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