Hello lammps expert
I never used lammps before and i am struggling to calculate CO2 adsorption isotherms with hMOFs. I am getting following error:
LAMMPS (29 Aug 2024 - Update 1)
using 1 OpenMP thread(s) per MPI task
Reading data file …
triclinic box = (0 0 0) to (19.077105 14.905516 18.991244) with tilt (-0.2992724 -0.025379158 -1.8057846)
4 by 2 by 4 MPI processor grid
reading atoms …
ERROR: Incorrect format in Atoms section of data file: 1 5 0.54025493137606906 7.4247784518991686 10.269818878376867
For more information see https://docs.lammps.org/err0002 (…/atom.cpp:1089)
Last command: read_data hMOF-9594.data
Following are the contents of my files. Please guide me if someone knows what’s wrong.
Have you read what is shown at the URL printed with the error?
I have read but i am unable to find the problem my data file has following contents:
(written by ASE)
334 atoms
5 atom types
0.0 19.077105 xlo xhi
0.0 14.905515912647122 ylo yhi
0.0 18.991243677259416 zlo zhi
-0.29927239803137828 -0.025379158068588033 -1.8057846000702804 xy xz yz
Masses
1 65.38 # Zn
2 15.999 # O
3 12.011 # C
4 14.007 # N
5 1.008 # H
Atoms # full
1 5 0.54025493137606906 7.4247784518991686 10.269818878376867
2 5 10.241133209426053 0.8749127956107472 0.77419703974715726
3 5 0.54006590393620391 5.0621903412553877 12.382670702446685
4 5 9.9416717839548081 13.41784059761409 2.8870488638169762
5 5 17.469834520789213 7.3832614682742577 12.600576232399559
6 5 8.0936077988391943 0.8333958119858369 3.1049543937698507
7 5 17.289543485175749 5.2738650398777907 10.241787802709229
8 5 7.6140443651943528 13.629515296236491 0.74616596407952251
9 4 18.498481892087877 6.2860266488133298 11.373722899604923
10 4 8.8229827721064851 14.64167690517203 1.8781010609752156
11 4 2.4130852760081778 7.0401710243280915 10.470632289020205
12 4 12.113963554058159 0.4903053680396714 0.97501045039049838
13 4 0.33058375581823674 5.2641263218654064 14.282953536036938
14 4 9.7321896358368409 13.619776578224108 4.7873316974072306
15 4 17.830230559925155 9.2603231544855422 12.39433132606452
16 4 8.4540038379751437 2.7104574981971217 2.8987094874348136
17 4 2.4129475781977656 5.3043739824636846 12.022919573468359?
18 4 11.81455345821637 13.660024238822386 2.5272977348386512
19 4 0.3309015877572129 9.2908308755481102 10.681928866173395
20 4 10.031779865807197 2.7409652192596896 1.1863070275436867
21 4 17.830050451175754 6.9694174484518463 14.443049720236234
22 4 8.4538237292257374 0.41955179216342553 4.9474278816065276
23 4 15.573060100802152 7.1746593584022929 12.367154856362363
24 4 6.1968333788521344 0.62479370211387275 2.8715330177326557
25 4 17.522950606164507 5.665136790926212 8.3741319257565063
26 4 7.8220723281145261 12.215002447214632 17.869753764386214
27 4 15.44058678378498 5.6248891303279338 10.634165888325084
28 4 5.7650876638035866 13.980539386686635 1.1385440496953794
29 4 0.15607587390873079 7.2454147400631408 8.3947184339026553
30 4 9.8315749938901256 -1.1102355162955617 17.890340272532367
31 4 0.15577711907476169 3.2187101863804353 11.9957431037662
32 4 9.5573829990933667 11.574360442739135 2.5001212651364932
33 4 17.522770472035944 3.3742292791079151 10.422869311171899
34 4 7.8472713520545501 11.729879535466615 0.92724747254219109
35 1 15.021217293013315 6.4182224251430506 11.521246880489874
36 1 5.6449905710632997 -0.13164323114536947 2.0256250418601667
37 1 13.533605753809958 6.4744830301905205 11.584031932086893
38 1 4.1573790318599437 -0.075382626097900043 2.0884100934571861
39 1 18.358602827428715 2.8111940252481498 11.182310154581824
40 1 8.683103707447323 11.166844281606849 1.686688315952118
41 1 18.299951604733248 1.3246303044730767 11.099926139509874
42 1 8.6244524847518527 9.680280560831779 1.6043043008801665
43 1 12.766097537140924 5.6926666018791741 10.712523759737458
44 1 3.0905984171595295 14.048316858237875 1.2169019211077516
45 1 11.368340130684583 5.7457015518655101 10.771453588867995
46 1 1.692841010703189 14.101351808224212 1.2758317502382879
47 1 10.738091737197838 6.5805009904770539 11.701967555322675
48 1 1.3618650152478204 0.03063533418863304 2.206345716692967
49 1 11.505693492999166 7.3624032403146753 12.573513710159464
50 1 2.1294667710491484 0.81253758402625587 3.0778918715297561
51 1 12.903430726777549 7.309435135530391 12.514507916054219
52 1 3.527204004827531 0.75956947924197094 3.018886077424511
53 1 6.5651375112370935 6.8256705597328944 11.975004665670635
54 1 16.266015789287074 0.27580490344447395 2.4793828270409257
55 1 5.1672876612214154 6.8785528429909037 12.033972477288524
56 1 14.868165939271398 0.32868718670248298 2.5383506386588164
57 1 5.0300297098109903 5.2618529603263369 10.231893364753377
58 1 14.431635589829595 13.617503216685037 0.73627152612367031
59 1 6.4278043216004699 5.2089020260816756 10.173020509353872
60 1 15.829410201619073 13.564552282440376 0.67739867072416615
61 1 7.1952907677129208 5.9908526040362382 11.044528681703307
62 1 16.596896647731526 14.346502860394938 1.548906843073601
63 3 9.3093446246008824 6.6346877983406705 11.762264753997973
64 3 19.010222902650867 0.084822142052251415 2.2666429153682657
65 3 8.6239989297993151 5.9367177358587568 10.984155518053301
66 3 18.025604809817917 14.292367992217459 1.4885336794235933
67 1 0.5958040625393124 13.275719459174956 12.581509023747591
68 1 10.296682340589296 6.7258538028865367 3.0858871851178824
69 1 0.5407704217562348 11.878961721148372 12.504138697006436
70 1 10.241648699806218 5.329096064859951 3.0085168583767277
71 1 17.835617412517315 12.039833703846504 10.867758185555379
72 1 8.4593906905672966 5.4899680475580857 1.37213634692567
73 1 17.890669831132993 13.436606347389006 10.945128512296533
74 1 8.5144431091829755 6.8867406911005817 1.449506673666825
75 1 0.031493576733366654 -0.85102337136108641 11.802051409501834
76 1 9.4330994567519699 7.5046268849976165 2.3064295708721243
77 1 0.086469311519170172 0.54575876034352455 11.879478709974018
78 1 9.4880751915377743 8.9014090167022246 2.3838568713443107
79 1 17.381412063215119 0.70662125487954419 10.243041224791929
80 1 7.7059129432337219 9.0622715112382455 0.7474193861622217
81 1 17.326359644599442 -0.690151388662954 10.165670898050776
82 1 7.6508605246180439 7.6654988676957476 0.67004905942106685
83 1 2.9121990187414251 6.1532924369543034 11.225591198922299
84 1 12.313804898760029 14.508942693313005 1.7299693602925921
85 1 4.3997984962782217 6.096734608894959 11.162483296182767
86 1 13.801404376296826 14.452384865253658 1.6668614575530591
87 1 18.35798944377586 6.4835287517938998 7.8856201646463644
88 1 8.6571111657258761 13.033394408082321 17.381242003276071
89 1 18.298112150823417 6.5676863418312843 6.3992135045146243
90 1 8.5972338727734385 13.117551998119707 15.894835343144331
91 1 18.639251165383559 9.7744133756296421 11.56555345198892
92 1 9.2630244434335438 3.2245477193412224 2.0699316133592127
93 1 18.699240119303237 11.260962159716954 11.647310756019523
94 1 9.3230133973532201 4.7110965034285321 2.1516889173898144
95 1 0.083263334901054767 7.4299470765679709 5.7115975446920926
96 1 9.758762454882449 -0.92570317979072891 15.207219383321798
97 1 0.026839198816647737 7.5090882303408115 4.314943502179081
98 1 9.7023383187980414 -0.84656202601789021 13.810565340808786
99 1 18.185341906571516 6.7258737989276893 3.6059623932196319
100 1 8.4844636285215369 13.275739455216108 13.101584231849339
101 1 17.322990808617888 5.863574224236177 4.2936733092605506
102 1 7.6221125305679047 12.413439880524598 13.789295147890256
103 1 17.379356267783624 5.784511209612103 5.6902893692862069
104 1 7.6784779897336382 12.334376865900524 15.185911207915915
105 1 17.895854324550452 5.0683687791213003 18.419094478994619
106 1 8.2203552045690547 13.424019035480001 8.9234726403649134
107 1 17.839583779260714 5.1474706337002001 17.022383462750579
108 1 8.1640846592793164 13.503120890058902 7.5267616241208701
109 1 0.54343144401888543 6.7930054219136577 17.043748611887494
110 1 10.244309722068868 0.2431397656252382 7.5481267732577857
111 1 0.59976141704704189 6.7138064518617702 18.440383663156826
112 1 10.300639695097024 0.16394079557334873 8.9447618245271219
113 1 18.839855552030595 7.6573452227112764 0.13675594571994326
114 1 9.4382496720119935 -0.69830503364742358 9.6323777843496536
115 3 18.127686709604646 6.8067194179932926 2.1783716147563643
116 3 8.4268084315546599 13.356585074281712 11.673993453386069
117 3 18.897470824532242 7.5765908425257482 1.5643277329395349
118 3 9.4958649445136363 -0.7790594138329513 11.059949571569243
119 1 18.639232109235774 6.090233036267362 14.848246895334242
120 1 9.263005387285757 -0.45963262002105904 5.352625056704535
121 1 18.701839963338351 6.0097313684368849 16.334767502928045
122 1 9.3256132413883339 -0.54013428785153461 6.8391456642983384
123 2 13.279145769750125 5.0128312451019204 9.9548491019895184
124 2 3.6036466497687307 13.36848150146062 0.45922726335981012
125 1 15.614029920242292 0.72527258897086688 8.6178655471104548
126 1 5.9131516421923109 7.2751382452592868 18.113487385740161
127 1 16.431979231781842 1.5626561672970229 9.3862322750486946
128 1 6.7311009537318576 8.1125218235854426 18.881854113678401
129 2 15.027823370391113 1.2537814279165942 8.0890733581608441
130 2 5.3269450923411323 7.8036470842050152 17.584695196790552
131 2 16.154612321811818 0.1881936820008201 8.050900958369553
132 2 6.453734043761834 6.7380593382892409 17.546522796999259
133 2 15.104723286791069 0.16610042122306035 9.1926165457590336
134 2 5.4038450087410883 6.7159660775114807 18.68823838438874
135 2 16.941363071470256 2.121783618497092 8.8114812764001158
136 2 7.2404847934202747 8.6716492747855121 18.307103115029822
137 2 15.891334709022313 2.0999663393832719 9.9532728287643035
138 2 6.2158355890409167 10.455616595741972 0.45765099013459754
139 1 16.960019398533031 9.9700388313338664 10.022666833161011
140 1 7.5837926765830153 3.4201731750454396 0.52704499453130327
141 1 16.825889749608255 11.360472035647977 9.9259254378690525
142 1 7.4496630276582394 4.810606379359557 0.43030359923934391
143 2 16.336565881116055 9.5506698723580747 9.4412688992253901
144 2 6.9349600010974468 1.1950196159993764 18.936890737855098
145 2 17.84208942736652 9.7191748272605647 9.7753438667520616
146 2 8.4658627054165017 3.1693091709721473 0.27972202812235403
147 2 16.792138748082277 9.6973105665752986 10.917002480410511
148 2 7.4159120261322569 3.1474449102868767 1.4213806417808035
149 2 16.993865161660057 11.633228305653757 9.0316087818632269
150 2 7.5922592816414518 3.2775780492950637 18.527230620492936
151 2 15.943607879229612 11.61144760147106 10.173172439303292
152 2 6.5673811572795948 5.0615819451826374 0.6775506006735843
153 1 1.8378598385792313 9.0645464148606223 5.5922945519115492
154 1 11.513358958560625 0.70889615850192178 15.087916390541256
155 1 1.0930194031416889 8.2909496636378055 6.4908462552574004
156 1 10.768518523123085 -0.064700592720895678 15.986468093887108
157 2 2.4611589687277373 9.5961805379793415 6.0733997279875602
158 2 12.136658088709133 1.2405302816206407 15.569021566617268
159 2 2.3042973574546721 8.4932144202763862 4.9938234899100724
160 2 11.979796477436068 0.13756416391768567 14.48944532853978
161 2 1.253233048201031 9.6290724309595532 5.1004403319142071
162 2 10.928732168182425 1.2734221746008523 14.596062170543915
163 2 1.6776289881867488 7.7263396317971988 6.9826435015237109
164 2 11.353128108168145 -0.62931062456150211 16.478265340153417
165 2 0.62654190376520147 8.8623327106018035 7.0895642034266819
166 2 10.302041023746597 0.50668245424310254 16.585186042056389
167 2 1.6430094433830706 -1.1266996786749743 13.279342272668488
168 2 11.044615323401674 7.2289505776837268 3.7837204340387798
169 1 0.2219188030217624 9.3901946523272404 2.8357535146446962
170 1 9.8974179230031574 1.0345443959685374 12.331375353274407
171 1 0.97460548708907224 8.4570884307076053 3.5592629250172512
172 1 10.650104607070466 0.10143817434890412 13.054884763646958
173 2 0.80705647020602667 9.9755833329176298 2.3693475611748842
174 2 10.482555590187422 1.6199330765589288 11.864969399804592
175 2 18.744086133581327 8.9351136626238148 2.2135813805340061
176 2 9.3424802535627265 0.5794634062651145 11.70920321916371
177 2 18.758535691210195 9.8928573631691741 3.433749795554244
…
Strange, because the solution is given by the first line after clicking the link:
This error happens when LAMMPS reads the contents of a section of a data file and the number of parameters in the line differs from what is expected.
Your data file will only work with the command:
atom_style atomic
in your input file. Please refer to the documentation of the read_data command to learn how the Data section should be formatted according to styles.
Thank you everyone for your response. I corrected the format and converted the atomic style in full format. But i am still not able to get any output. The job submission status show job is pending beause of AssocGrpCpuLimit. But the output of scontrol show partition reveals TotalCPUs=768, MaxCPUsPerNode=UNLIMITED, * DefMemPerCPU=4000, 'MaxMemPerCPU=4096`, TotalNodes=8. I am not sure if it’s issue with my files or resources? Will appreciate your responses.
Looks like i can now upload files as well… Here are the data and input files
config_co2_1.txt (1.0 KB)
hMOF-9594.data (50.8 KB)
in.test (1.5 KB)
32 cpus per 334+3 atoms are already too much, let alone 768!
For such a small system, it’s better to debug the input deck locally before submitting it to HPC centres. You will discover that your job fails at the script level, because you are changing the simulation box boundaries from a trigonal cell (which you want to keep, due to the structure of the MOF) to a huge orthogonal cell that contains a lonely CO2 molecule:
ERROR: Read_data subsequent file cannot switch to orthogonal
So, you have first to modify the second data file to have either a smaller periodic box, that fits inside the first box, or just use the same periodic vectors --which is what I have done. I have also translated the CO2 molecule from a random position to an empty pocket in the MOF:
config_co2_1.data
LAMMPS INPUT FILE FOR CO2
3 atoms
2 bonds
1 angles
2 atom types
1 bond types
1 angle types
9.194501 28.271501 xlo xhi
-14.114999 0.790998 ylo yhi
-16.945645 2.045644 zlo zhi
-0.299223 -0.026637 -1.806147 xy xz yz
Masses
1 0.120107000000000E+02
2 0.159990000000000E+02
Atoms
1 1 2 -0.350000 10.840000 -9.000000 0.000000
2 1 1 0.700000 12.000000 -9.000000 0.000000
3 1 2 -0.350000 13.160000 -9.000000 0.000000
Bonds
1 1 1 2
2 1 2 3
Angles
1 1 1 2 3
Then, you have to allow for extra atoms, bonds, and angles when the first data file is loaded:
read_data hMOF-9594.data extra/atom/types 2 extra/bond/types 1 extra/angle/types 1
Finally, the pair coefficients for atom types 4 and 5 are missing, plus I suspect that those for atom type 3 are assigned to the wrong atom type. Anyway, you sort out this mess as I have already gone too far.
