[lammps-users] I don't know which part my molecule file is wrong

I checked out the Types section and I got the same error before. (But I got ERROR on proc 0: Unknown section in molecule file (src/molecule.cpp:613))

Where is the “Unknown section in molecule file”?

The molecule file is

48 atoms

4 atom types

Types

1 4

2 2

3 2

4 4

5 2

6 2

7 3

8 3

9 1

10 2

11 1

12 2

13 1

14 1

15 2

16 1

17 2

18 2

19 2

20 1

21 2

22 2

23 2

24 1

25 2

26 2

27 2

28 1

29 2

30 2

31 2

32 1

33 2

34 2

35 2

36 1

37 2

38 2

39 2

40 1

41 2

42 2

43 2

44 1

45 2

46 2

47 2

48 2

Masses

1 12.0107 # C

2 1.00794 # H

3 14.0067 # N

4 28.085501 # Si

Coords

1 -1.39364 0.67237 0 # Si

2 -0.90366 -0.71356 0 # H

3 -0.90363 1.36533 -1.20025 # H

4 -0.61363 1.77545 1.9106 # Si

5 -1.10142 3.16216 1.90926 # H

6 -1.10583 1.08404 3.11085 # H

7 1.25637 1.77247 1.91231 # N

8 -3.26364 0.67239 0 # N

9 -3.75366 -0.71353 -0.00034 # C

10 -3.36253 -1.22992 -0.85196 # H

11 -3.75363 1.36566 -1.20008 # C

12 -3.36252 0.88673 -2.07333 # H

13 1.74416 1.07952 3.11347 # C

14 1.74858 3.15761 1.91184 # C

15 2.81682 3.15655 1.97314 # H

16 1.161 1.75532 4.36839 # C

17 0.27813 1.23495 4.67604 # H

18 1.884 1.72813 5.1567 # H

19 0.9157 2.77244 4.14434 # H

20 1.30073 -0.39465 3.07134 # C

21 1.34898 -0.75297 2.06427 # H

22 1.94893 -0.97989 3.68958 # H

23 0.29618 -0.47535 3.43088 # H

24 1.16566 3.90995 3.12254 # C

25 1.8218 3.79982 3.96055 # H

26 1.06461 4.9478 2.88264 # H

27 0.20557 3.50494 3.36563 # H

28 1.30967 3.85791 0.6124 # C

29 1.96452 4.67994 0.41153 # H

30 1.35136 3.16208 -0.19938 # H

31 0.30818 4.21829 0.72218 # H

32 -3.29109 2.83423 -1.16936 # C

33 -3.3145 3.19455 -0.16213 # H

34 -2.29309 2.90186 -1.54926 # H

35 -3.94431 3.42666 -1.77536 # H

36 -5.29241 1.31266 -1.23121 # C

37 -5.66294 2.08426 -1.87326 # H

38 -5.60907 0.35934 -1.59973 # H

39 -5.67435 1.45755 -0.24226 # H

40 -5.29243 -0.71393 -0.06184 # C

41 -5.66905 0.16165 0.42438 # H

42 -5.60852 -0.71809 -1.08408 # H

43 -5.66887 -1.58563 0.43143 # H

44 -3.29117 -1.42184 1.28652 # C

45 -2.29093 -1.77918 1.15718 # H

46 -3.3205 -0.73175 2.10373 # H

47 -3.94074 -2.24671 1.49277 # H

48 2.81251 1.12985 3.14514 # H

and my Si3N4 file is

LAMMPS data file written by OVITO Basic 3.4.2

208 atoms
4 atom types
0.0 15.1682033539 xlo xhi
0.0 13.1360494342 ylo yhi
0.0 22.0088653564 zlo zhi
-7.5841016769 0.0 0.0 xy xz yz

Masses

1 12.0107 # C
2 1.007940 # H
3 14.006700 # N
4 28.085501 # Si

Atoms # charge

1 2 0.0 4.531185041 0.3142901237 0.4271356899
2 2 0.0 0.7311957261 6.8697819725 0.4367035599
…(Skip)

INPUT file

LAMMPS input - silicon nitride with reaxff

boundary p p p

units real

atom_style charge

read_data Si3N4.data

molecule BDIPAS BDIPAS.data

timestep 0.25

pair_style reax/c lmp_control

pair_coeff * * ffield.reax.SiN C H N Si

fix 1 all nvt temp 500.0 500.0 50.0

fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq

fix 3 BDIPAS deposit 48 1 100 1 region near 10 vz -1.0 -1.0 box

dump dp1 all atom 50 bfadd.lammpstrj

thermo 50

run 100

You should have checked out the Masses section, too. You don’t need it since masses for your system are set through the mass keyword or the data file. As the documentation for the manual explains, you need a masses section only if you have per-atom masses (and not per-type masses) and in that case you need more entries (same as for Types).

Axel.

indeed the entire file is incorrect. you seem to be confusing the format of the “molecule” file with the format of the “data” file. those are not the same.

axel.