position of ions in OUTCAR not consistent with POSCAR

[Yuting]

Hi,

I am trying to calculate the density of states of a 128-atom amorphous graphene model. But the configuration given in OUTCAR is different from my POSCAR, and I always had this warning:

-----------------------------------------------------------------------------
| |
| W W AA RRRRR N N II N N GGGG !!! |
| W W A A R R NN N II NN N G G !!! |
| W W A A R R N N N II N N N G !!! |
| W WW W AAAAAA RRRRR N N N II N N N G GGG ! |
| WW WW A A R R N NN II N NN G G |
| W W A A R R N N II N N GGGG !!! |
| |
| The distance between some ions is very small |
| please check the nearest neigbor list in the OUTCAR file |
| I HOPE YOU KNOW, WHAT YOU ARE DOING |
| |
-----------------------------------------------------------------------------

The POSCAR I give is:

128a_static
1.0
19.507981 -0.106336 0.051970
-0.091677 16.978169 0.147340
0.019356 0.069231 9.111919
128
Cartesian
4.80237329000000 2.52092152000000 2.20688578000000
5.49297019000000 5.45382733000000 0.964398990000001
4.89581011000000 9.46195143000000 1.08121465000000
4.26819837000000 15.7652579600000 1.95137311000000
9.51791163000000 2.03071405000000 3.53162395000000
8.01138654000000 5.68353497000000 0.929771010000000
7.26989593000000 9.93997444000000 1.03757855000000
6.63530160000000 14.7584366800000 2.12884151000000
11.9584024900000 1.07359424000000 2.40263247000000
7.87625299000000 7.12763674000000 0.679423800000000
8.45894965000000 16.8219416200000 3.17847228000000
8.12729375000000 14.4953282700000 2.10535404000000
12.9552521900000 0.208248640000000 1.81344274000000
10.2964238400000 7.34063844000000 1.05643778000000
.... .... ....

And in OUTCAR, the position is ions are given as:

position of ions in cartesian coordinates (Angst):
6.06190856 11.81021030 2.55030302
0.02753618 10.68718689 0.31481769
7.88764598 10.79037011 1.40136512
15.12186963 15.89137230 0.28230173
0.56386228 3.54011549 5.42228028
10.13841932 14.59890937 9.17199657
15.23231371 1.88535680 0.94628966
2.77939190 15.85514548 1.86548272
9.15052172 4.21237236 4.27613064
7.54835395 5.15781305 6.80192413
18.84224112 16.84919563 2.36987608
12.40083178 11.33410389 1.63826923
9.08467266 6.52733332 8.03907680
15.71345304 8.68638267 1.17854593
13.10271354 8.46209829 3.67799704
6.65216557 14.45791663 2.08097101
17.13601883 2.49742305 5.94081912
8.97185518 15.06169535 4.06287489
... ... ....

This does not agree with the POSCAR. Why would I have this problem? Since before calculation, I already moved all the atoms into the unit cell. And I used SIESTA to check this model, and it gives me a reasonable DOS.

Thanks a lot for your help.

Yuting

[forsdan]

I would suggest that you do a clean start, i.e. remove everything except INCAR, KPOINTS, POTCAR and POSCAR. Then check the positions again. Because if you have not supplied the positions in direct coordinates or given the positions outside the computational unit cell, the caartesian coordinates should be preserved. Otherwise they are translated back and cause an unexpected geometriy if one is not careful.

I have assumed that you indeed compare the coordinates in the first ionic step and have not relaxed the ions.

Cheers,
/Dan
<span class='smallblacktext'>[ Edited Wed Dec 29 2010, 07:47PM ]</span>

[Yuting]

Hi, Dan:

Thanks a lot for your reply.

I did start with 4 required files, i.e. INCAR, KPOINTS, POTCAR and POSCAR. And I only did a static run.

The coordinates given in the OUTCAR seem really wired, since they cannot be calculated out by adding or subtracting the original coordinates with a certain lattice vector. It really puzzles me right now.

Best
Yuting

[quote="forsdan"]I would suggest that you do a clean start, i.e. remove everything except INCAR, KPOINTS, POTCAR and POSCAR. Then check the positions again. Because if you have not supplied the positions in direct coordinates or given the positions outside the computational unit cell, the caartesian coordinates should be preserved. Otherwise they are translated back and cause an unexpected geometriy if one is not careful.

I have assumed that you indeed compare the coordinates in the first ionic step and have not relaxed the ions.

Cheers,
/Dan
[/quote]