Unknown identifier in data file

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1

Hi, I am LAMMPS users.

I write data file as a input file, but LAMMPS give me error with command below.

"ERROR on proc 0 : Unknown identifier in data file : 7 2 2 yukawa 10.0 (read_data.cpp:1282)

What’s the problem on my data file?

I attach my data file below.

Please answer me. Thank you.

------------------------------------------------------------data.dna-------------------------------------------------------------------------------

LAMMPS Coarse-grained DNA Description

60 atoms
58 bonds
75 angles
74 dihedrals
18 impropers

6 atom types
6 bond types
10 angle types
10 dihedral types
4 improper types

-10.000000 150.00000 xlo xhi
-10.000000 10.000000 ylo yhi
-10.000000 150.00000 zlo zhi

Masses

1 132.120
2 236.920
3 134.100
4 110.100
5 150.100
6 125.100

Pair Coeffs

1 1 1 lj/cut/coul/cut 1.0 1.0 1.0 1.0
2 1 2 lj/cut/coul/cut 1.0 1.0 1.0 1.0
3 1 3 resquared 0.25 2.0 1.0 1.0 1.0 3.6229 5.0023 1.4057
4 1 4 resquared 0.25 2.0 1.0 1.0 1.0 2.5848 3.8092 1.3424
5 1 5 resquared 0.25 2.0 1.0 1.0 1.0 4.3347 2.3717 0.7752
6 1 6 resquared 0.25 2.0 1.0 1.0 1.0 3.6127 3.4088 0.9666
7 2 2 yukawa 10.0
8 2 3 resquared 729.67 4.2489 1.0 1.0 1.0 13.443 9.0257 2.6714
9 2 4 resquared 534.84 4.1348 1.0 1.0 1.0 12.917 8.0570 3.5227
10 2 5 resquared 244.45 4.1409 1.0 1.0 1.0 8.7902 4.1412 1.7311
11 2 6 resquared 934.79 4.2940 1.0 1.0 1.0 15.0740 12.8730 2.9361
12 3 3 resquared 3455.0 3.5969 3.6229 5.0023 1.4057 3.6229 5.0023 1.4057
13 3 4 resquared 17115.0 3.6915 4.3800 2.6585 2.4634 2.9957 7.8481 1.0379
14 3 5 resquared 4188.0 3.8501 3.6178 2.8420 1.5088 3.5849 4.4283 0.6581
15 3 6 resquared 6195.0 3.7700 3.7656 2.1395 1.6393 4.86454 5.5447 0.8189
16 4 4 resquared 7826.0 3.9060 2.5848 3.8092 1.3424 2.5848 3.8092 1.3424
17 4 5 resquared 3720.0 3.961 1.7108 3.6023 1.163 3.3655 2.4695 0.8089
18 4 6 resquared 4839.0 3.8553 1.1875 6.3381 1.2818 5.5485 4.9745 0.9895
19 5 5 resquared 4274.0 4.0250 4.3347 2.3717 0.7752 4.3347 2.3717 0.7752
20 5 6 resquared 51144.0 3.8664 5.4026 0.8356 1.1117 5.5485 4.9745 0.9895
21 6 6 resquared 2347.0 3.8096 3.6127 3.4088 0.9666 3.6127 3.4088 0.9666

Bond Coeffs

1 harmonic 330.800000 3.057000
2 harmonic 323.400000 3.169000
3 harmonic 229.200000 3.501000
4 harmonic 186.500000 3.572000
5 harmonic 40.4500000 4.581000
6 harmonic 5.59600000 5.194000

Angle Coeffs

1 9.755000 80.557900
2 5.645000 110.351700
3 3.925000 104.794000
4 1.726500 110.122500
5 12.09500 162.147100
6 10.34500 156.646700
7 14.06000 155.443500
8 16.06000 161.001200
9 16.28500 94.652700
10 32.79000 85.829100

Dihedral Coeffs

1 class2 -0.090000 -1.410000 0.030000 0.800000 -0.050000 -4.000000
2 class2 -0.100000 -1.260000 0.100000 -0.020000 -0.060000 -8.300000
3 class2 -0.100000 -0.790000 -0.040000 -1.500000 -0.080000 -3.900000
4 class2 -0.110000 -0.700000 -0.170000 1.850000 0.070000 -6.700000
5 class2 -0.130000 -1.620000 -0.260000 1.850000 -0.050000 -0.700000
6 class2 -0.070000 -0.900000 -0.220000 -0.720000 -0.050000 0.400000
7 class2 -0.120000 -14.71000 -0.230000 -1.240000 -0.020000 -0.200000
8 class2 -0.180000 0.200000 -0.220000 -0.480000 -0.140000 -0.100000
9 class2 0.100000 0.000000 0.150000 2.440000 0.210000 2.170000
10 class2 -0.080000 8.000000 -0.200000 -1.500000 0.044000 -0.900000

Improper Coeffs

1 class2 -1.400000 -0.770000 -0.300000 -0.770000 -0.300000 -0.600000
2 class2 -2.000000 -0.510000 -0.700000 -1.040000 -0.400000 -1.000000
3 class2 2.3600000 1.970000 0.000000 0.000000 0.000000 0.000000
4 class2 2.6600000 1.620000 0.000000 0.000000 0.000000 0.000000

Atoms

1 A 3 2.021384 0.000000 -5.567462
2 S 1 -0.000050 0.000000 -2.709000
3 P 2 0.000000 0.000000 1.872000
4 C 4 7.100604 0.000000 0.875086
5 S 1 4.896969 0.000000 3.603280
6 P 2 4.896969 0.000000 8.184280
7 G 5 13.162987 0.000000 8.723736
8 S 1 9.794810 0.000000 9.913092
9 P 2 9.794810 0.000000 14.494092
10 T 6 16.684062 0.000000 13.762072
11 S 1 14.691471 0.000000 16.226244
12 P 2 14.691471 0.000000 20.807244
13 A 3 21.788316 0.000000 19.815075
14 S 1 19.588421 0.000000 22.538577
15 P 2 19.588422 0.000000 27.119577
16 C 4 26.406274 0.000000 26.472805
17 S 1 24.485372 0.000000 28.850910
18 P 2 24.485372 0.000000 33.431910
19 G 5 31.628052 0.000000 32.385495
20 S 1 29.382322 0.000000 35.163243
21 P 2 29.382323 0.000000 39.744243
22 T 6 36.271575 0.000000 39.012223
23 S 1 34.278983 0.000000 41.476395
24 P 2 34.278984 0.000000 46.057395
25 A 3 41.375829 0.000000 45.065226
26 S 1 39.175934 0.000000 47.788728
27 P 2 39.175934 0.000000 52.369728
28 C 4 45.993786 0.000000 51.722956
29 S 1 44.072884 0.000000 54.101061
30 P 2 44.072885 0.000000 58.682061
31 G 5 51.214343 0.000000 57.634659
32 S 1 48.969835 0.000000 60.413394
33 P 2 48.969835 0.000000 64.994394
34 T 6 55.859087 0.000000 64.262374
35 S 1 53.866496 0.000000 66.726546
36 P 2 53.866496 0.000000 71.307546
37 A 3 60.963341 0.000000 70.315376
38 S 1 58.763446 0.000000 73.038879
39 P 2 58.763447 0.000000 77.619879
40 C 4 65.583208 0.000000 76.971410
41 S 1 63.661287 0.000000 79.348691
42 P 2 63.661287 0.000000 83.929691
43 G 5 70.802746 0.000000 82.882290
44 S 1 68.558238 0.000000 85.661024
45 P 2 68.558238 0.000000 90.242024
46 T 6 75.447490 0.000000 89.510004
47 S 1 73.454899 0.000000 91.974176
48 P 2 73.454899 0.000000 96.555176
49 A 3 80.551744 0.000000 95.563007
50 S 1 78.351849 0.000000 98.286509
51 P 2 78.351849 0.000000 102.867509
52 C 4 85.170747 0.000000 102.221581
53 S 1 83.248800 0.000000 104.598842
54 P 2 83.248800 0.000000 109.179842
55 G 5 90.390259 0.000000 108.132441
56 S 1 88.145750 0.000000 110.911175
57 P 2 88.145750 0.000000 115.49217
58 T 6 96.091478 0.000000 116.360756
59 S 1 93.042411 0.000000 117.224327

Bonds

1 3 1 2
2 5 2 3
3 6 3 5
4 1 5 4
5 5 5 6
6 6 6 8
7 4 8 7
8 5 8 9
9 6 9 11
10 2 11 10
11 5 11 12
12 6 12 14
13 3 14 13
14 5 14 15
15 6 15 17
16 1 17 16
17 5 17 18
18 6 18 20
19 4 20 19
20 5 20 21
21 6 21 23
22 2 23 22
23 5 23 24
24 6 24 26
25 3 26 25
26 5 26 27
27 6 27 29
28 1 29 28
29 5 29 30
30 6 30 32
31 4 32 31
32 5 32 33
33 6 33 35
34 2 35 34
35 5 35 36
36 6 36 38
37 3 38 37
38 5 38 39
39 6 39 41
40 1 41 40
41 5 41 42
42 6 42 44
43 4 44 43
44 5 44 45
45 6 45 47
46 2 47 46
47 5 47 48
48 6 48 50
49 3 50 49
50 5 50 51
51 6 51 53
52 1 53 52
53 5 53 54
54 6 54 56
55 4 56 55
56 5 56 57
57 6 57 59
58 2 59 58

Angles

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

Dihedrals

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

Impropers

1 2 3 5 4 6
2 3 6 8 7 9
3 4 9 11 10 12
4 1 12 14 13 15
5 2 15 17 16 18
6 3 18 20 19 21
7 4 21 23 22 24
8 1 24 26 25 27
9 2 27 29 28 30
10 3 30 32 31 33
11 4 33 35 34 36
12 1 36 38 37 39
13 2 39 41 40 42
14 3 42 44 43 45
15 4 45 47 46 48

2

Hi, I am LAMMPS users.

I write data file as a input file, but LAMMPS give me error with command
below.

"ERROR on proc 0 : Unknown identifier in data file : 7 2 2 yukawa 10.0
(read_data.cpp:1282)

What's the problem on my data file?

the PairCoeffs section is wrong.
for your system you cannot input
those in a data file. only with explicit
pair_coeff statements.

have a closer look at the read_data documentation.

axel.

3

Pair Coeffs

1 1 1 lj/cut/coul/cut 1.0 1.0 1.0 1.0
2 1 2 lj/cut/coul/cut 1.0 1.0 1.0 1.0
3 1 3 resquared 0.25 2.0 1.0 1.0 1.0 3.6229 5.0023 1.4057
4 1 4 resquared 0.25 2.0 1.0 1.0 1.0 2.5848 3.8092 1.3424

:

Hello.
Axel is right. Remove the "Pair Coeffs" section from your DATA file.
Instead put the following text in your input script (excerpt only):
pair_coeff 1 1 lj/cut/coul/cut 1.0 1.0 1.0 1.0
pair_coeff 1 2 lj/cut/coul/cut 1.0 1.0 1.0 1.0
pair_coeff 1 3 resquared 0.25 2.0 1.0 1.0 1.0 3.6229 5.0023 1.4057
pair_coeff 1 4 resquared 0.25 2.0 1.0 1.0 1.0 2.5848 3.8092 1.3424
:

Bond Coeffs

1 harmonic 330.800000 3.057000
2 harmonic 323.400000 3.169000
3 harmonic 229.200000 3.501000

Remove the "Bond Coeffs" section from your DATA file and put this your
input script:

bond_coeff 1 harmonic 330.800000 3.057000
bond_coeff 2 harmonic 323.400000 3.169000
bond_coeff 3 harmonic 229.200000 3.501000
:

Do the same thing for your Angle, Dihedral, and Improper Coeffs as well.

Dihedral Coeffs

1 class2 -0.090000 -1.410000 0.030000 0.800000 -0.050000 -4.000000
2 class2 -0.100000 -1.260000 0.100000 -0.020000 -0.060000 -8.300000
3 class2 -0.100000 -0.790000 -0.040000 -1.500000 -0.080000 -3.900000

:
dihedral_coeff 1 class2 -0.090000 -1.410000 0.030000 0.800000
-0.050000 -4.000000
dihedral_coeff 2 class2 -0.100000 -1.260000 0.100000 -0.020000
-0.060000 -8.300000
dihedral_coeff 3 class2 -0.100000 -0.790000 -0.040000 -1.500000
-0.080000 -3.900000
:

Improper Coeffs

improper_coeff 1 class2 -1.400000 -0.770000 -0.300000 -0.770000
-0.300000 -0.600000
improper_coeff 2 class2 -2.000000 -0.510000 -0.700000 -1.040000
-0.400000 -1.000000
improper_coeff 3 class2 2.3600000 1.970000 0.000000 0.000000 0.000000 0.000000
improper_coeff 4 class2 2.6600000 1.620000 0.000000 0.000000 0.000000 0.000000

If you are only using one type of improper and dihedral style, then
you don't need to use hybrid improper and dihedral styles. (That way
you can keep Dihedral Coeffs and Improper Coeffs in he data file.
However you would have to delete the "class2" from every line.) This
is optional. It's fine to use hybrid styles with only one style.

Finally, for the dihedral and improper coeffs, the phi1, phi2, phi3
and chi0 arguments should be in degrees, not radians.

Cheers.
Andrew

4

Incidentally, there is a bug in the "class2" dihedral implementation
in LAMMPS (which will prevent helical twisting)

http://lammps.sandia.gov/threads/msg28208.html
http://lammps.sandia.gov/threads/msg28261.html

Since you have non-zero phi1, phi2, phi3, parameters, your DNA
molecule won't be twisted the way you want it to. If this bothers you
then, then email Steve and ask him to fix it or put a warning in the
documentation. (It helps if more people complain. I'm sorry that I
don't have time to fix this problem.)

Fortunately the "charmm" dihedral and impropoer styles seems to work fine:
http://lammps.sandia.gov/doc/dihedral_charmm.html

5

(Each of these commands was supposed to fit one one line.)