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Segmentation fault in NEB calculations
Date: 2022/05/13 17:32
Name: Lovleen Kaur   <lovleenkaurkkr@gmail.com>

Hello Developers,
I am trying to do NEB calculations and my system contains 110 atoms. The calculations stop with segmentation error. My computer system contains 20 cores and 104 GB.
My input file is as follows:


#
# File Name
#

System.CurrrentDirectory ./ # default=./
System.Name graphene
DATA.PATH ../../../../../DFT_DATA13
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)

#
# Definition of Atomic Species
#

Species.Number 4
<Definition.of.Atomic.Species
H H6.0-s2p1 H_PBE13
C C6.0-s2p2d1 C_PBE13
Al Al8.0-s3p3d2 Al_PBE13
F F6.0-s2p2d1 F_PBE13
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 112
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0.7513522 1.2662413 -0.1401993 2.00000 2.00000
2 C 2.1276835 1.2633663 -0.1528914 2.00000 2.00000
3 C 5.0776875 1.2657172 -0.2201496 2.00000 2.00000
4 C 9.4082870 1.3040051 -0.3317847 2.00000 2.00000
5 C 6.4553041 1.2713504 -0.2286952 2.00000 2.00000
6 C 10.7846957 1.3061701 -0.2993031 2.00000 2.00000
7 C 0.0076515 2.4713267 -0.0895370 2.00000 2.00000
8 C 0.0086420 4.9428750 -0.0219027 2.00000 2.00000
9 C 0.0149998 7.4068080 -0.0557685 2.00000 2.00000
10 C 0.0291251 9.8740132 -0.2092606 2.00000 2.00000
11 C 2.8777346 2.4647626 -0.1112654 2.00000 2.00000
12 C 2.8892588 4.9366934 -0.0192483 2.00000 2.00000
13 C 2.8945415 7.3995311 -0.0538351 2.00000 2.00000
14 C 2.8946980 9.8611911 -0.2557744 2.00000 2.00000
15 C 0.7276224 3.7009930 -0.0517637 2.00000 2.00000
16 C 0.7317685 6.1733393 -0.0291367 2.00000 2.00000
17 C 0.7401801 8.6429250 -0.1310989 2.00000 2.00000
18 C 0.7778487 11.0709557 -0.3165314 2.00000 2.00000
19 C 2.1648115 3.6976710 -0.0566935 2.00000 2.00000
20 C 2.1709436 6.1694055 -0.0251667 2.00000 2.00000
21 C 2.1754856 8.6382439 -0.1418399 2.00000 2.00000
22 C 2.1537956 11.0647430 -0.3434057 2.00000 2.00000
23 C 4.3246986 2.4631393 -0.1233610 2.00000 2.00000
24 C 4.3198638 4.9351583 0.0068612 2.00000 2.00000
25 C 4.3222724 7.3990531 -0.0103633 2.00000 2.00000
26 C 4.3417681 9.8547949 -0.2714249 2.00000 2.00000
27 C 8.6483884 2.4822515 -0.1042945 2.00000 2.00000
28 C 8.5993249 4.9198396 0.2798069 2.00000 2.00000
29 C 8.6075879 7.4219264 0.5278148 2.00000 2.00000
30 C 8.6334378 9.8680879 -0.0403950 2.00000 2.00000
31 C 7.1992632 2.4733522 -0.1202159 2.00000 2.00000
32 C 7.1827340 4.9284591 0.1352523 2.00000 2.00000
33 C 7.2068568 7.4058807 0.2369893 2.00000 2.00000
34 C 7.1956906 9.8539781 -0.1830595 2.00000 2.00000
35 C 11.5241167 2.4854257 -0.0147588 2.00000 2.00000
36 C 11.4965338 4.8828217 0.5987839 2.00000 2.00000
37 Al 11.5058020 7.4709644 1.6471464 1.50000 1.50000
38 C 11.4872003 9.9639704 0.4351478 2.00000 2.00000
39 C 5.0376322 3.6938981 -0.0383519 2.00000 2.00000
40 C 5.0429125 6.1679756 0.0543248 2.00000 2.00000
41 C 5.0515917 8.6322700 -0.0892486 2.00000 2.00000
42 C 5.0886840 11.0421745 -0.4640415 2.00000 2.00000
43 C 9.3525374 3.6966435 0.1472151 2.00000 2.00000
44 C 9.2950227 6.1224770 0.6176122 2.00000 2.00000
45 C 9.2938325 8.7333154 0.5095613 2.00000 2.00000
46 C 9.4384626 10.9832113 -0.4140066 2.00000 2.00000
47 C 6.4712464 3.6945902 -0.0124892 2.00000 2.00000
48 C 6.4766562 6.1682468 0.1547417 2.00000 2.00000
49 C 6.4839745 8.6351131 0.0007881 2.00000 2.00000
50 C 6.4645339 11.0371280 -0.4422685 2.00000 2.00000
51 C 10.7981101 3.6842210 0.2193203 2.00000 2.00000
52 C 10.6678201 5.9808345 0.9549211 2.00000 2.00000
53 C 10.6493784 8.9269716 0.9046838 2.00000 2.00000
54 C 10.8176911 11.0078013 -0.2668651 2.00000 2.00000
55 H 0.2340289 0.3090175 -0.1702484 0.50000 0.50000
56 H 2.6407140 0.3040471 -0.1919927 0.50000 0.50000
57 H 4.5668307 0.3072293 -0.2933611 0.50000 0.50000
58 H 6.9741352 0.3169766 -0.3023840 0.50000 0.50000
59 H 8.9008956 0.3680146 -0.5594738 0.50000 0.50000
60 H 11.3032127 0.3701841 -0.5007214 0.50000 0.50000
61 H 11.3716936 11.8322853 -0.7188971 0.50000 0.50000
62 H 8.9648312 11.8276683 -0.9153084 0.50000 0.50000
63 H 6.9959425 11.9772237 -0.5845522 0.50000 0.50000
64 H 4.5764875 11.9869440 -0.6355840 0.50000 0.50000
65 H 2.6720235 12.0185604 -0.4206996 0.50000 0.50000
66 H 0.2659524 12.0294090 -0.3777016 0.50000 0.50000
67 C 13.7189829 1.3142848 -0.1217548 2.00000 2.00000
68 C 15.0929256 1.3061527 -0.1188456 2.00000 2.00000
69 C 18.0323558 1.2893158 -0.0994487 2.00000 2.00000
70 C 19.4090916 1.2822256 -0.1171827 2.00000 2.00000
71 C 12.9694726 2.5068512 0.0439942 2.00000 2.00000
72 C 12.9676116 4.9464944 0.5522020 2.00000 2.00000
73 C 13.2101164 7.4298903 0.9511100 2.00000 2.00000
74 C 12.9913077 9.9029894 0.5042547 2.00000 2.00000
75 C 15.8419562 2.5060797 0.0062894 2.00000 2.00000
76 C 15.8825175 4.9568395 0.1956332 2.00000 2.00000
77 C 15.8945112 7.4307926 0.2769866 2.00000 2.00000
78 C 15.8859593 9.9169364 0.1423268 2.00000 2.00000
79 C 13.6832368 3.7379439 0.2518539 2.00000 2.00000
80 C 13.7728392 6.1826668 0.6387863 2.00000 2.00000
81 C 13.7861956 8.6841051 0.6157578 2.00000 2.00000
82 C 13.7316702 11.0823027 0.2866868 2.00000 2.00000
83 C 15.1330119 3.7294212 0.1616960 2.00000 2.00000
84 C 15.1829929 6.1836329 0.3406344 2.00000 2.00000
85 C 15.1924880 8.6875825 0.3322541 2.00000 2.00000
86 C 15.1164725 11.1001547 0.1450436 2.00000 2.00000
87 C 17.2913113 2.4960977 -0.0270526 2.00000 2.00000
88 C 17.3078550 4.9579356 0.0946576 2.00000 2.00000
89 C 17.3176646 7.4259156 0.1237866 2.00000 2.00000
90 C 17.3287831 9.9034207 -0.0050358 2.00000 2.00000
91 C 20.1656032 2.4805479 -0.0758378 2.00000 2.00000
92 C 20.1837407 4.9518609 -0.0040899 2.00000 2.00000
93 C 20.1906736 7.4165710 -0.0286619 2.00000 2.00000
94 C 20.1880345 9.8857367 -0.1672471 2.00000 2.00000
95 C 18.0212394 3.7195930 0.0158388 2.00000 2.00000
96 C 18.0299403 6.1925668 0.0779565 2.00000 2.00000
97 C 18.0376993 8.6664334 0.0206475 2.00000 2.00000
98 C 18.0720112 11.0973386 -0.1460366 2.00000 2.00000
99 C 19.4573480 3.7136894 -0.0181249 2.00000 2.00000
100 C 19.4681893 6.1865710 0.0158767 2.00000 2.00000
101 C 19.4710257 8.6587584 -0.0592982 2.00000 2.00000
102 C 19.4473004 11.0900199 -0.2236449 2.00000 2.00000
103 H 13.2000695 0.3663357 -0.2514940 0.50000 0.50000
104 H 15.6038947 0.3533196 -0.2430148 0.50000 0.50000
105 H 17.5140594 0.3327661 -0.1300117 0.50000 0.50000
106 H 19.9168898 0.3205009 -0.1639987 0.50000 0.50000
107 H 19.9630493 12.0433669 -0.3220869 0.50000 0.50000
108 H 17.5542914 12.0545139 -0.1850894 0.50000 0.50000
109 H 15.6017257 12.0664564 0.0137408 0.50000 0.50000
110 H 13.2046206 12.0357978 0.2336712 0.50000 0.50000
111 F 11.5058020 7.4709644 4.6471464 3.50000 3.50000
112 H 11.5058020 7.4709644 5.5795464 0.50000 0.50000
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
21.51329 0.00000 -0.00000
0.00000 30.03302 0.00000
-0.00000 0.00000 29.99564
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization on
scf.ElectronicTemperature 300.0
scf.energycutoff 250.0
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 5 1 1
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15
scf.criterion 1.0e-7

#
# vdW
#

scf.dftD on
version.dftD 3
DFTD3.damp bj
DFTD.IntDirection 0 0 0
DFT.scale6 1.0
DFT.scale8 0.7875
DFTD.a1 0.4289
DFT.a2 4.4407



#
# MD or Geometry Optimization
#

MD.Type NEB # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 30 # default=5
#MD.Opt.EveryDIIS 10000 # default=10
MD.maxIter 800 #
MD.Opt.criterion 2.0e-4 # default=1.0e-4 (a.u.)

MD.NEB.Number.Images 8 # default=10

MD.NEB.Parallel.Number 2

<NEB.Atoms.SpeciesAndCoordinates
1 C 0.75111 1.32340 -0.15373 2.0 2.0
2 C 2.12602 1.31801 -0.16142 2.0 2.0
3 C 5.06657 1.31731 -0.20405 2.0 2.0
4 C 9.38025 1.36140 -0.25416 2.0 2.0
5 C 6.44221 1.32235 -0.18905 2.0 2.0
6 C 10.75306 1.37015 -0.21379 2.0 2.0
7 C 0.01191 2.53017 -0.09417 2.0 2.0
8 C 0.01650 5.00116 -0.01268 2.0 2.0
9 C 0.02763 7.46556 -0.05194 2.0 2.0
10 C 0.04514 9.93019 -0.24290 2.0 2.0
11 C 2.87352 2.51868 -0.10288 2.0 2.0
12 C 2.88537 4.98820 0.00886 2.0 2.0
13 C 2.89670 7.44974 -0.04038 2.0 2.0
14 C 2.91569 9.90523 -0.31248 2.0 2.0
15 C 0.73060 3.75819 -0.04743 2.0 2.0
16 C 0.73836 6.23029 -0.02215 2.0 2.0
17 C 0.75390 8.69904 -0.14813 2.0 2.0
18 C 0.80007 11.11799 -0.40441 2.0 2.0
19 C 2.16358 3.75142 -0.04398 2.0 2.0
20 C 2.17284 6.22246 -0.00967 2.0 2.0
21 C 2.18829 8.69002 -0.16213 2.0 2.0
22 C 2.17748 11.10576 -0.44537 2.0 2.0
23 C 4.31676 2.51498 -0.09699 2.0 2.0
24 C 4.31061 4.98257 0.06370 2.0 2.0
25 C 4.31924 7.44339 0.03472 2.0 2.0
26 C 4.36488 9.88814 -0.31149 2.0 2.0
27 C 8.62356 2.53696 -0.01735 2.0 2.0
28 C 8.57763 4.96840 0.40725 2.0 2.0
29 C 8.57373 7.45278 0.71183 2.0 2.0
30 C 8.65690 9.83204 0.02078 2.0 2.0
31 C 7.18062 2.52347 -0.04545 2.0 2.0
32 C 7.16497 4.97159 0.25561 2.0 2.0
33 C 7.18158 7.43807 0.36993 2.0 2.0
34 C 7.22208 9.84531 -0.16937 2.0 2.0
35 C 11.48236 2.55252 0.07820 2.0 2.0
36 C 11.45316 4.95294 0.70111 2.0 2.0
37 Al 11.53644 7.36749 2.12089 1.5 1.5
38 C 11.48555 9.95093 0.63006 2.0 2.0
39 C 5.02654 3.74265 0.02102 2.0 2.0
40 C 5.03078 6.21227 0.12990 2.0 2.0
41 C 5.05462 8.66818 -0.05934 2.0 2.0
42 C 5.13853 11.04978 -0.55364 2.0 2.0
43 C 9.32257 3.75065 0.24887 2.0 2.0
44 C 9.27281 6.16333 0.78190 2.0 2.0
45 C 9.26042 8.73370 0.68865 2.0 2.0
46 C 9.49872 10.88549 -0.43409 2.0 2.0
47 C 6.45635 3.74230 0.07492 2.0 2.0
48 C 6.45699 6.20791 0.27206 2.0 2.0
49 C 6.48118 8.65790 0.07019 2.0 2.0
50 C 6.51730 11.02278 -0.51464 2.0 2.0
51 C 10.76035 3.75228 0.31434 2.0 2.0
52 C 10.63967 6.04802 1.11357 2.0 2.0
53 C 10.60105 8.97664 1.21812 2.0 2.0
54 C 10.87325 10.87701 -0.24718 2.0 2.0
55 H 0.23157 0.36817 -0.19174 0.5 0.5
56 H 2.63973 0.35972 -0.20419 0.5 0.5
57 H 4.55410 0.36285 -0.30615 0.5 0.5
58 H 6.96388 0.37100 -0.27279 0.5 0.5
59 H 8.87410 0.42789 -0.49185 0.5 0.5
60 H 11.27874 0.44004 -0.41866 0.5 0.5
61 H 11.48844 11.60022 -0.78398 0.5 0.5
62 H 9.06282 11.67940 -1.04058 0.5 0.5
63 H 7.06623 11.94558 -0.69925 0.5 0.5
64 H 4.64431 11.99297 -0.77993 0.5 0.5
65 H 2.69990 12.05309 -0.56665 0.5 0.5
66 H 0.29133 12.07564 -0.49816 0.5 0.5
67 C 13.66182 1.37109 -0.01544 2.0 2.0
68 C 15.03262 1.36382 -0.02528 2.0 2.0
69 C 17.95216 1.34899 -0.07907 2.0 2.0
70 C 19.32621 1.34019 -0.11771 2.0 2.0
71 C 12.91996 2.56854 0.13869 2.0 2.0
72 C 12.91619 5.00435 0.65089 2.0 2.0
73 C 13.14041 7.46910 1.13306 2.0 2.0
74 C 12.95653 9.93644 0.76155 2.0 2.0
75 C 15.77579 2.56788 0.07674 2.0 2.0
76 C 15.81388 5.01899 0.27122 2.0 2.0
77 C 15.83234 7.48367 0.38733 2.0 2.0
78 C 15.82106 9.96632 0.31842 2.0 2.0
79 C 13.62831 3.80014 0.33864 2.0 2.0
80 C 13.70749 6.24317 0.74816 2.0 2.0
81 C 13.73574 8.71188 0.82636 2.0 2.0
82 C 13.68327 11.13332 0.57101 2.0 2.0
83 C 15.07158 3.79098 0.23782 2.0 2.0
84 C 15.11490 6.24431 0.43537 2.0 2.0
85 C 15.13289 8.73213 0.49350 2.0 2.0
86 C 15.05922 11.15596 0.39367 2.0 2.0
87 C 17.21856 2.55728 0.01672 2.0 2.0
88 C 17.23565 5.01831 0.15256 2.0 2.0
89 C 17.25035 7.48206 0.20609 2.0 2.0
90 C 17.25572 9.95773 0.11134 2.0 2.0
91 C 20.08077 2.53824 -0.07283 2.0 2.0
92 C 20.10283 5.00845 0.01428 2.0 2.0
93 C 20.11320 7.47281 -0.00861 2.0 2.0
94 C 20.11127 9.94070 -0.15988 2.0 2.0
95 C 17.94534 3.78027 0.05628 2.0 2.0
96 C 17.95835 6.25042 0.13299 2.0 2.0
97 C 17.96625 8.72168 0.09876 2.0 2.0
98 C 17.99467 11.15138 -0.05915 2.0 2.0
99 C 19.37727 3.77207 0.00183 2.0 2.0
100 C 19.39195 6.24383 0.04728 2.0 2.0
101 C 19.39603 8.71512 -0.02525 2.0 2.0
102 C 19.36632 11.14385 -0.19411 2.0 2.0
103 H 13.14024 0.42275 -0.12183 0.5 0.5
104 H 15.54551 0.41153 -0.13795 0.5 0.5
105 H 17.43066 0.39506 -0.11249 0.5 0.5
106 H 19.83308 0.37971 -0.18313 0.5 0.5
107 H 19.87774 12.09706 -0.31439 0.5 0.5
108 H 17.47641 12.10868 -0.08079 0.5 0.5
109 H 15.54871 12.12308 0.29153 0.5 0.5
110 H 13.14530 12.08206 0.57680 0.5 0.5
111 F 11.41622 7.55620 3.79901 3.5 3.5
112 H 10.59854 9.02034 2.33251 0.5 0.5
NEB.Atoms.SpeciesAndCoordinates>



With regards,
Lovleen Kaur
メンテ
Page: [1]

Re: Segmentation fault in NEB calculations ( No.1 )
Date: 2022/05/13 18:34
Name: Naoya Yamaguchi

Hi,

Which version of the OpenMX did you use in your calculation?

Regards,
Naoya Yamaguchi
メンテ
Re: Segmentation fault in NEB calculations ( No.2 )
Date: 2022/05/13 19:15
Name: lovleen kaur  <lovleenkaurkkr@gmail.com>

Hello Naoya Yamaguchi,


I am using OpenMX 3.8
メンテ
Re: Segmentation fault in NEB calculations ( No.3 )
Date: 2022/05/13 19:17
Name: Naoya Yamaguchi

Dear Lovleen Kaur,

The bug was resolved in Ver. 3.9, but you can resolve it in 3.8 as follows:
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2459

Regards,
Naoya Yamaguchi
メンテ

Page: [1]

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