Dear lammps users,
I have only recently started to familiarize myself with lammps. I have written a molecule file for a medium chain alkane (decane). I would now like to insert this molecule into a lammps simulation using the create_atoms command.
Here you can find my input file and my molecule file:
Input file:
input file dacane simulation
units real
dimension 3
molecule decane decane_mol.txt
atom_style template decane
processors * * *
boundary p p p
set up styles
pair_style lj/cut 8.75
bond_style harmonic
angle_style harmonic
dihedral_style multi/harmonic
set up simulation box
region 1 block -20 20 -20 20 -20 20
create_box 1 1 bond/types 2 angle/types 3 dihedral/types 1
create atoms
create_atoms 0 single 0 0 0 mol decane 1234
set up coefficients
mass 1 12.011
mass 2 1.008
pair_coeff 1 1 0.066 3.5 8.75
pair_coeff 2 2 0.03 2.5 6.25
bond_coeff 1 200.0 1.54
bond_coeff 2 125.0 0.99
angle_coeff 1 57.5 109.5
angle_coeff 2 25.0 109.5
angle_coeff 3 40.0 109.5
dihedral_coeff 1 2.2 2.9 -3.1 6.3 7.5
outputs
thermo 100
thermo_style custom step temp pe press vol lx density
dump 2 all custom 1000 md.decanetrj id type x y z
initial minimization
minimize 1.0e-10 1.0e-10 100000 100000
relaxation
fix 1 all nvt temp 100 500 10
run 100000
unfix 1
write_data decane_10_result.dat
write_restart decane_10_restart.rest
Molecule file:
alkane data file
header section:
32 atoms
31 bonds
60 angles
7 dihedrals
body section:
Coords
1 0 0 0
2 1.500 0 0.348
3 3 0 0
4 4.501 0 0.348
5 6.001 0 0
6 7.501 0 0.348
7 9.001 0 0
8 10.501 0 0.348
9 12.002 0 0
10 13.502 0 0.348
11 -0.964 0 0.224
12 0 0.964 -0.224
13 0 -0.964 -0.224
14 1.500 0.964 0.572
15 1.500 -0.964 0.572
16 3 0.964 -0.224
17 3 -0.964 -0.224
18 4.501 0.964 0.572
19 4.501 -0.964 0.572
20 6.001 0.964 -0.224
21 6.001 -0.964 -0.224
22 7.501 0.964 0.572
23 7.501 -0.964 0.572
24 9.001 0.964 -0.224
25 9.001 -0.964 -0.224
26 10.501 0.964 0.572
27 10.501 -0.964 0.572
28 12.002 0.964 -0.224
29 12.002 -0.964 -0.224
30 13.502 0.964 0.572
31 13.502 -0.964 0.572
32 14.466 0 0.124
Types
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 2
12 2
13 2
14 2
15 2
16 2
17 2
18 2
19 2
20 2
21 2
22 2
23 2
24 2
25 2
26 2
27 2
28 2
29 2
30 2
31 2
32 2
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
6 1 6 7
7 1 7 8
8 1 8 9
9 1 9 10
10 2 1 11
11 2 1 12
12 2 1 13
13 2 2 14
14 2 2 15
15 2 3 16
16 2 3 17
17 2 4 18
18 2 4 19
19 2 5 20
20 2 5 21
21 2 6 22
22 2 6 23
23 2 7 24
24 2 7 25
25 2 8 26
26 2 8 27
27 2 9 28
28 2 9 29
29 2 10 30
30 2 10 31
31 2 10 32
Angles
1 1 1 2 3
2 1 2 3 4
3 1 3 4 5
4 1 4 5 6
5 1 5 6 7
6 1 6 7 8
7 1 7 8 9
8 1 8 9 10
9 2 11 1 12
10 2 11 1 13
11 2 12 1 13
12 2 14 2 15
13 2 16 3 17
14 2 18 4 19
15 2 20 5 21
16 2 22 6 23
17 2 24 7 25
18 2 26 8 27
19 2 28 9 29
20 2 30 10 31
21 2 30 10 32
22 2 31 10 32
23 3 1 2 14
24 3 1 2 15
25 3 3 2 14
26 3 3 2 15
27 3 2 3 16
28 3 2 3 17
29 3 4 3 16
30 3 4 3 17
31 3 3 4 18
32 3 3 4 19
33 3 5 4 18
34 3 5 4 19
35 3 4 5 20
36 3 4 5 21
37 3 6 5 20
38 3 6 5 21
39 3 5 6 22
40 3 5 6 23
41 3 7 6 22
42 3 7 6 23
43 3 6 7 24
44 3 6 7 25
45 3 8 7 24
46 3 8 7 25
47 3 7 8 26
48 3 7 8 27
49 3 9 8 26
50 3 9 8 27
51 3 8 9 28
52 3 8 9 29
53 3 10 9 28
54 3 10 9 29
55 3 11 1 2
56 3 12 1 2
57 3 13 1 2
58 3 30 10 9
59 3 31 10 9
60 3 32 10 9
Dihedrals
1 1 1 2 3 4
2 1 2 3 4 5
3 1 3 4 5 6
4 1 4 5 6 7
5 1 5 6 7 8
6 1 6 7 8 9
7 1 7 8 9 10
Special Bond Counts
1 4 3 3
2 4 6 3
3 4 6 6
4 4 6 6
5 4 6 6
6 4 6 6
7 4 6 6
8 4 6 6
9 4 6 3
10 4 3 3
11 1 3 3
12 1 3 3
13 1 3 3
14 1 3 6
15 1 3 6
16 1 3 6
17 1 3 6
18 1 3 6
19 1 3 6
20 1 3 6
21 1 3 6
22 1 3 6
23 1 3 6
24 1 3 6
25 1 3 6
26 1 3 6
27 1 3 6
28 1 3 6
29 1 3 6
30 1 3 3
31 1 3 3
32 1 3 3
Special Bonds
1 2 11 12 13 3 14 15 4 16 17
2 1 3 14 15 4 11 12 13 16 17 5 18 19
3 2 4 16 17 1 6 14 15 18 19 6 11 12 13 20 21
4 3 5 18 19 2 6 16 17 20 21 1 7 14 15 22 23
5 4 6 20 21 3 7 18 19 22 23 2 8 16 17 24 25
6 5 7 22 23 4 8 20 21 24 25 3 9 18 19 26 27
7 6 8 24 25 5 9 22 23 26 27 4 10 20 21 28 29
8 7 9 26 27 6 10 24 25 28 29 5 22 23 30 31 32
9 8 10 28 29 7 26 27 30 31 32 6 24 25
10 9 30 31 32 8 28 29 7 26 27
11 1 2 12 13 3 14 15
12 1 2 11 13 3 14 15
13 1 2 11 12 3 14 15
14 2 1 3 15 4 11 12 13 16 17
15 2 1 3 14 4 11 12 13 16 17
16 3 2 4 17 1 5 14 15 18 19
17 3 2 4 16 1 5 14 15 18 19
18 4 3 5 19 2 6 16 17 20 21
19 4 3 5 18 2 6 16 17 20 21
20 5 4 6 21 3 7 18 19 22 23
21 5 4 6 20 3 7 18 19 22 23
22 6 5 7 23 4 8 20 21 24 25
23 6 5 7 22 4 8 20 21 24 25
24 7 6 8 25 5 9 22 23 26 27
25 7 6 8 24 5 9 22 23 26 27
26 8 7 9 27 6 10 24 25 28 29
27 8 7 9 26 6 10 24 25 28 29
28 9 8 10 29 7 26 27 30 31 32
29 9 8 10 28 7 26 27 30 31 32
30 10 9 31 32 8 28 29
31 10 9 30 32 8 28 29
32 10 9 30 31 8 28 29
When I run the input file with lammps, I get the following error message:
ERROR: Invalid atom type in create_atoms mol command (src/create_atoms.cpp:300)
Last command: create_atoms 0 single 0 0 0 mol decane 1234
I unfortunately don’t understand right now what the problem is. I would therefore be very grateful for any tips and hints.
Many thanks and best regards