of the material, water 4.57E-5 bar-1, in bar-1
# Room temperature simulation (300K, 0.1 fs time step, atmospheric pressure)
dyn = NPTBerendsen(atoms, timestep=0.1*units.fs, temperature=300,
taut=0.1*1000*units.fs, pressure = 1.01325,
taup=1.0*1000*units.fs, compressibility=4.57e-5)
7.22 Density Functional Theory
7.22.1 Brillouin zone sampling
The k-points are always given relative to the basis vectors of the reciprocal unit cell.
Monkhorst-Pack
ase.dft.kpoints.monkhorst_pack(size)
Construct a uniform sampling of k-space of given size.
The k-points are given as [MonkhorstPack]:
�
i=1,2,3
2ni − Ni − 1
bi,
2Ni
where ni = 1, 2, ..., Ni, size = (N1, N2, N3) and the bi‘s are reciprocal lattice vectors.
ase.dft.kpoints.get_monkhorst_pack_size_and_offset(kpts)
Find Monkhorst-Pack size and offset.
Example:
Returns (size, offset), where:
kpts = monkhorst_pack(size) + offset.
The set of k-points must not have been symmetry reduced.
>>> from ase.dft.kpoints import *
>>> monkhorst_pack((4, 1, 1))
array([[-0.375, 0. , 0. ],
[-0.125, 0. , 0. ],
[ 0.125, 0. , 0. ],
[ 0.375, 0. , 0. ]])
156 Chapter 7. Documentation for modules in ASE