Problem to creating vacuum for preparing spacegroup.in file

[Santu Baidya]

Dear Elk users,

I am making a few layers system from a hexagonal bulk using bulk. During the procedure of preparing spacegroup.in file I am facing problem to creating vacuum in spacegroup.in keeping system symmetry. Can anyone please tell me if this is possible. My spacegroup is R-3:H, a,b= 13.239596 a.u. and c kept as 14 a.u. How to tell in spacegroup.in that I need to keep vacuum along z direction for R-3:H symmetry.

Thanks,

Santu B

[Vitaliy Romaka]

you will not be able to keep symmetry by adding vacuum slab. But in the case symmetry is not the limiting factor, just make 1 1 2, or 1 1 3 and primcel - false in spacegroup.in, then delete unnecessary atoms in the desired from generated geometry.out. (You may use VESTA program to determine which atoms to remove). I would also advise to use cif2cell program (on sourceforge).

[Santu Baidya]

Many thanks for your reply.

[Eleni Chatzikyriakou]

Hello, I have tried this too, but I'm not sure the results are what I want.

I don't understand why one of my atoms ends up at 0 0 0 ater running elk optimization.

spacegroup.in

'P1'                                       : hrmg
6.028830615883  6.028830615883  14.05861649203  : a, b, c  
90.0     90.0     120.0000           : bc, ac, ab
1  1  3                              : ncell
.false.                               : primcell
2                                    : nspecies
’Mo’                                 : spsymb
1                                    : nwpos
 0.66667    0.33333    0.50000  : wpos
’S’
2
0.33333    0.66667    0.28965
0.33333    0.66667    0.71035

GEOMETRY.OUT

! Atomic positions generated by spacegroup version 1.2.01
!  Hermann-Mauguin symbol : P1
!  Hall symbol            : P 1
!  Schoenflies symbol     : C1^1
!  space group number     : 1
!  lattice constants (a,b,c) :    6.028830616       6.028830616       14.05861649    
!  angles in degrees (bc,ac,ab) :    90.00000000       90.00000000       120.0000000    
!  number of conventional unit cells :    1   1   3
!  reduction to primitive cell : F
!  Wyckoff positions :
!   species :    1, ’Mo’
!     0.6666700000      0.3333300000      0.5000000000    
!   species :    2, ’S’
!     0.3333300000      0.6666700000      0.2896500000    
!     0.3333300000      0.6666700000      0.7103500000    

avec
   6.028830616       0.000000000       0.000000000    
  -3.014415308       5.221120468       0.000000000    
   0.000000000       0.000000000       42.17584948    

atoms
   2                                    : nspecies
'’Mo’.in'                           : spfname
   3                                    : natoms; atposl, bfcmt below
    0.66667000    0.33333000    0.16666667    0.00000000  0.00000000  0.00000000
    0.66667000    0.33333000    0.50000000    0.00000000  0.00000000  0.00000000
    0.66667000    0.33333000    0.83333333    0.00000000  0.00000000  0.00000000
'’S’.in'                            : spfname
   6                                    : natoms; atposl, bfcmt below
    0.33333000    0.66667000    0.09655000    0.00000000  0.00000000  0.00000000
    0.33333000    0.66667000    0.42988333    0.00000000  0.00000000  0.00000000
    0.33333000    0.66667000    0.76321667    0.00000000  0.00000000  0.00000000
    0.33333000    0.66667000    0.23678333    0.00000000  0.00000000  0.00000000
    0.33333000    0.66667000    0.57011667    0.00000000  0.00000000  0.00000000
    0.33333000    0.66667000    0.90345000    0.00000000  0.00000000  0.00000000

elk.in

tasks
2

xctype
1

autolinengy
true

mixtype
3

!spinpol
! .true.

!bfieldc
!  0.0  0.0  0.01

!reducebf
! 0.5

maxscl
200

latvopt
1

nempty
  10 

sppath
 '../species/'

avec
   6.028830616       0.000000000       0.000000000    
  -3.014415308       5.221120468       0.000000000    
   0.000000000       0.000000000       42.17584948    

atoms
   2                                    : nspecies
'Mo.in'                           : spfname
   1                                    : natoms; atposl, bfcmt below
    0.66667000    0.33333000    0.16666667    0.00000000  0.00000000  0.00000000
'S.in'                            : spfname
   2                                    : natoms; atposl, bfcmt below
    0.33333000    0.66667000    0.09655000    0.00000000  0.00000000  0.00000000
    0.33333000    0.66667000    0.23678333    0.00000000  0.00000000  0.00000000

ngridk
9 9 1

GEOMETRY.OUT

! Atomic position optimisation step :      4

scale
 1.0

scale1
 1.0

scale2
 1.0

scale3
 1.0

avec
   6.028830616       0.000000000       0.000000000    
  -3.014415308       5.221120468       0.000000000    
   0.000000000       0.000000000       42.17584948    

atoms
   2                                    : nspecies
'Mo.in'                                 : spfname
   1                                    : natoms; atpos, bfcmt below
   -0.00000215    0.00000215    0.00000000    0.00000000  0.00000000  0.00000000
'S.in'                                  : spfname
   2                                    : natoms; atpos, bfcmt below
    0.66680354    0.33319646    0.91042789    0.00000000  0.00000000  0.00000000
    0.66680354    0.33319646    0.08957210    0.00000000  0.00000000  0.00000000

[mfechner]

Dear Eleni,

by default elk shifts the entire lattice that the first atom (Mo in your case) exhibit 0 0 0 coordinates, which I guess is the source of your observation. You can suppress this by setting

tshift
.false.

or just ignore it and go on with the shifted coordinates.

best regards
Michael

[Eleni Chatzikyriakou]

Dear Michael,

It still doesn't work as I would like it:
a) The lattice vectors do not change either with latvopt 1 or 2 (I am using elk v. 5.2.10)
b) The atoms are spread inside the unit cell and the structure is broken (either with tshift=true or false)

[DEBARATI PAL]

Dear Eleni,
Can you please tell me how to upgrade elk v.5.2.10,I am using elk v 4.3.06,in case I need to uninstall my current version how to do it and how to install the new one.

[mfechner]

Okay,

could you post the default output to check wether elk already computed the strain ? Anyway if you are trying to relax a surface, as I guess this from you input card. You may want to keep the lattice vectors fixed! The reason for this is that you should have enough vacuum to allow the atoms to relax in c-direction. Number two: what do you mean the atoms are spread inside the unit cell. From your previous post (elk.in and geometry.out)

1.) the elk shift was obvious and the atoms relaxed a bit inside the cell. So I suppose that this configuration might be the groundstate for a free standing layer. Please note that also your initial set up had a similiar ''roughness''

best regards
Michael

[Eleni Chatzikyriakou]

This is indeed one layer of material. I have tried different configurations, and the structure breaks every time. It looks like I should reduce the optimization step, although I have not ried it yet.
By "default", you mean INFO.OUT?
I see this line at the begining of INFO.OUT
+---------------------------------------------------+
| Geometry optimisation run resuming from STATE.OUT |
+---------------------------------------------------+

Although I am using

tasks
2

Does this mean I should run 0 first?

[com foru]

You may now not be capable of keep symmetry with the aid of adding vacuum slab. But in the case symmetry is not the proscribing thing, simply make 1 1 2, or 1 1 three and primcel - false in spacegroup.In, then delete pointless atoms within the favored from generated geometry.Out.

[com foru]

You may now not be capable of keep symmetry with the aid of adding vacuum slab. But in the case symmetry is not the proscribing thing, simply make 1 1 2, in the hardwood floor or 1 1 three and primcel - false in spacegroup.In, then delete pointless atoms within the favored from generated geometry.Out.