[ase-users] ASE made Pt(111) surface, cannot converge in VASP
Zhang, Qiang
zhang.5671 at buckeyemail.osu.edu
Fri Jun 23 00:09:52 CEST 2017
Hello Tristan,
The POSCAR made with VESTA, it converges in 15 geometric steps. Using all the same file (INCAR, KPOINTS, POTCAR), just change to use the POSCAR made by ASE, it never converges for the first geometric step. That is why I think it might related to the way I am using ASE. From VASP output in the calculation with ASE POSCAR, the energy bounce around with dE in the magnitude of e+4 or e+5 and never reduce to a low level. As far as I know, it might because the initial POSCAR guess is really bad. Below is the script I used to make the POSCAR.
from ase.build import fcc111
from ase.io import write
from ase.constraints import FixAtoms
slab = fcc111('Pt', size=(2,2,6), a=3.98, vacuum=7.5)
c = FixAtoms(indices=[atom.index for atom in slab if atom.index < 8])
slab.set_constraint(c)
slab.write('POSCAR', vasp5=True)
Thanks for your time.
Sincerely,
Qiang Zhang
________________________________
From: Tristan Maxson <tgmaxson at gmail.com>
Sent: Wednesday, June 21, 2017 8:23:39 PM
To: Zhang, Qiang
Cc: Protik Das; ase-users at listserv.fysik.dtu.dk
Subject: Re: [ase-users] ASE made Pt(111) surface, cannot converge in VASP
I just looked at both of these cells, I don't see any real difference. What do you mean by they won't converge? This is less of an ASE issue I think but we can still try to help you.
Can you converge an electronic step with both POSCAR? If geometric convergence is the problem, you need to constrain the lower layers of the ASE generated POSCAR to be comparable. You can do this by opening it in the gui and using the constraints in tools or by setting FixConstraints if you are doing this via code.
Thank you,
Tristan Maxson
On Wed, Jun 21, 2017 at 8:17 PM, Zhang, Qiang <zhang.5671 at buckeyemail.osu.edu<mailto:zhang.5671 at buckeyemail.osu.edu>> wrote:
Hello,
Here is a vesta POSCAR
Pt
3.98000000
1.414212380000 0.000000000000 0.000000000000
0.707106810000 1.224745380000 0.000000000000
0.000000000000 0.000000000000 6.655684221105
24
Select Dynamics
Direct
0.0000000000000000 0.0000000000000000 1.0000000000000000 T T T
0.5000000000000000 0.0000000000000000 1.0000000000000000 T T T
0.0000000000000000 0.5000000000000000 1.0000000000000000 T T T
0.5000000000000000 0.5000000000000000 1.0000000000000000 T T T
0.6666700000000000 0.1666700000000000 0.9132500910771759 T T T
0.1666700000000000 0.1666700000000000 0.9132500910771759 T T T
0.1666700000000000 0.6666700000000000 0.9132500910771759 T T T
0.6666700000000000 0.6666700000000000 0.9132500910771759 T T T
0.3333300000000000 0.8333300000000000 0.8265091970051182 T T T
0.8333300000000000 0.8333300000000000 0.8265091970051182 T T T
0.8333300000000000 0.3333300000000000 0.8265091970051182 T T T
0.3333300000000000 0.3333300000000000 0.8265091970051182 T T T
0.0000000000000000 0.0000000000000000 0.7397592880822941 T T T
0.5000000000000000 0.0000000000000000 0.7397592880822941 T T T
0.0000000000000000 0.5000000000000000 0.7397592880822941 T T T
0.5000000000000000 0.5000000000000000 0.7397592880822941 T T T
0.6666700000000000 0.1666700000000000 0.6530093791594700 F F F
0.1666700000000000 0.1666700000000000 0.6530093791594700 F F F
0.1666700000000000 0.6666700000000000 0.6530093791594700 F F F
0.6666700000000000 0.6666700000000000 0.6530093791594700 F F F
0.3333300000000000 0.8333300000000000 0.5662594702366459 F F F
0.8333300000000000 0.8333300000000000 0.5662594702366459 F F F
0.8333300000000000 0.3333300000000000 0.5662594702366459 F F F
0.3333300000000000 0.3333300000000000 0.5662594702366459 F F F
Below is the ase version for similar size (I don't know how to output fractional positions and add "T T T" or "F F F" using ASE)
Pt
1.0000000000000000
5.6285699782449186 0.0000000000000000 0.0000000000000000
2.8142849891224593 4.8744845881385244 0.0000000000000000
0.0000000000000000 0.0000000000000000 26.4892703568735577
Pt
24
Cartesian
1.4071424945612296 0.8124140980230874 7.5000000000000000
4.2214274836836889 0.8124140980230874 7.5000000000000000
2.8142849891224593 3.2496563920923496 7.5000000000000000
5.6285699782449186 3.2496563920923496 7.5000000000000000
0.0000000000000000 1.6248281960461748 9.7978540713747115
2.8142849891224593 1.6248281960461748 9.7978540713747115
1.4071424945612296 4.0620704901154365 9.7978540713747115
4.2214274836836889 4.0620704901154365 9.7978540713747115
0.0000000000000000 0.0000000000000000 12.0957081427494213
2.8142849891224593 0.0000000000000000 12.0957081427494213
1.4071424945612296 2.4372422940692622 12.0957081427494213
4.2214274836836889 2.4372422940692622 12.0957081427494213
1.4071424945612296 0.8124140980230874 14.3935622141241311
4.2214274836836889 0.8124140980230874 14.3935622141241311
2.8142849891224593 3.2496563920923496 14.3935622141241311
5.6285699782449186 3.2496563920923496 14.3935622141241311
0.0000000000000000 1.6248281960461748 16.6914162854988426
2.8142849891224593 1.6248281960461748 16.6914162854988426
1.4071424945612296 4.0620704901154365 16.6914162854988426
4.2214274836836889 4.0620704901154365 16.6914162854988426
0.0000000000000000 0.0000000000000000 18.9892703568735541
2.8142849891224593 0.0000000000000000 18.9892703568735541
1.4071424945612296 2.4372422940692622 18.9892703568735541
4.2214274836836889 2.4372422940692622 18.9892703568735541
Thanks for your time.
Sincerely,
Qiang Zhang
________________________________
From: Zhang, Qiang
Sent: Monday, June 19, 2017 6:13:43 PM
To: Tristan Maxson
Cc: Protik Das; ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] ASE made Pt(111) surface, cannot converge in VASP
Hello,
Here is a vesta POSCAR
Pt
3.98000000
1.414212380000 0.000000000000 0.000000000000
0.707106810000 1.224745380000 0.000000000000
0.000000000000 0.000000000000 6.655684221105
24
Select Dynamics
Direct
0.0000000000000000 0.0000000000000000 1.0000000000000000 T T T
0.5000000000000000 0.0000000000000000 1.0000000000000000 T T T
0.0000000000000000 0.5000000000000000 1.0000000000000000 T T T
0.5000000000000000 0.5000000000000000 1.0000000000000000 T T T
0.6666700000000000 0.1666700000000000 0.9132500910771759 T T T
0.1666700000000000 0.1666700000000000 0.9132500910771759 T T T
0.1666700000000000 0.6666700000000000 0.9132500910771759 T T T
0.6666700000000000 0.6666700000000000 0.9132500910771759 T T T
0.3333300000000000 0.8333300000000000 0.8265091970051182 T T T
0.8333300000000000 0.8333300000000000 0.8265091970051182 T T T
0.8333300000000000 0.3333300000000000 0.8265091970051182 T T T
0.3333300000000000 0.3333300000000000 0.8265091970051182 T T T
0.0000000000000000 0.0000000000000000 0.7397592880822941 T T T
0.5000000000000000 0.0000000000000000 0.7397592880822941 T T T
0.0000000000000000 0.5000000000000000 0.7397592880822941 T T T
0.5000000000000000 0.5000000000000000 0.7397592880822941 T T T
0.6666700000000000 0.1666700000000000 0.6530093791594700 F F F
0.1666700000000000 0.1666700000000000 0.6530093791594700 F F F
0.1666700000000000 0.6666700000000000 0.6530093791594700 F F F
0.6666700000000000 0.6666700000000000 0.6530093791594700 F F F
0.3333300000000000 0.8333300000000000 0.5662594702366459 F F F
0.8333300000000000 0.8333300000000000 0.5662594702366459 F F F
0.8333300000000000 0.3333300000000000 0.5662594702366459 F F F
0.3333300000000000 0.3333300000000000 0.5662594702366459 F F F
Below is the ase version for similar size (I don't know how to output fractional positions and add "T T T" or "F F F" using ASE)
Pt
1.0000000000000000
5.6285699782449186 0.0000000000000000 0.0000000000000000
2.8142849891224593 4.8744845881385244 0.0000000000000000
0.0000000000000000 0.0000000000000000 26.4892703568735577
Pt
24
Cartesian
1.4071424945612296 0.8124140980230874 7.5000000000000000
4.2214274836836889 0.8124140980230874 7.5000000000000000
2.8142849891224593 3.2496563920923496 7.5000000000000000
5.6285699782449186 3.2496563920923496 7.5000000000000000
0.0000000000000000 1.6248281960461748 9.7978540713747115
2.8142849891224593 1.6248281960461748 9.7978540713747115
1.4071424945612296 4.0620704901154365 9.7978540713747115
4.2214274836836889 4.0620704901154365 9.7978540713747115
0.0000000000000000 0.0000000000000000 12.0957081427494213
2.8142849891224593 0.0000000000000000 12.0957081427494213
1.4071424945612296 2.4372422940692622 12.0957081427494213
4.2214274836836889 2.4372422940692622 12.0957081427494213
1.4071424945612296 0.8124140980230874 14.3935622141241311
4.2214274836836889 0.8124140980230874 14.3935622141241311
2.8142849891224593 3.2496563920923496 14.3935622141241311
5.6285699782449186 3.2496563920923496 14.3935622141241311
0.0000000000000000 1.6248281960461748 16.6914162854988426
2.8142849891224593 1.6248281960461748 16.6914162854988426
1.4071424945612296 4.0620704901154365 16.6914162854988426
4.2214274836836889 4.0620704901154365 16.6914162854988426
0.0000000000000000 0.0000000000000000 18.9892703568735541
2.8142849891224593 0.0000000000000000 18.9892703568735541
1.4071424945612296 2.4372422940692622 18.9892703568735541
4.2214274836836889 2.4372422940692622 18.9892703568735541
Thanks for your time.
Sincerely,
Qiang Zhang
________________________________
From: Tristan Maxson <tgmaxson at gmail.com<mailto:tgmaxson at gmail.com>>
Sent: Monday, June 19, 2017 4:20:05 PM
To: Zhang, Qiang
Cc: Protik Das; ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] ASE made Pt(111) surface, cannot converge in VASP
Can you include POSCARs you made using VESTA compared to ASE? Maybe we will see an obvious problem if you include both and we can look at both as the POSCAR's origin cannot influence convergence directly.
On Mon, Jun 19, 2017 at 1:57 PM, Zhang, Qiang via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>> wrote:
Hi Protik Das,
3.98 should be right and I do not think it is the problem of ismear. I use the same INCAR for my previous Pt calculations, they converge well. Also for vacuum, reducing the vacuum (5 A) does not make the convergence better.
I used to make these using VESTA and it converge really quick. Now I just try to use ase since it is easier. I think I might just made some stupid mistake in the script which I do not realize or do not know. Thanks for help any way.
Sincerely,
Qiang Zhang
________________________________
From: Protik Das <protik77 at gmail.com<mailto:protik77 at gmail.com>>
Sent: Monday, June 19, 2017 1:28:50 PM
To: Zhang, Qiang; ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] ASE made Pt(111) surface, cannot converge in VASP
It seems like a vasp issue rather than ASE issue. Your POSCAR should be alright. Some comments regarding vasp:
1. You used 3.98 angstrom for the bulk lattice constant. Are you sure that is the optimized lattice constant for the theory level (LDA/GGA) you are using? If this is not, it might effect convergence. I would suggest doing a full relaxation of bulk Pt and then using that lattice constant to create surface.
2. When you used 15 angstrom as vacuum value, it basically adding 15 angstrom vacuum in each direction. That means you are adding 30 angstrom vacuum which may be little too large.
3. As Pt is a metal, you need to pay close attention to ISMEAR and SIGMA values. Take a look here: http://cms.mpi.univie.ac.at/vasp/guide/node124.html .
On Mon, Jun 19, 2017 at 6:39 AM Zhang, Qiang <zhang.5671 at buckeyemail.osu.edu<mailto:zhang.5671 at buckeyemail.osu.edu>> wrote:
Hello Protik Das,
I just try to relax this created surface POSCAR. It is not converging. Thanks for your time.
Sincerely,
Qiang Zhang
________________________________
From: Protik Das <protik77 at gmail.com<mailto:protik77 at gmail.com>>
Sent: Monday, June 19, 2017 2:09:52 AM
To: Zhang, Qiang; ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] ASE made Pt(111) surface, cannot converge in VASP
What calculation are you doing? Did you relax your surface before these calculations?
On Sun, Jun 18, 2017 at 10:54 PM Zhang, Qiang via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>> wrote:
Dear ASE users,
I use ase to to make a Pt(111) surface
from ase.build import fcc111
from ase.io<http://ase.io> import write
slab = fcc111('Pt', size=(3,3,4), a=3.98, vacuum=15.0)
#write('pt111.xyz<http://pt111.xyz>', slab)
slab.write('POSCAR', vasp5=True)
I use the POSCAR (fix the bottom two Pt layers) for VASP calculation, but it is take long time without converging. Is there something wrong with my script? Thanks for your time.
Sincerely,
Qiang Zhang
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--
Protik Das,
ECE Graduate Student,
LATTE (http://latte.ece.ucr.edu),
University of California, Riverside.
--
Protik Das,
ECE Graduate Student,
LATTE (http://latte.ece.ucr.edu),
University of California, Riverside.
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