Phonon Dispersion Calculation for NbO2 #259

Zhennan-Lin · 2025-04-22T08:59:11Z

Zhennan-Lin
Apr 22, 2025

Dear Professor Tadano,

I am currently calculating the phonon dispersion of NbO2 using the harmonic approximation but have encountered significant imaginary frequencies in my results, indicating a clear issue with the calculation.

To troubleshoot this, I have tried two approaches:

Primitive cell: Generated a 384-atom supercell

Conventional cell: Generated a 192-atom supercell

Unfortunately, both methods still produce problematic results. After reviewing previous discussions, I understand that version 1.5.0 cannot handle conventional cells properly. However, even with the primitive cell, the calculation remains incorrect, and I am unsure how to proceed.

Could you kindly provide any suggestions or guidance on resolving this issue? Your insights would be greatly appreciated.

Thank you very much for your time and assistance.

Best regards,
Zhennan-Lin

Attaching the calculating details
1 &general
2 PREFIX = BCT
3 MODE = suggest
4 NAT = 384
5 NKD = 2 ; KD = Nb O
6 TOLERANCE = 1.0e-3
7 /
8
9 &interaction
10 NORDER = 1
11 /
12
13 &cell
14 1.8897161646320724 # factor in Bohr unit
15 20.5695111091158864 0.0277340741564612 0.0000013849920752
16 -16.9815119072779126 11.6074753914152566 0.0000025901809630
17 -1.7940135556606107 -5.8176479589404506 19.6478631348407227
18
19
20
21 /
22
23 &cutoff
24
25 - None
26 /

&general
2 PREFIX = BCT222
3 MODE = optimize
4 NAT = 384
5 NKD = 2 ; KD = Nb O
6 /
7
8 &interaction
9 NORDER = 1
10 /
11
12 &optimize
13 DFSET = DFSET_harmonic
14 /
15 &cell
16 1.8897161646320724 # factor in Bohr unit
17 20.5695111091158864 0.0277340741564612 0.0000013849920752
18 -16.9815119072779126 11.6074753914152566 0.0000025901809630
19 -1.7940135556606107 -5.8176479589404506 19.6478631348407227
20
21
22
23 /
24
25 &cutoff
26
27 - None
28 /

&general
PREFIX = BCT222
MODE = phonons
FCSXML = BCT112.xml
NKD = 2; KD = Nb O
MASS = 92.90638 16
/

&cell
1.8897161646320724
10.2847555545579432 0.0138670370782306 0.0000006924960376
-8.4907559536389563 5.8037376957076283 0.0000012950904815
-0.8970067778303054 -2.9088239794702253 9.8239315674203613

/

&kpoint
1 # KPMODE = 1: line mode
G 0.0000000000 0.0000000000 0.0000000000 X 0.0000000000 0.5000000000 0.0000000000 51

X 0.0000000000 0.5000000000 0.0000000000 M 0.5000000000 0.5000000000 0.0000000000 51

M 0.5000000000 0.5000000000 0.0000000000 G 0.0000000000 0.0000000000 0.0000000000 51

G 0.0000000000 0.0000000000 0.0000000000 Z 0.0000000000 0.0000000000 0.5000000000 51

Z 0.0000000000 0.0000000000 0.5000000000 R 0.0000000000 0.5000000000 0.5000000000 51

R 0.0000000000 0.5000000000 0.5000000000 A 0.5000000000 0.5000000000 0.5000000000 51

A 0.5000000000 0.5000000000 0.5000000000 Z 0.0000000000 0.0000000000 0.5000000000 51

X 0.0000000000 0.5000000000 0.0000000000 R 0.0000000000 0.5000000000 0.5000000000 51

M 0.5000000000 0.5000000000 0.0000000000 A 0.5000000000 0.5000000000 0.5000000000 51

/

BCT.pattern_HARMONIC:
Basis : C
1: 1
9 0 1 0
2: 1
9 -0 -1 -0
3: 1
17 0 0 1
4: 1
17 -0 -0 -1
5: 1
25 0 0 1
6: 1
25 -0 -0 -1
7: 1
73 0 1 0
8: 1
73 -0 -1 -0
9: 1
81 0 0 1
10: 1
81 -0 -0 -1
11: 1
89 0 0 1
12: 1
89 -0 -0 -1
13: 1
137 0 1 0
14: 1
137 -0 -1 -0
15: 1
145 0 0 1
16: 1
145 -0 -0 -1
17: 1
153 0 0 1
18: 1
153 -0 -0 -1
19: 1
201 0 1 0
20: 1
201 -0 -1 -0
21: 1
209 0 0 1
22: 1
209 -0 -0 -1
23: 1
217 0 0 1
24: 1
217 -0 -0 -1
25: 1
265 0 1 0
26: 1
265 -0 -1 -0
27: 1
273 0 0 1
28: 1
273 -0 -0 -1
29: 1
281 0 0 1
30: 1
281 -0 -0 -1
31: 1
329 0 1 0
32: 1
329 -0 -1 -0
33: 1
337 0 0 1
34: 1
337 -0 -0 -1
35: 1
345 0 0 1
36: 1
345 -0 -0 -1

Answered by ttadano

Apr 24, 2025

Please consider the following procedure:

Find a (standardized) primitive cell using spglib. Make sure that the detected space group is what you expect. If a non-standardized cell is preferred, you may set no_idealize=True.
Perform structure optimization using the detected primitive cell
Generate a supercell from the primitive cell
Use the generated supercell for ALM. Make sure that the alm code detects the same space group as step 1.
Use the relaxed primitive cell for the &cell field of anphon.

View full answer

ttadano · 2025-04-23T03:51:49Z

ttadano
Apr 23, 2025
Maintainer

In the &cell field for anphon, you need to give primitive lattice vectors. Is this requirement satisfied?
According to your input, the lattice vectors in the anphon's &cell field is 1/8 size of the alm's supercell, indicating that the primitive cell contains 384/8 = 48 atoms.

6 replies

Zhennan-Lin Apr 23, 2025
Author

10.2847555545579432 0.0138670370782306 0.0000006924960376
-8.4907559536389563 5.8037376957076283 0.0000012950904815
-0.8970067778303054 -2.9088239794702253 9.8239315674203613
vectors were used in the &cell field for anphon, but the results were unchanged exceptly

Zhennan-Lin Apr 23, 2025
Author

Dear Professor Tadano,

I attempted to calculate the phonon dispersion again using a primitive cell with only 24 atoms from the crystal database, followed by a 2×2×2 supercell expansion. Unfortunately, the results still appear incorrect, with obvious anomalies. I have attached all the relevant calculation files for your reference.

Could you kindly take a look and give some suggestions? I greatly appreciate your time and expertise.

Thank you in advance for your help.

Best regards,

#POSCAR-primitive cell
Nb8 O16
1.00000000000000
7.5123368864979465 0.0050318030092551 0.0000001455041152
-5.0792376600137166 5.5350316719424484 -0.0000001468575444
-1.2165496706341261 -2.7700315046004924 6.8762026710840614
Nb O
8 16
Direct
0.2792478379331900 0.5106990841611890 0.7433438674867728
0.2346825371549764 0.9786882115047297 0.7692282758011514
0.7606990841614013 0.5173552166746461 0.7314512462281322
0.7673552166745363 0.5359039704465374 0.2566561325133310
0.7859039704463252 0.0292478379330804 0.2685487537719713
0.2286882115046867 0.9594599357034911 0.2440056743496687
0.2094599357034733 0.4654542613537203 0.2307717241987366
0.7154542613537629 0.9846825371549591 0.7559943256502191
0.5961628694619610 0.8383279630723606 0.9733533333869572
0.1308109711477939 0.8726854052056238 0.4739851418021981
0.8895138207913906 0.1341520177943071 0.5496281454082527
0.8649746296853661 0.6228095360749657 0.0266466666129786
0.8728095360748805 0.3461628694618627 0.2578349063895385
0.6110865897621461 0.1612897867042857 0.7557009808083921
0.4055888058959638 0.8553856089538314 0.2442990191916301
0.3987002634032430 0.6568258293454062 0.5260148581978926
0.0883279630724460 0.6149746296854638 0.7421650936103970
0.1226854052055264 0.1487002634034595 0.2418744340578922
0.5898856753830339 0.6395138207912614 0.2553618029970390
0.4112897867044719 0.1555888058960798 0.0502031969422346
0.9068258293455034 0.8808109711475776 0.7581255659421984
0.1053856089536447 0.3610865897620297 0.9497968030577876
0.5845238723859616 0.3398856753830453 0.4503718545917071
0.3841520177943183 0.3345238723860908 0.7446381970029210

SPOSCAR (222)

1.000000
15.0246737729958930 0.0100636060185102 0.0000002910082304
-10.1584753200274331 11.0700633438848968 -0.0000002937150888
-2.4330993412682522 -5.5400630092009848 13.7524053421681227
Nb O
64 128
Direct
0.1396239189665950 0.2553495420805945 0.3716719337433865 Nb001
0.1396239189665950 0.2553495420805945 0.8716719337433865 Nb002
0.1396239189665950 0.7553495420805945 0.3716719337433865 Nb003
0.1396239189665950 0.7553495420805945 0.8716719337433865 Nb004
0.6396239189665950 0.2553495420805945 0.3716719337433865 Nb005
0.6396239189665950 0.2553495420805945 0.8716719337433865 Nb006
0.6396239189665950 0.7553495420805945 0.3716719337433865 Nb007
0.6396239189665950 0.7553495420805945 0.8716719337433865 Nb008
0.1173412685774882 0.4893441057523649 0.3846141379005756 Nb009
0.1173412685774882 0.4893441057523649 0.8846141379005756 Nb010
0.1173412685774882 0.9893441057523649 0.3846141379005756 Nb011
0.1173412685774882 0.9893441057523649 0.8846141379005756 Nb012
0.6173412685774882 0.4893441057523649 0.3846141379005756 Nb013
0.6173412685774882 0.4893441057523649 0.8846141379005756 Nb014
0.6173412685774882 0.9893441057523649 0.3846141379005756 Nb015
0.6173412685774882 0.9893441057523649 0.8846141379005756 Nb016
0.3803495420807006 0.2586776083373230 0.3657256231140661 Nb017
0.3803495420807006 0.2586776083373230 0.8657256231140661 Nb018
0.3803495420807006 0.7586776083373230 0.3657256231140661 Nb019
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0.8803495420807006 0.2586776083373230 0.3657256231140661 Nb021
0.8803495420807006 0.2586776083373230 0.8657256231140661 Nb022
0.8803495420807006 0.7586776083373230 0.3657256231140661 Nb023
0.8803495420807006 0.7586776083373230 0.8657256231140661 Nb024
0.3836776083372682 0.2679519852232687 0.1283280662566655 Nb025
0.3836776083372682 0.2679519852232687 0.6283280662566655 Nb026
0.3836776083372682 0.7679519852232687 0.1283280662566655 Nb027
0.3836776083372682 0.7679519852232687 0.6283280662566655 Nb028
0.8836776083372682 0.2679519852232687 0.1283280662566655 Nb029
0.8836776083372682 0.2679519852232687 0.6283280662566655 Nb030
0.8836776083372682 0.7679519852232687 0.1283280662566655 Nb031
0.8836776083372682 0.7679519852232687 0.6283280662566655 Nb032
0.3929519852231627 0.0146239189665403 0.1342743768859856 Nb033
0.3929519852231627 0.0146239189665403 0.6342743768859856 Nb034
0.3929519852231627 0.5146239189665403 0.1342743768859856 Nb035
0.3929519852231627 0.5146239189665403 0.6342743768859856 Nb036
0.8929519852231627 0.0146239189665403 0.1342743768859856 Nb037
0.8929519852231627 0.0146239189665403 0.6342743768859856 Nb038
0.8929519852231627 0.5146239189665403 0.1342743768859856 Nb039
0.8929519852231627 0.5146239189665403 0.6342743768859856 Nb040
0.1143441057523433 0.4797299678517455 0.1220028371748343 Nb041
0.1143441057523433 0.4797299678517455 0.6220028371748343 Nb042
0.1143441057523433 0.9797299678517455 0.1220028371748343 Nb043
0.1143441057523433 0.9797299678517455 0.6220028371748343 Nb044
0.6143441057523433 0.4797299678517455 0.1220028371748343 Nb045
0.6143441057523433 0.4797299678517455 0.6220028371748343 Nb046
0.6143441057523433 0.9797299678517455 0.1220028371748343 Nb047
0.6143441057523433 0.9797299678517455 0.6220028371748343 Nb048
0.1047299678517366 0.2327271306768601 0.1153858620993683 Nb049
0.1047299678517366 0.2327271306768601 0.6153858620993683 Nb050
0.1047299678517366 0.7327271306768601 0.1153858620993683 Nb051
0.1047299678517366 0.7327271306768601 0.6153858620993683 Nb052
0.6047299678517366 0.2327271306768601 0.1153858620993683 Nb053
0.6047299678517366 0.2327271306768601 0.6153858620993683 Nb054
0.6047299678517366 0.7327271306768601 0.1153858620993683 Nb055
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0.3577271306768814 0.4923412685774795 0.3779971628251095 Nb057
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0.8577271306768814 0.9923412685774795 0.3779971628251095 Nb063
0.8577271306768814 0.9923412685774795 0.8779971628251095 Nb064
0.2980814347309805 0.4191639815361803 0.4866766666934785 O001
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0.7949428376915170 0.3197569103956307 0.6276809014985195 O086
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0.7949428376915170 0.8197569103956307 0.6276809014985195 O088
0.2056448933522359 0.0777944029480399 0.0251015984711173 O089
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0.6920760088971591 0.1672619361930454 0.3723190985014605 O125
0.6920760088971591 0.1672619361930454 0.8723190985014605 O126
0.6920760088971591 0.6672619361930454 0.3723190985014605 O127
0.6920760088971591 0.6672619361930454 0.8723190985014605 O128

####BCT_alma1.n#####
&general
PREFIX = BCT
MODE = suggest
NAT = 192
NKD = 2 ; KD = Nb O
TOLERANCE = 1.0e-3
/

&interaction
NORDER = 1
/

&cell
1.8897161646320724 # factor in Bohr unit
15.0246737729958930 0.0100636060185102 0.0000002910082304
-10.1584753200274331 11.0700633438848968 -0.0000002937150888
-2.4330993412682522 -5.5400630092009848 13.7524053421681227

/

&cutoff

- None
/

&position
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###BCT_alm2.in ###############
&general
PREFIX = BCT222
MODE = optimize
NAT = 192
NKD = 2 ; KD = Nb O
/

&interaction
NORDER = 1
/

&optimize
DFSET = DFSET_harmonic
/
&cell
1.8897161646320724 # factor in Bohr unit
15.0246737729958930 0.0100636060185102 0.0000002910082304
-10.1584753200274331 11.0700633438848968 -0.0000002937150888
-2.4330993412682522 -5.5400630092009848 13.7524053421681227

/

&cutoff

- None
/

&position
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########bct_phband.in#############
&general
PREFIX = BCT222
MODE = phonons
FCSXML = BCT222.xml
NKD = 2; KD = Nb O
MASS = 92.90638 16
/

&cell
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-5.0792376600137166 5.5350316719424484 -0.0000001468575444
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