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Unfolding cannot assign atoms in supercell-slab calculations
Date: 2020/08/20 21:43
Name: Eike F. Schwier   <schwier@physik.uni-wuerzburg.de>

Hi everybody,

does anyone have some experience with unfolding from slap-supercells? I am trying to calculate the surface structure of Pd intercalated Bi2Te3 and for the bulk 2x2x2 supercell its works without a problem. But when I try to construct a slab from said supercell (2x2x6 with vacuum) unfolding to a "primitive" slab (1x1x6 with vacuum) does not work.I tried setting the reference origin to 0/0/0, but to no avail. Any ideas what I did wrong?

best regards,
Eike



System.CurrrentDirectory ./ # default=./

System.Name P0.2BT_2x2x6_01_noSO
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

#
# Definition of Atomic Species
#

Species.Number 3
<Definition.of.Atomic.Species
Te Te7.0-s2p2d1 Te_CA19
Bi Bi8.0-s2p2d1 Bi_CA19
Pd Pd7.0-s2p2d1 Pd_CA19
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 126
Atoms.SpeciesAndCoordinates.Unit FRAC # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Pd 0.31 0.31 0.015 8 8
2 Te 0.1 0.6 0.031 8 8
3 Te 0.6 0.1 0.031 8 8
4 Te 0.6 0.6 0.031 8 8
5 Te 0.1 0.1 0.031 8 8
6 Bi 0.71 0.71 0.053 7.5 7.5
7 Bi 0.21 0.21 0.053 7.5 7.5
8 Bi 0.21 0.71 0.053 7.5 7.5
9 Bi 0.71 0.21 0.053 7.5 7.5
10 Te 0.81 0.31 0.078 8 8
11 Te 0.31 0.81 0.078 8 8
12 Te 0.81 0.81 0.078 8 8
13 Te 0.31 0.31 0.078 8 8
14 Bi 0.91 0.91 0.102 7.5 7.5
15 Bi 0.41 0.41 0.102 7.5 7.5
16 Bi 0.41 0.91 0.102 7.5 7.5
17 Bi 0.91 0.41 0.102 7.5 7.5
18 Te 0.52 0.02 0.124 8 8
19 Te 0.02 0.02 0.124 8 8
20 Te 0.02 0.52 0.124 8 8
21 Te 0.52 0.52 0.124 8 8
22 Pd 0.31 0.31 0.14 8 8
23 Te 0.1 0.6 0.156 8 8
24 Te 0.6 0.1 0.156 8 8
25 Te 0.6 0.6 0.156 8 8
26 Te 0.1 0.1 0.156 8 8
27 Bi 0.71 0.71 0.178 7.5 7.5
28 Bi 0.21 0.21 0.178 7.5 7.5
29 Bi 0.21 0.71 0.178 7.5 7.5
30 Bi 0.71 0.21 0.178 7.5 7.5
31 Te 0.31 0.81 0.203 8 8
32 Te 0.81 0.31 0.203 8 8
33 Te 0.81 0.81 0.203 8 8
34 Te 0.31 0.31 0.203 8 8
35 Bi 0.91 0.91 0.227 7.5 7.5
36 Bi 0.41 0.41 0.227 7.5 7.5
37 Bi 0.41 0.91 0.227 7.5 7.5
38 Bi 0.91 0.41 0.227 7.5 7.5
39 Te 0.52 0.02 0.249 8 8
40 Te 0.02 0.02 0.249 8 8
41 Te 0.02 0.52 0.249 8 8
42 Te 0.52 0.52 0.249 8 8
43 Pd 0.31 0.31 0.265 8 8
44 Te 0.1 0.6 0.281 8 8
45 Te 0.6 0.1 0.281 8 8
46 Te 0.6 0.6 0.281 8 8
47 Te 0.1 0.1 0.281 8 8
48 Bi 0.71 0.71 0.303 7.5 7.5
49 Bi 0.21 0.21 0.303 7.5 7.5
50 Bi 0.21 0.71 0.303 7.5 7.5
51 Bi 0.71 0.21 0.303 7.5 7.5
52 Te 0.31 0.81 0.328 8 8
53 Te 0.81 0.31 0.328 8 8
54 Te 0.81 0.81 0.328 8 8
55 Te 0.31 0.31 0.328 8 8
56 Bi 0.91 0.91 0.352 7.5 7.5
57 Bi 0.41 0.41 0.352 7.5 7.5
58 Bi 0.41 0.91 0.352 7.5 7.5
59 Bi 0.91 0.41 0.352 7.5 7.5
60 Te 0.52 0.02 0.374 8 8
61 Te 0.02 0.02 0.374 8 8
62 Te 0.02 0.52 0.374 8 8
63 Te 0.52 0.52 0.374 8 8
64 Pd 0.31 0.31 0.39 8 8
65 Te 0.1 0.6 0.406 8 8
66 Te 0.6 0.1 0.406 8 8
67 Te 0.6 0.6 0.406 8 8
68 Te 0.1 0.1 0.406 8 8
69 Bi 0.71 0.71 0.428 7.5 7.5
70 Bi 0.21 0.21 0.428 7.5 7.5
71 Bi 0.21 0.71 0.428 7.5 7.5
72 Bi 0.71 0.21 0.428 7.5 7.5
73 Te 0.31 0.81 0.453 8 8
74 Te 0.81 0.31 0.453 8 8
75 Te 0.81 0.81 0.453 8 8
76 Te 0.31 0.31 0.453 8 8
77 Bi 0.91 0.91 0.477 7.5 7.5
78 Bi 0.41 0.41 0.477 7.5 7.5
79 Bi 0.41 0.91 0.477 7.5 7.5
80 Bi 0.91 0.41 0.477 7.5 7.5
81 Te 0.52 0.02 0.499 8 8
82 Te 0.02 0.02 0.499 8 8
83 Te 0.02 0.52 0.499 8 8
84 Te 0.52 0.52 0.499 8 8
85 Pd 0.31 0.31 0.515 8 8
86 Te 0.1 0.6 0.531 8 8
87 Te 0.6 0.1 0.531 8 8
88 Te 0.6 0.6 0.531 8 8
89 Te 0.1 0.1 0.531 8 8
90 Bi 0.71 0.71 0.553 7.5 7.5
91 Bi 0.21 0.21 0.553 7.5 7.5
92 Bi 0.21 0.71 0.553 7.5 7.5
93 Bi 0.71 0.21 0.553 7.5 7.5
94 Te 0.31 0.81 0.578 8 8
95 Te 0.81 0.31 0.578 8 8
96 Te 0.81 0.81 0.578 8 8
97 Te 0.31 0.31 0.578 8 8
98 Bi 0.91 0.91 0.602 7.5 7.5
99 Bi 0.41 0.41 0.602 7.5 7.5
100 Bi 0.41 0.91 0.602 7.5 7.5
101 Bi 0.91 0.41 0.602 7.5 7.5
102 Te 0.52 0.02 0.624 8 8
103 Te 0.02 0.02 0.624 8 8
104 Te 0.02 0.52 0.624 8 8
105 Te 0.52 0.52 0.624 8 8
106 Pd 0.31 0.31 0.64 8 8
107 Te 0.1 0.6 0.656 8 8
108 Te 0.6 0.1 0.656 8 8
109 Te 0.6 0.6 0.656 8 8
110 Te 0.1 0.1 0.656 8 8
111 Bi 0.71 0.71 0.678 7.5 7.5
112 Bi 0.21 0.21 0.678 7.5 7.5
113 Bi 0.21 0.71 0.678 7.5 7.5
114 Bi 0.71 0.21 0.678 7.5 7.5
115 Te 0.31 0.81 0.703 8 8
116 Te 0.81 0.31 0.703 8 8
117 Te 0.81 0.81 0.703 8 8
118 Te 0.31 0.31 0.703 8 8
119 Bi 0.91 0.91 0.727 7.5 7.5
120 Bi 0.41 0.41 0.727 7.5 7.5
121 Bi 0.41 0.91 0.727 7.5 7.5
122 Bi 0.91 0.41 0.727 7.5 7.5
123 Te 0.52 0.02 0.749 8 8
124 Te 0.02 0.02 0.749 8 8
125 Te 0.02 0.52 0.749 8 8
126 Te 0.52 0.52 0.749 8 8
Atoms.SpeciesAndCoordinates>


<Unfolding.ReferenceOrigin
0 0 0
Unfolding.ReferenceOrigin>


Atoms.UnitVectors.Unit Ang


<Atoms.UnitVectors
8.7370796204 0.0000000000 0.0000000000
4.3685398102 7.5665329062 0.0000000000
34.9483452008 20.1774365096 81.1284823144
Atoms.UnitVectors>


Unfolding.Electronic.Band on # on|off, default=off

<Unfolding.ReferenceVectors
4.3685398102 0.0000000000 0.0000000000
2.1842699051 3.7832664531 0.0000000000
34.9483452008 20.1774365096 81.1284823144
Unfolding.ReferenceVectors>
Unfolding.LowerBound -1.5
Unfolding.UpperBound 1.0

<Unfolding.Map
1 1
2 2
3 2
4 2
5 2
6 3
7 3
8 3
9 3
10 4
11 4
12 4
13 4
14 5
15 5
16 5
17 5
18 6
19 6
20 6
21 6
22 7
23 8
24 8
25 8
26 8
27 9
28 9
29 9
30 9
31 10
32 10
33 10
34 10
35 11
36 11
37 11
38 11
39 12
40 12
41 12
42 12
43 13
44 14
45 14
46 14
47 14
48 15
49 15
50 15
51 15
52 16
53 16
54 16
55 16
56 17
57 17
58 17
59 17
60 18
61 18
62 18
63 18
64 19
65 20
66 20
67 20
68 20
69 21
70 21
71 21
72 21
73 22
74 22
75 22
76 22
77 23
78 23
79 23
80 23
81 24
82 24
83 24
84 24
85 25
86 26
87 26
88 26
89 26
90 27
91 27
92 27
93 27
94 28
95 28
96 28
97 28
98 29
99 29
100 29
101 29
102 30
103 30
104 30
105 30
106 31
107 32
108 32
109 32
110 32
111 33
112 33
113 33
114 33
115 34
116 34
117 34
118 34
119 35
120 35
121 35
122 35
123 36
124 36
125 36
126 36
Unfolding.Map>

Unfolding.desired_totalnkpt 500
Unfolding.Nkpoint 5

<Unfolding.kpoint
G 0.0 0.0 0.0
M 0.5 0.5 0.0
X 0.5 0.0 0.0
G 0.0 0.0 0.0
Y 0.0 0.5 0.0
Unfolding.kpoint>

#
# SCF or Electronic System
#

scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 600.0 # default=300 (K)
scf.energycutoff 75.0 # default=150 (Ry)
#scf.Ngrid 24 24 24
scf.maxIter 400 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band
scf.Kgrid 4 4 1 # means n1 x n2 x n3
scf.ProExpn.VNA on # default=on
scf.Generation.Kpoint regular
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.05 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.350 # default=0.40
scf.Mixing.History 12 # default=5
scf.Mixing.StartPulay 20 # default=6
scf.Mixing.EveryPulay 1 # default=5
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstevx
scf.restart on

メンテ
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Re: Unfolding cannot assign atoms in supercell-slab calculations ( No.1 )
Date: 2020/08/22 18:20
Name: Naoya Yamaguchi

Dear Eike,

I might find the cause and you might solve it by modifying "Unfolding_Bands.c".
Please try to replace lines 2873 and 2961 with
for (i=-2*atomnum; i<=2*atomnum; i++) for (j=-2*atomnum; j<=2*atomnum; j++) for (k=-2*atomnum; k<=2*atomnum; k++) {
Because I haven't checked the whole result, please check it by yourself.

Regards,
Naoya Yamaguchi
メンテ
Re: Unfolding cannot assign atoms in supercell-slab calculations ( No.2 )
Date: 2020/08/22 22:05
Name: Chi-Cheng  <cclee.physics@gmail.com>

Hi Eike,

You can try to skip the loop between line 2965 and line 2973,
and then replace them by "esti=0; estj=0; estk=0;".

The estimated i, j, and k failed because the slab is not-orthogonal
and too long along the c axis. Hope this will help.

Regards,
Chi-Cheng
メンテ
Re: Unfolding cannot assign atoms in supercell-slab calculations ( No.3 )
Date: 2020/08/22 22:40
Name: Chi-Cheng  <cclee.physics@gmail.com>

Hi Eike,

Sorry, line 2965 and line 2973 I mentioned previously should be 2961 and 2969, respectively.

-------------------------
replace the following

for (i=-2*atomnum; i<=2*atomnum; i+=5) for (j=-2*atomnum; j<=2*atomnum; j+=5) for (k=-2*atomnum; k<=2*atomnum; k+=5) {
double x=(double)i*a[0]+(double)j*b[0]+(double)k*c[0]+origin[0];
double y=(double)i*a[1]+(double)j*b[1]+(double)k*c[1]+origin[1];
double z=(double)i*a[2]+(double)j*b[2]+(double)k*c[2]+origin[2];
tmp[0]=X-x;
tmp[1]=Y-y;
tmp[2]=Z-z;
if (dis(tmp)<estl) { estl=dis(tmp); esti=i; estj=j; estk=k; }
}

by

esti=0; estj=0; estk=0;
----------------------------

If the loop does not take a long time, you can also follow Naoya's suggestion.

Regards,
Chi-Cheng

メンテ
Re: Unfolding cannot assign atoms in supercell-slab calculations ( No.4 )
Date: 2020/08/26 23:47
Name: Eike F. Schwier  <schwier@physik.uni-wuerzburg.de>

Dear Yamaguchi-san & Chi-Cheng,

thank you very much for your advice. For now I was able, with Yamaguchi-san's code lines, to successfully obtain an unfolded bandstructure. I will need to check if there is any inconsistency in the structure exist or if the unfolding worked as it was originally implemented.

best regards,
Eike
メンテ
Re: Unfolding cannot assign atoms in supercell-slab calculations ( No.5 )
Date: 2020/09/17 22:05
Name: Eike F. Schwier  <schwier@physik.uni-wuerzburg.de>

Dear Yamaguchi-san & Chi-Cheng,

in the meantime I was able to test the unfolding. It works if I do not include SO coupling and seems to produce reasonable results. However, if SO coupling is included the unfolding produces no error, but empty unfold_orb files. I tested with 3.8.5 (without scalapack) and 3.9.2 on a smaller system (orthorhombic bulk with 17 atoms) and on a different PC. 3.8.5 works. 3.9.2 works up to a certain number of atoms (10) in an otherwise identical unit cell (I simply remmoved the atoms from the unit cell one by one). Above it produces zero size output.

Do you have any advice at to why this may happen?

best regards,
Eike

メンテ
Re: Unfolding cannot assign atoms in supercell-slab calculations ( No.6 )
Date: 2020/09/17 23:44
Name: Naoya Yamaguchi

Dear Eike-san,

Can you show each of the actual examples of the inputs?

Regards,
Naoya Yamaguchi
メンテ
Re: Unfolding cannot assign atoms in supercell-slab calculations ( No.7 )
Date: 2020/09/18 00:17
Name: Chi-Cheng  <cclee.physics@gmail.com>

Hi Eike,

Could you also try to reduce the number of k points?
Maybe the file size is too large to handle. If reducing
# of kpoints works, you can calculate the unfolding
piece by piece by dividing the entire k path smartly.

Regards,
Chi-Cheng
メンテ

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