[ase-users] Relaxation of structure
Abid Channa
abid_channa04 at yahoo.com
Mon Aug 13 20:51:39 CEST 2018
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 readfrom ase.visualize import viewfrom ase.constraints import FixAtomsfrom ase.optimize import QuasiNewtonfrom ase.neb import NEBfrom ase.calculators.emt import EMT
initial = read('initial')c = initial.get_positions()initial[230].x = 1.000initial[230].y = 18.30initial[230].z = 20.51# view(initial)# exit()
final = initial.copy()
# move adatom to row atom 168final.positions[-1, :] = initial.positions[168]# Move row atom 168 to the next rowfinal.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) FellowTheoretical 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) FellowTheoretical Chemistry
Dunhagi 3, VR-II1, Science Institute, 107 Reykjavik University of Iceland.Mobile : +3547835935
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