error in band unfolding of 2D

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error in band unfolding of 2D

Date: 2023/08/11 08:05
Name: Roozbeh Anvari <roozbeh.anvari@austin.utexas.edu>: Dear experts,

I am facing the following error message when trying to unfold bands of a (√3 ×√3) reconstruction of MoS2 into unit cell:

"
Cannot assign atoms in the reference cell properly! Could be due to more than one same atom in the reference cell!
Check the input file, maybe the structure is highly disordered or you need to set the reference origin by yourself!
"

I am wondering if band-unfolding module works for reconstructed supercells ? or may be this is due to the length of c-vector as discussed in this thread :

https://www.openmx-square.org/forum/patio.cgi?mode=view&no=2671

setting/un-setting the origin does not make a difference,

Thank you for your help,
regards,
Roozbeh

#-------------------------------------------------------------

here is the input script,

File Name , MoS2, standard accuracy,
System.CurrrentDirectory ./ # default=./
System.Name MoS2
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)
DATA.PATH /scratch/ranvari/openmx/DFT_DATA19 # CC

Species.Number 4
<Definition.of.Atomic.Species
Mo Mo7.0-s3p2d2 Mo_PBE19
S S7.0-s2p2d1f1 S_PBE19
Au Au7.0-s3p2d2f1 Au_PBE19
E S7.0-s2p2d1f1 E
Definition.of.Atomic.Species>

Atoms.Number 36
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Mo 5.17021496257605 1.69269482383582 32.84527946368422 7.0 7.0
2 Mo 2.22595562180673 0.00062118019171 32.85636220203556 7.0 7.0
3 Mo 8.10543749520870 3.37597309067890 32.85848406938854 7.0 7.0
4 Mo 13.99477444433331 6.77861609979504 32.83844969499939 7.0 7.0
5 Mo 11.12080171639627 5.00151242460014 32.83712338311516 7.0 7.0
6 Mo 16.92184016851574 8.49182072376890 32.84633242188106 7.0 7.0
7 Mo 7.98916586090044 6.78645830947599 32.81545798106036 7.0 7.0
8 Mo 5.16841917401078 5.07042194226625 32.84608482304930 7.0 7.0
9 Mo 11.11245122914105 8.55408015364740 32.84154077731986 7.0 7.0
10 Mo 11.04593288442700 1.68538388265577 32.84469182646005 7.0 7.0
11 Mo 8.12347096098679 -0.00630158209698 32.85173489612149 7.0 7.0
12 Mo 14.00564804066109 3.38470080882278 32.85117925410249 7.0 7.0
13 S 1.25853320505355 1.69225133790223 31.33578200148131 3.0 3.0
14 S 7.11469828721247 5.04296668711318 31.31515380278173 3.0 3.0
15 S 4.19409964826992 3.39668905594181 31.32047377788701 3.0 3.0
16 S 1.24764478303706 1.69661637203488 34.36538014625864 3.0 3.0
17 S 7.12071093789306 5.07933792255724 34.36339120163856 3.0 3.0
18 S 4.20015598306174 3.38090486452737 34.37074169869526 3.0 3.0
19 S 10.07305266648584 6.77818154918764 31.45275532320302 3.0 3.0
20 S 15.94554729528137 10.16171567780813 31.32043645584893 3.0 3.0
21 S 13.02573694637688 8.50798040964937 31.31266010792494 3.0 3.0
22 Au 10.04874921156424 6.77390729963104 34.67859297964308 8.5 8.5
23 S 15.95177119347215 10.17878196280291 34.37086034097744 3.0 3.0
24 S 13.03261809152093 8.47321229524314 34.36890559092445 3.0 3.0
25 S 4.19940126328275 6.78044484529582 31.32904611038892 3.0 3.0
26 S 10.06805078075999 10.16487994834728 31.32172010704462 3.0 3.0
27 S 7.10933251175784 8.51777054940868 31.31239553219098 3.0 3.0
28 S 4.19360706894176 6.77988728274890 34.35466836901708 3.0 3.0
29 S 10.07212072453103 10.17946430277841 34.36628763332808 3.0 3.0
30 S 7.11731159984772 8.48449571367431 34.36654562280687 3.0 3.0
31 S 7.13655857019585 1.68695776106287 31.33640070365824 3.0 3.0
32 S 13.03158147891535 5.04804747701040 31.31089061160834 3.0 3.0
33 S 10.06641447571694 3.39162627155429 31.32201305298240 3.0 3.0
34 S 7.12501827200038 1.68037854157690 34.36751757571043 3.0 3.0
35 S 13.03686200083370 5.08218926780999 34.36973295507907 3.0 3.0
36 S 10.07555979205321 3.37887076258852 34.36575743337900 3.0 3.0
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
0.000000000000000 0.000000000000000 77.000000000000000
11.755499839800001 0.000000000000000 0.000000000000000
5.877749919900000 10.180561495399999 0.000000000000000
Atoms.UnitVectors>

# SCF
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization On # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 300.0 # default=150 (Ry)

scf.maxIter 100 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band

scf.Kgrid 1 12 12 # means n1 x n2 x n3 ,
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.010 # default=0.30
scf.Min.Mixing.Weight 0.01 # default=0.001
scf.Max.Mixing.Weight 0.100 # default=0.40
scf.Mixing.History 30 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.criterion 1.0e-10 # default=1.0e-6 (Hartree)

ESM.switch on2 # off, on1=v|v|v, on2=m|v|m, on3=v|v|m, on4=on2+EF
ESM.potential.difference 0.0 # default=0.0 (eV)
ESM.wall.switch off
ESM.wall.position 6.0 # default=10.0 (ang)
ESM.wall.height 100.0 # default=100.0 (eV)
ESM.buffer.range 10 # default=10.0 (ang)
ESM.direction z # x|y|z, default=x

scf.dftD on # on|off, default=off
version.dftD 3 # 2|3, default=2
DFTD3.damp bj # zero|bj, default=bj
DFTD.Unit AU # Ang|AU
DFTD.rcut_dftD 100.0 # default=100 (DFTD.Unit)
DFTD.cncut_dftD 40 # default=40 (DFTD.Unit)
DFTD.IntDirection 1 1 1 # default=1 1 1 (1:on 0:off)

<DFTD.periodicity
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
DFTD.periodicity>

MD.Type nomd # Nomd|Opt|NVE|NVT_VS|NVT_NH
MD.maxIter 1 # default=1
MD.TimeStep 1 # default=0.5 (fs)
MD.Opt.criterion 2.0e-5 # default=1.0e-4 (Hartree/bohr)

# ------------
#------------------------------------------------------------------------
Unfolding.Electronic.Band on # on|off, default=off
Unfolding.LowerBound -3.0 # default=-10 eV
Unfolding.UpperBound 3.0 # default= 10 eV

Unfolding.Nkpoint 4

<Unfolding.kpoint
G 0.0 0.0 0.0
M 0.0 -0.5 0.0
K 0.0 0.3333 -0.6666
G 0.0 0.0 0.0
Unfolding.kpoint>

Unfolding.desired_totalnkpt 30

<Unfolding.ReferenceVectors
-0.000000000000000 0.000000000000000 77.000000000000000
3.163477557887240 -0.000426431984253 0.000000000000000
-1.582522944036001 2.740067493643488 0.000000000000000
Unfolding.ReferenceVectors>

<Unfolding.Map
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 2
14 2
15 2
16 2
17 2
18 2
19 2
20 2
21 2
22 3
23 2
24 2
25 2
26 2
27 2
28 2
29 2
30 2
31 2
32 2
33 2
34 2
35 2
36 2
Unfolding.Map>

# <unfolding.referenceorigin
# 0 0 0
# unfolding.referenceorigin>

Page: [1]

Re: error in band unfolding of 2D ( No.1 )

Date: 2023/08/11 16:19
Name: Naoya Yamaguchi

Hi,

The mapping rule given by `Unfolding.Map` is not appropriate. How about the following?

```
<Unfolding.Map
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 2
14 2
15 2
16 4
17 4
18 4
19 2
20 2
21 2
22 3
23 4
24 4
25 2
26 2
27 2
28 4
29 4
30 4
31 2
32 2
33 2
34 4
35 4
36 4
Unfolding.Map>
```

Regards,
Naoya Yamaguchi

Re: error in band unfolding of 2D ( No.2 )

Date: 2023/10/06 11:32
Name: Roozbeh Anvari <roozbeh.anvari@gmail.com>

Dear Yamaguchi,

Thank you for your solution, but I am afraid the same error message still persists for the above structure,

I applied the method you suggested (by assigning top and bottom S atoms to different classes) to a 6x6 supercell with very large vacuum and it worked, however I have not found a solution around highly disturbed structures yet,

Best regards,

Roozbeh

Re: error in band unfolding of 2D ( No.3 )

Date: 2023/10/06 12:58
Name: Naoya Yamaguchi

Dear Roozbeh,

Although I forgot to mention it, it is necessary to adjust `Unfolding.ReferenceVectors` according to the given mapping rules.

The lattice constant c should be given as the bulk unit cell.

<Unfolding.ReferenceVectors
-0.000000000000000 0.000000000000000 c
3.163477557887240 -0.000426431984253 0.000000000000000
-1.582522944036001 2.740067493643488 0.000000000000000
Unfolding.ReferenceVectors>

Regards,
Naoya Yamaguchi

Page: [1]