[gpaw-users] Optimizing the unit cell using stress tensor

[sollebac]

Dear Marcin,
Ok, Thank you very much, Im going try in that way.
All the best
Jose Luis



On Mon, Feb 9, 2015 at 3:20 AM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
wrote:

>  On 02/09/2015 09:19 AM, Filip Anselm Rasmussen wrote:
>
> Dear Jose,
>
> This is actually more a ASE-related question, but let's take it here
> anyway:
> As is written on the ASE web site (
> https://wiki.fysik.dtu.dk/ase/ase/constraints.html#ase.constraints.UnitCellFilter)
> both the UnitCellFilter and StrainFilter objects come with an optional mask
> parameter that specifies which stress tensor components are allowed to be
> non-zero (i.e. applied in the relaxation). If you only want to relax in the
> z-direction you thus simply do this:
>
> mask = [0, 0, 1, 0, 0, 0] # = [xx, yy, zz, yz, xz, xy] - we only need
> zz-component
> uf = UnitCellFilter(a, mask=mask)
>
> If you only want your lattice constant to be relaxed and not the internal
> atomic positions I would suggest you use the StrainFilter class instead, it
> should also make the relaxation more stable.
> One is also sometimes required to use a rather high PW cut-off when
> relaxing units cells because the number of plane waves will change as the
> unit cell changes and this can introduce small variations in the energy.
> Personally I've in some cases needed as much as 750 eV to make the
> relaxation stable.
>
> the exercise
> https://wiki.fysik.dtu.dk/gpaw/exercises/stress/stress.html
> shows how to fix the number of plane waves based on the starting cell
> geometry:
>
> mode=PW(400, cell=a.get_cell()),  # fix no of planewaves!
>
> but even doing this I think you will still need a large cutoff.
>
> Best regards,
>
> Marcin
>
>
>
> - Filip
>
> On 2015-02-08 05:51, sollebac wrote:
>
>     Dear gpaw users,
>
>  I'm trying to relax a nanotube C  using the stress tensor, then
>  i set periodic boundary conditions only in z direction  [
> pbc=(False,False True) ]
>  im wondering if there is a way to fix the  "X" and "Y"  sides of the unit
> cell and let  move only in "z" direction?
>
>  The nanotube is in a supercell and only is peridic in z ,
>  here is the script that im using that is similar to example in the web :
>  https://wiki.fysik.dtu.dk/gpaw/exercises/stress/stress.html
>
>   i just  want  relax the nanotube  and find the lattice parameter but
> only in z direction
>
> from ase import Atoms
> from ase.lattice import bulk
> from ase.optimize.bfgs import BFGS
> from ase.constraints import UnitCellFilter
> from gpaw import GPAW
> from gpaw import PW
> import numpy as np
> from ase.structure import nanotube
> from ase.io import read,write
>
> a=nanotube(7, 0, length=1, bond=1.4, symbol='C')
> a.center()
> a.set_pbc((False,False,True))
> write('a.traj', a)
> calc = GPAW(xc='PBE',
>             mode=PW(100),
>             # mode=PW(400, cell=a.get_cell()),  # fix no of planewaves!
>             kpts=(1, 1, 3),
>             # convergence={'eigenstates': 1.e-10},  # converge tightly!
>             txt='stress.txt')
>
> a.set_calculator(calc)
>
> uf = UnitCellFilter(a)
> relax = BFGS(uf)
> relax.run(fmax=0.05)  # Consider much tighter fmax!
>
>
> b=a.get_cell()[0]
> #b=a.get_cell()
> print "Unit cell = ",a.get_cell()
>
>
>
>  any advice is welcome
>  thank you very much
>
>  Jose Luis
>
>
>
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