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SiC + buffer layer 2x2 unfolding error
Date: 2020/11/07 22:18
Name: Malone

Dear OpenMX maintainers,

I have encountered an unfolding problem that I fail to resolve myself, so I heed your help.

A SiC 2x2 crystal with the buffer layer on C-terminated side is being investigated. I have successfully unfolded (partially for surface
carbon layer) the bandstructure, using this graphene reference cell: https://ibb.co/T0x3WkH
by assigning groups 1,3,5,7=1, 2,4,6,8=2, other atoms each one in its own group (so the 'bulk' was not unfolded).

Now I am trying to use the bulk SiC-cell: https://ibb.co/mT8t5bt
and it fails with a somewhat cryptic message:

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 have added two lines of code into the Unfolding_Bands.c::buildtab4RN() function (lines 3590, 3582) to track where the failure actually occurs, and here is the output:

FAIL: [iR][iN]=[0][28] coincide with [iRp][iNp]=[2][2]
FAIL: [iR][iN]=[0][29] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][30] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][30] coincide with [iRp][iNp]=[2][2]
FAIL: [iR][iN]=[0][31] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][32] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][33] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][34] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][35] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][36] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][37] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][38] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][39] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][40] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][41] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][42] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][43] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][44] coincide with [iRp][iNp]=[19][19]
FAIL: [iR][iN]=[0][45] coincide with [iRp][iNp]=[19][19]

Unfortunately, I could not understand what the variable iR exactly corresponds to, so I ask you to help in these two points:
1) What am I missing regarding the system itself? I understand that as soon as 2x2 cell is the minimal cell where the 'graphene' layer
can be constructed, thus the system is irreducible and I cannot simultaneously unfold all bands -- either graphene layer or SiC bulk.
But why do I receive this error when I take a proper SiC-bulk's cell? Do my actions have any sense?

2) It will be highly appreciated if you could invest some time into explaining the magic behind the `buildtabr4RN' function, so that I would be able to perform unfolding debugging myself (to some extent, greater than current one, though).


This is the system

Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 C 0.00324524363256 1.48664415886461 18.118475910832712 2.0 2.0
2 C 1.28311893831066 0.74671781726372 18.117981815336423 2.0 2.0
3 C 2.55703857095221 1.47661374148216 18.183016487714084 2.0 2.0
4 C -0.00282452625590 2.95440559482601 18.182641803901805 2.0 2.0
5 C -1.27581444254790 3.68238409813573 18.123712792587746 2.0 2.0
6 C 3.82431849469757 0.73877455655615 18.117877282422767 2.0 2.0
7 C 1.26565114270063 3.69180344447668 18.115387353482178 2.0 2.0
8 C 2.56215738516977 2.94328476605010 18.122149301066939 2.0 2.0
9 Si 1.68444707976490 0.00253203506553 15.9690190747356710 2.0 2.0
10 Si -0.83760066316124 1.45665204059686 15.9708378637095611 2.0 2.0
11 Si 1.72028878664208 2.97998800650180 15.9692209866193012 2.0 2.0
12 C 3.40293143147223 0.00228252457502 15.3026834785986613 2.0 2.0
13 C -1.69725891489095 2.94630318747320 15.3066437502781514 2.0 2.0
14 C 0.86092959241991 1.48912422737823 15.3061328662388215 2.0 2.0
15 Si 3.40969002899243 0.00010151176771 13.4014185136412316 2.0 2.0
16 Si -1.70242837798359 2.95150295271441 13.4031988217192617 2.0 2.0
17 Si 0.85615787123948 1.48046367318679 13.4031367226045518 2.0 2.0
18 C 0.00109758782428 2.95424067925589 12.7292994768435319 2.0 2.0
19 C 2.55975089335264 1.47730748298141 12.7292474899198220 2.0 2.0
20 Si 2.55921045027294 1.47664500172362 10.8370932671614321 2.0 2.0
21 Si 0.00052021888161 2.95374971264254 10.8371205683758822 2.0 2.0
22 C -0.85191068311225 1.47552641015339 10.1643750553581623 2.0 2.0
23 C 1.70569704182936 -0.00103700733054 10.1642798862132224 2.0 2.0
24 C 1.70636922953515 2.95433386639622 10.1642693229194425 2.0 2.0
25 Si -0.85368251557652 4.43086619944899 8.2668834517741626 2.0 2.0
26 Si 4.26436749811787 1.47573850993789 8.2669162769110927 2.0 2.0
27 Si 1.70569830689987 2.95400799354222 8.2668739769092928 2.0 2.0
28 C -0.00009948824623 2.95366716948947 7.5893414703461629 2.0 2.0
29 C 2.55856197553034 1.47637241336102 7.5893535674485130 2.0 2.0
30 Si 2.55821995448622 1.47629246181792 5.6969158489287131 2.0 2.0
31 Si -0.00046331093220 2.95361956718066 5.6969062703667132 2.0 2.0
32 C 0.85229660350768 4.43113265242596 5.0210413014877533 2.0 2.0
33 C 3.41107894330547 2.95372369851485 5.0210099892912134 2.0 2.0
34 C 0.85276930282136 1.47657042966827 5.0209955055010035 2.0 2.0
35 Si 0.85207870567210 4.43097005741617 3.1300437134737736 2.0 2.0
36 Si 3.41079932274796 2.95360116727883 3.1300205999346537 2.0 2.0
37 Si 0.85248570794137 1.47636893881557 3.1299793789883538 2.0 2.0
38 C -0.85323562282113 1.47640999003541 2.4875329687628539 2.0 2.0
39 C 1.70541238425970 -0.00090725296463 2.4875445007636740 2.0 2.0
40 C 1.70511177020177 2.95380559886956 2.4874450451564341 2.0 2.0
41 C 0.00194331471832 -0.00032825245817 12.7388806392142842 2.0 2.0
42 Si 2.55912497917804 4.43111720617694 10.8409189716216843 2.0 2.0
43 C 0.00027576067198 -0.00097170622280 7.5882147553186744 2.0 2.0
44 Si 2.55790330999001 4.43097491334740 5.6963244529581245 2.0 2.0
45 H -0.85315069513872 1.47656366978237 1.3795801831773446 0.5 0.5
46 H 1.70557061249230 -0.00079097275300 1.3795938229854647 0.5 0.5
47 H 1.70526006884019 2.95408594964264 1.37948364504858 0.5 0.5
Atoms.SpeciesAndCoordinates>

And this is the unfolding map that fails:
<unfolding.referenceorigin
0 0 0
unfolding.referenceorigin>


<unfolding.referencevectors
2.55921 1.4767 0
-2.55921 1.4767 0
0 0 30
unfolding.referencevectors>

<unfolding.map
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 9
11 9
12 10
13 10
14 10
15 11
16 11
17 11
18 12
19 12
20 13
21 13
22 14
23 14
24 14
25 15
26 15
27 15
28 16
29 16
30 17
31 17
32 18
33 18
34 18
35 19
36 19
37 19
38 20
39 20
40 20
41 12
42 13
43 16
44 17
45 21
46 21
47 21
unfolding.map>

メンテ
Page: [1]

Re: SiC + buffer layer 2x2 unfolding error ( No.1 )
Date: 2020/11/07 22:18
Name: Malone

I have checked that this problem arises just in graphene as well. using this input

1 C 0.003239 1.486618 18.11 2 2
2 C 1.283108 0.746700 18.11 2 2
3 C 2.557032 1.476602 18.11 2 2
4 C -0.002808 2.954401 18.11 2 2
5 C -1.275819 3.682353 18.11 2 2
6 C 3.824339 0.738766 18.11 2 2
7 C 1.265666 3.691793 18.11 2 2
8 C 2.562166 2.943276 18.11 2 2

and setting unfold map to identity

1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8

I do get this error too, starting with

FAIL: [iR][iN]=[0][0] coincide with [iRp][iNp]=[195645263][195645263]
FAIL: [iR][iN]=[0][1] coincide with [iRp][iNp]=[17][17]
FAIL: [iR][iN]=[0][2] coincide with [iRp][iNp]=[17][17]
FAIL: [iR][iN]=[0][3] coincide with [iRp][iNp]=[17][17]
FAIL: [iR][iN]=[0][3] coincide with [iRp][iNp]=[2][2]
FAIL: [iR][iN]=[0][4] coincide with [iRp][iNp]=[17][17]
FAIL: [iR][iN]=[0][5] coincide with [iRp][iNp]=[17][17]
FAIL: [iR][iN]=[0][6] coincide with [iRp][iNp]=[17][17]
FAIL: [iR][iN]=[0][7] coincide with [iRp][iNp]=[5][5]

メンテ
Re: SiC + buffer layer 2x2 unfolding error ( No.2 )
Date: 2020/11/07 00:54
Name: Naoya Yamaguchi

Hi,

Can you add the information of "Atoms.UnitVectors"?

Regards,
Naoya Yamaguchi
メンテ
Re: SiC + buffer layer 2x2 unfolding error ( No.3 )
Date: 2020/11/07 22:19
Name: Malone

Ouch, my fault. Sorry.

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
5.117000000000000 -0.000000000000000 0.000000000000000
-2.559000000000000 4.432000000000000 0.000000000000000
0.000000000000000 0.000000000000000 30.000000000000000
Atoms.UnitVectors>
メンテ
Re: SiC + buffer layer 2x2 unfolding error ( No.4 )
Date: 2020/11/07 16:57
Name: Naoya Yamaguchi

Dear Malone,

I tried the following input for the graphene, and get no errors.
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 C 0.003239 1.486618 18.11 2 2
2 C 1.283108 0.746700 18.11 2 2
3 C 2.557032 1.476602 18.11 2 2
4 C -0.002808 2.954401 18.11 2 2
5 C -1.275819 3.682353 18.11 2 2
6 C 3.824339 0.738766 18.11 2 2
7 C 1.265666 3.691793 18.11 2 2
8 C 2.562166 2.943276 18.11 2 2
Atoms.SpeciesAndCoordinates>

<unfolding.referenceorigin
0 0 0
unfolding.referenceorigin>


<unfolding.referencevectors
2.55921 1.4767 0
-2.55921 1.4767 0
0 0 30
unfolding.referencevectors>

<unfolding.map
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
unfolding.map>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
5.117000000000000 -0.000000000000000 0.000000000000000
-2.559000000000000 4.432000000000000 0.000000000000000
0.000000000000000 0.000000000000000 30.000000000000000
Atoms.UnitVectors>

System.CurrrentDirectory ./
System.Name 2714_1
level.of.fileout 0

Species.Number 1
<Definition.of.Atomic.Species
C C5.0-s2p2d1 C_PBE19
Definition.of.Atomic.Species>

Atoms.Number 8
Atoms.UnitVectors.Unit Ang

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.ElectronicTemperature 300.0
scf.energycutoff 300.0
scf.SpinOrbit.Coupling off
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 8 8 1
scf.Mixing.Type rmm-diish
scf.Init.Mixing.Weight 0.10
scf.Min.Mixing.Weight 0.001
scf.Max.Mixing.Weight 0.300
scf.Mixing.History 10
scf.Mixing.StartPulay 5
scf.criterion 1.0e-8

Unfolding.Electronic.Band on
Unfolding.LowerBound -1.0
Unfolding.UpperBound 1.0
Unfolding.desired_totalnkpt 10
Unfolding.Nkpoint 2

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

And, I also tried the first input you showed with the following input, and get the error.
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 C 0.00324524363256 1.48664415886461 18.118475910832712 2.0 2.0
2 C 1.28311893831066 0.74671781726372 18.117981815336423 2.0 2.0
3 C 2.55703857095221 1.47661374148216 18.183016487714084 2.0 2.0
4 C -0.00282452625590 2.95440559482601 18.182641803901805 2.0 2.0
5 C -1.27581444254790 3.68238409813573 18.123712792587746 2.0 2.0
6 C 3.82431849469757 0.73877455655615 18.117877282422767 2.0 2.0
7 C 1.26565114270063 3.69180344447668 18.115387353482178 2.0 2.0
8 C 2.56215738516977 2.94328476605010 18.122149301066939 2.0 2.0
9 Si 1.68444707976490 0.00253203506553 15.9690190747356710 2.0 2.0
10 Si -0.83760066316124 1.45665204059686 15.9708378637095611 2.0 2.0
11 Si 1.72028878664208 2.97998800650180 15.9692209866193012 2.0 2.0
12 C 3.40293143147223 0.00228252457502 15.3026834785986613 2.0 2.0
13 C -1.69725891489095 2.94630318747320 15.3066437502781514 2.0 2.0
14 C 0.86092959241991 1.48912422737823 15.3061328662388215 2.0 2.0
15 Si 3.40969002899243 0.00010151176771 13.4014185136412316 2.0 2.0
16 Si -1.70242837798359 2.95150295271441 13.4031988217192617 2.0 2.0
17 Si 0.85615787123948 1.48046367318679 13.4031367226045518 2.0 2.0
18 C 0.00109758782428 2.95424067925589 12.7292994768435319 2.0 2.0
19 C 2.55975089335264 1.47730748298141 12.7292474899198220 2.0 2.0
20 Si 2.55921045027294 1.47664500172362 10.8370932671614321 2.0 2.0
21 Si 0.00052021888161 2.95374971264254 10.8371205683758822 2.0 2.0
22 C -0.85191068311225 1.47552641015339 10.1643750553581623 2.0 2.0
23 C 1.70569704182936 -0.00103700733054 10.1642798862132224 2.0 2.0
24 C 1.70636922953515 2.95433386639622 10.1642693229194425 2.0 2.0
25 Si -0.85368251557652 4.43086619944899 8.2668834517741626 2.0 2.0
26 Si 4.26436749811787 1.47573850993789 8.2669162769110927 2.0 2.0
27 Si 1.70569830689987 2.95400799354222 8.2668739769092928 2.0 2.0
28 C -0.00009948824623 2.95366716948947 7.5893414703461629 2.0 2.0
29 C 2.55856197553034 1.47637241336102 7.5893535674485130 2.0 2.0
30 Si 2.55821995448622 1.47629246181792 5.6969158489287131 2.0 2.0
31 Si -0.00046331093220 2.95361956718066 5.6969062703667132 2.0 2.0
32 C 0.85229660350768 4.43113265242596 5.0210413014877533 2.0 2.0
33 C 3.41107894330547 2.95372369851485 5.0210099892912134 2.0 2.0
34 C 0.85276930282136 1.47657042966827 5.0209955055010035 2.0 2.0
35 Si 0.85207870567210 4.43097005741617 3.1300437134737736 2.0 2.0
36 Si 3.41079932274796 2.95360116727883 3.1300205999346537 2.0 2.0
37 Si 0.85248570794137 1.47636893881557 3.1299793789883538 2.0 2.0
38 C -0.85323562282113 1.47640999003541 2.4875329687628539 2.0 2.0
39 C 1.70541238425970 -0.00090725296463 2.4875445007636740 2.0 2.0
40 C 1.70511177020177 2.95380559886956 2.4874450451564341 2.0 2.0
41 C 0.00194331471832 -0.00032825245817 12.7388806392142842 2.0 2.0
42 Si 2.55912497917804 4.43111720617694 10.8409189716216843 2.0 2.0
43 C 0.00027576067198 -0.00097170622280 7.5882147553186744 2.0 2.0
44 Si 2.55790330999001 4.43097491334740 5.6963244529581245 2.0 2.0
45 H -0.85315069513872 1.47656366978237 1.3795801831773446 0.5 0.5
46 H 1.70557061249230 -0.00079097275300 1.3795938229854647 0.5 0.5
47 H 1.70526006884019 2.95408594964264 1.37948364504858 0.5 0.5
Atoms.SpeciesAndCoordinates>

<unfolding.referenceorigin
0 0 0
unfolding.referenceorigin>


<unfolding.referencevectors
2.55921 1.4767 0
-2.55921 1.4767 0
0 0 30
unfolding.referencevectors>

<unfolding.map
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 9
11 9
12 10
13 10
14 10
15 11
16 11
17 11
18 12
19 12
20 13
21 13
22 14
23 14
24 14
25 15
26 15
27 15
28 16
29 16
30 17
31 17
32 18
33 18
34 18
35 19
36 19
37 19
38 20
39 20
40 20
41 12
42 13
43 16
44 17
45 21
46 21
47 21
unfolding.map>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
5.117000000000000 -0.000000000000000 0.000000000000000
-2.559000000000000 4.432000000000000 0.000000000000000
0.000000000000000 0.000000000000000 30.000000000000000
Atoms.UnitVectors>

System.CurrrentDirectory ./
System.Name 2714
level.of.fileout 0

Species.Number 3
<Definition.of.Atomic.Species
C C5.0-s2p2d1 C_PBE19
H H6.0-s2p1 H_PBE19
Si Si7.0-s2p2d1 Si_PBE19
Definition.of.Atomic.Species>

Atoms.Number 47
Atoms.UnitVectors.Unit Ang

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.ElectronicTemperature 300.0
scf.energycutoff 300.0
scf.SpinOrbit.Coupling off
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 8 8 1
scf.Mixing.Type rmm-diish
scf.Init.Mixing.Weight 0.10
scf.Min.Mixing.Weight 0.001
scf.Max.Mixing.Weight 0.300
scf.Mixing.History 10
scf.Mixing.StartPulay 5
scf.criterion 1.0e-8

Unfolding.Electronic.Band on
Unfolding.LowerBound -1.0
Unfolding.UpperBound 1.0
Unfolding.desired_totalnkpt 2
Unfolding.Nkpoint 2

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

I found that unsetting "unfolding.referenceorigin" solved it, that is, the manual setting of the origin was not appropriate.
And, I also found that modification shown in No.1 in the following thread was another solution.
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2671

Regards,
Naoya Yamaguchi
メンテ
Re: SiC + buffer layer 2x2 unfolding error ( No.5 )
Date: 2020/11/11 07:01
Name: Malone

I have tracked down the graphene unfolding problem. It is due to this diff:

--- C C6.0-s2p2d1 C_PBE19
+++ C C5.0-s2p2d1 C_PBE19

the first variant being mine, the last is Yamaguchi-san's.

Unbelievable...
メンテ
Re: SiC + buffer layer 2x2 unfolding error ( No.6 )
Date: 2020/11/11 01:52
Name: Naoya Yamaguchi

Dear Malone,

>--- C C6.0-s2p2d1 C_PBE19
I have tried the above, and the error appeared, but when I comment out "unfolding.referenceorigin", the unfolding code worked well. In my experience, I think that it is better to omit "unfolding.referenceorigin" for the first time.

Regards,
Naoya Yamaguchi
メンテ
Re: SiC + buffer layer 2x2 unfolding error ( No.7 )
Date: 2020/11/11 07:01
Name: Malone

The second system works too.

Thank you very much, dear Yamaguchi-san. You helped a lot.
メンテ

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