[ase-users] Relaxation of structure
Oscar Xavier Guerrero
oscarxavier.ox at gmail.com
Mon Aug 13 23:09:16 CEST 2018
You are creating a list named mask to filter the atoms with tag = 4, you
are then printing it with the print(mask) statement. That's why it is
printing the list.
That mask is all False because your initial doesn't have tags and your
constraint doesn't do anything and you are not using it.
Le lun. 13 août 2018 à 13:51, Abid Channa <abid_channa04 at yahoo.com> a
écrit :
> Hi Oscar,
>
> Thanks for your prompt response. I am doing NEB calculation and have
> defined initial and final configurations in my structure named initial in
> this script, and trying to relax these both configurations, here is the
> script
>
> from ase.io import read
> from ase.visualize import view
> from ase.constraints import FixAtoms
> from ase.optimize import QuasiNewton
> from ase.neb import NEB
> from ase.calculators.emt import EMT
>
> initial = read('initial')
> c = initial.get_positions()
> initial[230].x = 1.000
> initial[230].y = 18.30
> initial[230].z = 20.51
> # view(initial)
> # exit()
>
> final = initial.copy()
>
> # move adatom to row atom 168
> final.positions[-1, :] = initial.positions[168]
> # Move row atom 168 to the next row
> final.positions[168, :] = initial.positions[156] + [0.0, 2.60, 4.10]
> # view([initial, final])
> # exit()
>
> mask = [atom.tag > 4 for atom in initial]
> constraint = FixAtoms(mask=mask)
> print(mask)
>
> initial.set_calculator(EMT())
> final.set_calculator(EMT())
>
>
> # Relax the initial and final states:
>
> qn = QuasiNewton(initial, trajectory='initial.traj')
>
> qn.run(fmax=0.001)
>
>
> qn = QuasiNewton(final, trajectory='final.traj')
>
> qn.run(fmax=0.001)
>
>
> view([initial, final])
>
>
> exit()
>
>
> *_________________________________** ABID ALI *
>
>
> PhD (Marie Curie-ITN) Fellow
> Theoretical Chemistry
> Dunhagi 3, VR-II1,
> Science Institute, 107 Reykjavik
> University of Iceland.
> Mobile : +3547835935
>
>
>
> On Monday, August 13, 2018, 6:42:00 PM GMT, Oscar Xavier Guerrero <
> oscarxavier.ox at gmail.com> wrote:
>
>
> Hello,
>
> It's impossible to know where this list is coming from without knowing
> what the script does. Can you attach the script?
>
>
>
> Le lun. 13 août 2018 à 13:16, Abid Channa via ase-users <
> ase-users at listserv.fysik.dtu.dk> a écrit :
>
> Hello ASE users,
>
> I am relaxing my structure and it fully optimised according to my choice.
> After giving my script I am getting False some thing like below and then
> it start
>
> -bash-4.2$ python relax.py
> [False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False,
> False, False, False, False, False, False, False, False, False, False, False]
>
> Step[ FC] Time Energy fmax
>
> *Force-consistent energies used in optimization.
>
> BFGSLineSearch: 0[ 0] 16:09:40 25.143031* 1.9155
>
> BFGSLineSearch: 1[ 1] 16:09:40 23.464833* 0.5100
>
> BFGSLineSearch: 2[ 2] 16:09:40 23.283974* 0.4838
>
> BFGSLineSearch: 3[ 3] 16:09:40 23.171580* 0.0858
>
> BFGSLineSearch: 4[ 4] 16:09:40 23.112214* 0.0767
>
> BFGSLineSearch: 5[ 5] 16:09:41 23.092067* 0.0710
>
> BFGSLineSearch: 6[ 6] 16:09:41 23.079306* 0.0298
>
> BFGSLineSearch: 7[ 7] 16:09:41 23.073434* 0.0230
>
> BFGSLineSearch: 8[ 8] 16:09:41 23.069540* 0.0267
>
> BFGSLineSearch: 9[ 9] 16:09:41 23.067205* 0.0181
>
> BFGSLineSearch: 10[ 10] 16:09:41 23.065940* 0.0104
>
> BFGSLineSearch: 11[ 11] 16:09:42 23.065366* 0.0080
>
> BFGSLineSearch: 12[ 12] 16:09:42 23.064974* 0.0093
>
> BFGSLineSearch: 13[ 13] 16:09:42 23.064721* 0.0080
>
> BFGSLineSearch: 14[ 14] 16:09:42 23.064599* 0.0047
>
> BFGSLineSearch: 15[ 15] 16:09:42 23.064538* 0.0024
>
> BFGSLineSearch: 16[ 17] 16:09:42 23.064473* 0.0029
>
> BFGSLineSearch: 17[ 19] 16:09:43 23.064396* 0.0020
>
> BFGSLineSearch: 18[ 21] 16:09:43 23.064344* 0.0020
>
> BFGSLineSearch: 19[ 23] 16:09:43 23.064317* 0.0019
>
> BFGSLineSearch: 20[ 25] 16:09:43 23.064292* 0.0020
>
> BFGSLineSearch: 21[ 27] 16:09:44 23.064284* 0.0014
>
> BFGSLineSearch: 22[ 29] 16:09:44 23.064281* 0.0010
>
> BFGSLineSearch: 23[ 31] 16:09:44 23.064279* 0.0012
>
> BFGSLineSearch: 24[ 33] 16:09:44 23.064277* 0.0004
>
> Could some one explain what is this ? Is this for periodic boundary
> conditions but I have already described in script pbc as fixed like
> pbc=True
>
> Best,
>
>
> *_________________________________** ABID ALI *
>
>
> PhD (Marie Curie-ITN) Fellow
> Theoretical Chemistry
> Dunhagi 3, VR-II1,
> Science Institute, 107 Reykjavik
> University of Iceland.
> Mobile : +3547835935
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20180813/d7872715/attachment-0001.html>
More information about the ase-users
mailing list