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

I’m a newbie user, and I’m trying to insert a molecule on Silicon Nitride (Si3N4) surface. I used two commands to insert a molecule “molecule + fix deposit” in my input file.

I’ve read molecule document several times and finally finished (my opinion) like following;

LAMMPS data file. CGCMM style. atom_style charge generated by VMD/TopoTools v1.7 on Sat Feb 27 15:14:48 +0900 2021

48 atoms

Types

1 1

2 2

3 3

4 4

Masses

1 12.010700 # C

2 1.007940 # H

3 14.006700 # N

4 28.085501 # Si

Coords

1 4 0.000000 -1.393640 0.672370 0.000000 # Si

2 2 0.000000 -0.903660 -0.713560 0.000000 # H

3 2 0.000000 -0.903630 1.365330 -1.200250 # H

4 4 0.000000 -0.613630 1.775450 1.910600 # Si

5 2 0.000000 -1.101420 3.162160 1.909260 # H

6 2 0.000000 -1.105830 1.084040 3.110850 # H

7 3 0.000000 1.256370 1.772470 1.912310 # N

8 3 0.000000 -3.263640 0.672390 0.000000 # N

9 1 0.000000 -3.753660 -0.713530 -0.000340 # C

10 2 0.000000 -3.362530 -1.229920 -0.851960 # H

11 1 0.000000 -3.753630 1.365660 -1.200080 # C

12 2 0.000000 -3.362520 0.886730 -2.073330 # H

13 1 0.000000 1.744160 1.079520 3.113470 # C

14 1 0.000000 1.748580 3.157610 1.911840 # C

15 2 0.000000 2.816820 3.156550 1.973140 # H

16 1 0.000000 1.161000 1.755320 4.368390 # C

17 2 0.000000 0.278130 1.234950 4.676040 # H

18 2 0.000000 1.884000 1.728130 5.156700 # H

19 2 0.000000 0.915700 2.772440 4.144340 # H

20 1 0.000000 1.300730 -0.394650 3.071340 # C

21 2 0.000000 1.348980 -0.752970 2.064270 # H

22 2 0.000000 1.948930 -0.979890 3.689580 # H

23 2 0.000000 0.296180 -0.475350 3.430880 # H

24 1 0.000000 1.165660 3.909950 3.122540 # C

25 2 0.000000 1.821800 3.799820 3.960550 # H

26 2 0.000000 1.064610 4.947800 2.882640 # H

27 2 0.000000 0.205570 3.504940 3.365630 # H

28 1 0.000000 1.309670 3.857910 0.612400 # C

29 2 0.000000 1.964520 4.679940 0.411530 # H

30 2 0.000000 1.351360 3.162080 -0.199380 # H

31 2 0.000000 0.308180 4.218290 0.722180 # H

32 1 0.000000 -3.291090 2.834230 -1.169360 # C

33 2 0.000000 -3.314500 3.194550 -0.162130 # H

34 2 0.000000 -2.293090 2.901860 -1.549260 # H

35 2 0.000000 -3.944310 3.426660 -1.775360 # H

36 1 0.000000 -5.292410 1.312660 -1.231210 # C

37 2 0.000000 -5.662940 2.084260 -1.873260 # H

38 2 0.000000 -5.609070 0.359340 -1.599730 # H

39 2 0.000000 -5.674350 1.457550 -0.242260 # H

40 1 0.000000 -5.292430 -0.713930 -0.061840 # C

41 2 0.000000 -5.669050 0.161650 0.424380 # H

42 2 0.000000 -5.608520 -0.718090 -1.084080 # H

43 2 0.000000 -5.668870 -1.585630 0.431430 # H

44 1 0.000000 -3.291170 -1.421840 1.286520 # C

45 2 0.000000 -2.290930 -1.779180 1.157180 # H

46 2 0.000000 -3.320500 -0.731750 2.103730 # H

47 2 0.000000 -3.940740 -2.246710 1.492770 # H

48 2 0.000000 2.812510 1.129850 3.145140 # H

But I got ERROR on proc 0: Unknown section in molecule file (src/molecule.cpp:613)

In my understanding, I need to put “types” section and “Coords” section which describes the xyz coordinate to use “fix deposit” command.

Which part is the unknown section in my molecule file?

If it is not enough to figure out what the problem is, I will upload more information.

These are Si3N4 data file and input file.

LAMMPS data file written by OVITO Basic 3.4.2

204 atoms

3 atom types

0.0 15.1682033539 xlo xhi

0.0 13.1360494342 ylo yhi

0.0 29.5382137299 zlo zhi

-7.5841016769 0.0 0.0 xy xz yz

Masses

1 1.007940 # H

2 14.006700 # N

3 28.085501 # Si

Atoms # charge

1 1 0.0 5.5730789412 11.0804019973 9.3849674292

2 1 0.0 9.3973074318 4.527285028 9.3532323404

3 1 0.0 -1.9997459578 11.0747059041 9.3433852156

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 H N Si C

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

I’m a newbie user, and I’m trying to insert a molecule on Silicon Nitride (Si3N4) surface. I used two commands to insert a molecule “molecule + fix deposit” in my input file.

I’ve read molecule document several times and finally finished (my opinion) like following;

you need to read the documentation again. the “Types” section is wrong. it should have one line per atom, not one line per type.

axel.