error about N2 model

Hello, LAMMPS users:

I test a three three-charge-site N2 model these days. In this model, there are two Lennard-Jones interaction nitrogen sites and a massless point charge placed in the middle of the N-N. The mass of point charge/massless atom (at the center of N2) is set to 0.000000001. no matter how small the timestep is, when I run it, I got the error:

Out of range atoms - cannot compute PPPM already at the first step.

I paste the input and data file at the end of the e-mail

What could be the reason of this, what could I do?

Thanks in advance for any support.

Kind regards.

units real
atom_style full
dimension 3
boundary p p p

read_data data.n

neighbor 2.0 bin
neigh_modify delay 5

pair_style lj/cut/coul/long 12 11
pair_coeff 1 1 0 0
pair_coeff 1 2 0 1.655
pair_coeff 2 2 0.0742 3.31

bond_style harmonic
bond_coeff 1 420 0.547
angle_style harmonic
angle_coeff 1 147.7 180
kspace_style pppm 0.0001

group all type 1 2

min_style cg
minimize 1.0e-8 1.0e-9 4000 4000

velocity all create 200.0 1836584

fix

fix 1 all shake 0.0001 20 0 b 1
fix 2 all nvt temp 200.0 200.0 200.0 drag 1.7

run 1

timestep 0.1
thermo_style custom step temp pe etotal press vol
thermo 100
dump a all custom 100 dump.replace id mol type xu yu zu fx fy fz
run 40000

data file
LAMMPS 2005 data file for n

90 atoms
60 bonds
30 angles
0 dihedrals
0 impropers

2 atom types
1 bond types
1 angle types

-3.000000000 38 xlo xhi
-3.000000000 38 ylo yhi
-3.000000000 38 zlo zhi

Masses

1 0.000000001
2 14.006700

Atoms

1 1 1 0.9908 21.72082099 14.66368908 14.70658726
2 1 2 -0.4954 22.20936852 14.59478398 14.94629467
3 1 2 -0.4954 21.23227345 14.73259417 14.46687986
4 2 1 0.9908 22.46606137 21.20534952 7.515282493
5 2 2 -0.4954 22.92174451 20.90077986 7.493382953
6 2 2 -0.4954 22.01037823 21.50991918 7.537182033
7 3 1 0.9908 38.42674881 29.72242413 34.68976794
8 3 2 -0.4954 38.67513884 30.15202238 34.45322386
9 3 2 -0.4954 38.17835878 29.29282588 34.92631203
10 4 1 0.9908 18.67208801 14.01745153 6.513753399
11 4 2 -0.4954 18.51734045 14.48290622 6.267793331
12 4 2 -0.4954 18.82683557 13.55199684 6.759713466
13 5 1 0.9908 32.93323338 4.777773132 35.33875323
14 5 2 -0.4954 33.40615829 5.043800848 35.25784562
15 5 2 -0.4954 32.46030847 4.511745416 35.41966084
16 6 1 0.9908 33.85135852 5.271709289 25.55941129
17 6 2 -0.4954 33.76240968 5.613137949 25.12460382
18 6 2 -0.4954 33.94030736 4.930280628 25.99421876
19 7 1 0.9908 5.68671005 14.27287082 23.7027261
20 7 2 -0.4954 5.63273723 13.81465153 23.44112451
21 7 2 -0.4954 5.74068287 14.73109011 23.9643277
22 8 1 0.9908 22.75228709 28.21829179 28.31349515
23 8 2 -0.4954 22.59224137 28.23736666 27.8018004
24 8 2 -0.4954 22.9123328 28.19921692 28.82518991
25 9 1 0.9908 23.58348349 30.65183024 27.14127286
26 9 2 -0.4954 24.09046297 30.53802428 27.31830058
27 9 2 -0.4954 23.07650401 30.76563619 26.96424514
28 10 1 0.9908 5.7253782 22.41101916 26.73749787
29 10 2 -0.4954 6.11898808 22.12121326 26.48773773
30 10 2 -0.4954 5.33176832 22.70082506 26.987258
31 11 1 0.9908 33.85413967 13.96978419 26.0859608
32 11 2 -0.4954 33.48900925 14.37045824 26.00149443
33 11 2 -0.4954 34.21927009 13.56911014 26.17042717
34 12 1 0.9908 32.79268141 22.3389132 15.81293978
35 12 2 -0.4954 32.48965921 22.18614429 15.38161774
36 12 2 -0.4954 33.09570361 22.49168211 16.24426182
37 13 1 0.9908 29.92075017 30.55950143 30.83362374
38 13 2 -0.4954 30.17892195 30.54025929 30.3495918
39 13 2 -0.4954 29.66257839 30.57874356 31.31765568
40 14 1 0.9908 38.14875175 34.26571547 34.60247028
41 14 2 -0.4954 37.96736341 34.7826881 34.55002585
42 14 2 -0.4954 38.3301401 33.74874283 34.65491471
43 15 1 0.9908 10.13814747 34.54612343 18.25131048
44 15 2 -0.4954 9.89163387 34.70925366 17.78935353
45 15 2 -0.4954 10.38466107 34.38299319 18.71326744
46 16 1 0.9908 26.26282705 24.32854995 4.77388998
47 16 2 -0.4954 25.85824274 24.00353735 4.951944887
48 16 2 -0.4954 26.66741137 24.65356255 4.595835073
49 17 1 0.9908 13.19558508 28.4126858 9.238054619
50 17 2 -0.4954 12.73397915 28.41029479 8.941373416
51 17 2 -0.4954 13.65719101 28.41507681 9.534735822
52 18 1 0.9908 20.51452069 3.132896271 20.02787796
53 18 2 -0.4954 20.33491944 3.041460517 19.51624952
54 18 2 -0.4954 20.69412194 3.224332025 20.53950639
55 19 1 0.9908 37.8415258 6.428017574 26.92857407
56 19 2 -0.4954 37.92322199 6.959950983 26.88034635
57 19 2 -0.4954 37.75982962 5.896084164 26.97680178
58 20 1 0.9908 35.91149136 35.14980962 9.595579574
59 20 2 -0.4954 35.60696579 34.91348408 9.204885776
60 20 2 -0.4954 36.21601693 35.38613516 9.986273371
61 21 1 0.9908 6.62774553 22.45414167 6.409302911
62 21 2 -0.4954 6.62317168 21.89206205 6.442141514
63 21 2 -0.4954 6.63231939 23.01622129 6.376464307
64 22 1 0.9908 34.23145853 9.536305813 24.23009001
65 22 2 -0.4954 34.14349112 10.06250339 24.32882149
66 22 2 -0.4954 34.31942594 9.010108239 24.13135853
67 23 1 0.9908 38.47230674 6.839983763 15.82037863
68 23 2 -0.4954 38.33949898 6.341002431 16.02532361
69 23 2 -0.4954 38.60511449 7.338965094 15.61543366
70 24 1 0.9908 6.89844163 16.03885223 34.01585891
71 24 2 -0.4954 7.20946717 16.46278845 34.17470049
72 24 2 -0.4954 6.58741609 15.61491602 33.85701732
73 25 1 0.9908 9.00787549 14.77778244 8.873381564
74 25 2 -0.4954 8.99192207 14.24197272 8.854172966
75 25 2 -0.4954 9.0238289 15.31359217 8.892590162
76 26 1 0.9908 13.19736999 24.30784673 21.59540081
77 26 2 -0.4954 13.73730866 24.36727878 21.66765921
78 26 2 -0.4954 12.65743132 24.24841468 21.52314241
79 27 1 0.9908 14.19567989 6.407230215 11.440295
80 27 2 -0.4954 14.70215089 6.251875247 11.29649536
81 27 2 -0.4954 13.68920888 6.562585182 11.58409464
82 28 1 0.9908 14.96355009 29.34119435 6.35494307
83 28 2 -0.4954 15.40913046 29.66126942 6.368563461
84 28 2 -0.4954 14.51796973 29.02111927 6.341322678
85 29 1 0.9908 19.57121838 1.928521235 31.17559129
86 29 2 -0.4954 19.12770635 1.665455092 30.99182527
87 29 2 -0.4954 20.01473041 2.191587377 31.35935732
88 30 1 0.9908 8.22532501 34.06620441 22.49601477
89 30 2 -0.4954 8.37669335 34.42175671 22.88568995
90 30 2 -0.4954 8.07395666 33.71065211 22.10633958

Bonds

1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
5 1 7 8
6 1 7 9
7 1 10 11
8 1 10 12
9 1 13 14
10 1 13 15
11 1 16 17
12 1 16 18
13 1 19 20
14 1 19 21
15 1 22 23
16 1 22 24
17 1 25 26
18 1 25 27
19 1 28 29
20 1 28 30
21 1 31 32
22 1 31 33
23 1 34 35
24 1 34 36
25 1 37 38
26 1 37 39
27 1 40 41
28 1 40 42
29 1 43 44
30 1 43 45
31 1 46 47
32 1 46 48
33 1 49 50
34 1 49 51
35 1 52 53
36 1 52 54
37 1 55 56
38 1 55 57
39 1 58 59
40 1 58 60
41 1 61 62
42 1 61 63
43 1 64 65
44 1 64 66
45 1 67 68
46 1 67 69
47 1 70 71
48 1 70 72
49 1 73 74
50 1 73 75
51 1 76 77
52 1 76 78
53 1 79 80
54 1 79 81
55 1 82 83
56 1 82 84
57 1 85 86
58 1 85 87
59 1 88 89
60 1 88 90

Angles

1 1 2 1 3
2 1 5 4 6
3 1 8 7 9
4 1 11 10 12
5 1 14 13 15
6 1 17 16 18
7 1 20 19 21
8 1 23 22 24
9 1 26 25 27
10 1 29 28 30
11 1 32 31 33
12 1 35 34 36
13 1 38 37 39
14 1 41 40 42
15 1 44 43 45
16 1 47 46 48
17 1 50 49 51
18 1 53 52 54
19 1 56 55 57
20 1 59 58 60
21 1 62 61 63
22 1 65 64 66
23 1 68 67 69
24 1 71 70 72
25 1 74 73 75
26 1 77 76 78
27 1 80 79 81
28 1 83 82 84
29 1 86 85 87
30 1 89 88 90

in.n (696 Bytes)

data.n (5.79 KB)

Hello, LAMMPS users:

first off, there is no need to copy steve or me on e-mails to the
mailing list. we are subscribed and thus copying us will only cause
irritation by receiving the message twice or it not being properly
pre-sorted and tagged.

     I test a three three-charge-site N2 model these days. In this model,
there are two Lennard-Jones interaction nitrogen sites and a massless point
charge placed in the middle of the N-N. The mass of point charge/massless
atom (at the center of N2) is set to 0.000000001. no matter how small the
timestep is, when I run it, I got the error:

this model cannot work this way. you have to use one of the rigid fixes.

Out of range atoms - cannot compute PPPM already at the first step.

yes. after shake was called for the first time.

axel.