[lammps-users] 'nan' in E_mol, Total energy and pressure

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1

Dear everyone,

Thank you very much for answering my trivial questions, Paul and Steve.
It helps me a lot.
I could make Lammps, and could create input script with a data file.
Now I tried to run with the input script, but I got 'nan' in E_mol,
Totla energy and pressure...
If you don't mind, would you tell me what is going on with this and what
I should check first?
Does 'E_mol' mean energy per mol?
I thought that atoms are too close, so changed timestep, but it did not
work...
Thank you very much.

Best regards,
Nanako Takahashi

2

Dear everyone,

Thank you very much for answering my trivial questions, Paul and Steve.
It helps me a lot.
I could make Lammps, and could create input script with a data file.
Now I tried to run with the input script, but I got 'nan' in E_mol,
Totla energy and pressure...

what input? did you try any of the reference examples?

those _have_ to work or else you have a miscompiled executable.
in the latter case we need to know what compiler/platform you
are running on and what compiler flags you have been using.

cheers,
   axel.

3

Hi Axel,

Thank you very much for your prompt reply.
I have already tried examples, and I could run them.
I got 'nan' with my input script which I created....
The following is my input script and data file.
Actually I am not sure what I need to select for "fix" command, but,
I get 'nan' at the first step, so I thought something is wrong with my initial settings...
Thank you very much.

Best regards,
Nanako Takahashi

* input script*-----------------------

units real
atom_style full
bond_style harmonic
special_bonds amber
angle_style harmonic
dihedral_style charmm
improper_style cvff
pair_style lj/cut/coul/cut 200.0

read_data data.EMI_BF4

neighbor 17. bin

# Temperature T=300 K
velocity all create 300.00 376847

minimize 1.0e-4 1.0e-6 100 10000

fix 1nn all nvt 300.0 300.0 3000.0

thermo 100
timestep 0.00001

dump myDump all atom 10 dump.EMI._BF4

run 500

*data file*----------------------
LAMMPS data file

24 atoms
23 bonds
39 angles
39 dihedrals
14 impropers

10 atom types
10 bond types
15 angle types
11 dihedral types
3 improper types

-20.000000 20.000000 xlo xhi
-20.000000 20.000000 ylo yhi
-20.000000 20.000000 zlo zhi

Masses

1 14.0070
2 12.0010
3 12.0010
4 12.0010
5 1.0080
6 0.0080
7 1.0080
8 1.0080
9 10.8110
10 18.9984

Atoms

1 1 1 -0.0100 -1.543 0.630 -0.795
2 1 2 0.0581 -0.169 0.630 -0.795
3 1 1 0.0795 0.270 1.934 -0.795
4 1 3 -0.1671 -0.853 2.780 -0.803
5 1 3 -0.1925 -1.988 1.964 -0.807
6 1 4 0.0328 -2.370 -0.556 -0.690
7 1 4 -0.0795 -2.694 -1.214 -2.019
8 1 4 -0.1657 1.644 2.336 -0.684
9 1 5 0.2587 -3.047 2.227 -0.805
10 1 6 0.2046 0.492 -0.288 -0.737
11 1 5 0.2482 -0.765 3.868 -0.798
12 1 7 0.1293 1.693 3.363 -0.235
13 1 7 0.1293 2.116 2.346 -1.703
14 1 7 0.1293 2.188 1.604 -0.015
15 1 7 0.0892 -1.815 -1.288 -0.020
16 1 7 0.0892 -3.324 -0.250 -0.173
17 1 8 0.0556 -1.767 -1.554 -2.540
18 1 8 0.0556 -3.330 -2.110 -1.811
19 1 8 0.0556 -3.255 -0.526 -2.695
20 2 9 0.8275 1.233 -1.338 1.219
21 2 10 -0.4569 1.465 -1.697 -0.075
22 2 10 -0.4569 -0.114 -1.329 1.392
23 2 10 -0.4569 1.834 -2.182 2.072
24 2 10 -0.4569 1.691 -0.068 1.366

Bond Coeffs

1 309.99 1.526
2 339.99 1.090
3 339.99 1.090
4 336.99 1.475
5 366.99 1.080
6 476.99 1.343
7 366.99 1.080
8 426.99 1.381
9 548.99 1.350
10 289.99 1.393

Bonds

1 6 2 1
2 6 3 2
3 8 4 3
4 9 5 4
5 8 1 5
6 4 1 6
7 1 6 7
8 2 6 15
9 2 6 16
10 3 7 17
11 3 7 18
12 3 7 19
13 4 3 8
14 2 8 12
15 2 8 13
16 2 8 14
17 5 2 10
18 7 4 11
19 7 5 9
20 10 20 21
21 10 20 22
22 10 20 23
23 10 20 24

Angle Coeffs

1 35.00 109.5
2 50.00 109.5
3 70.00 128.8
4 70.00 121.2
5 70.00 121.2
6 35.00 119.7
7 50.00 109.5
8 50.00 109.5
9 35.00 109.5
10 50.00 109.5
11 70.00 120.0
12 35.00 120.0
13 70.00 120.0
14 35.00 120.0
15 50.00 109.5

Angles

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

Dihedral Coeffs

1 1.7000 2 180 0.0
2 1.7000 2 180 0.0
3 2.3249 2 180 0.0
4 2.3249 2 180 0.0
5 0.1555 3 0 0.0
6 0.0000 2 0 0.0
7 6.6498 2 180 0.0
8 1.8500 2 180 0.0
9 1.8500 2 180 0.0
10 1.5000 2 180 0.0
11 1.8500 2 180 0.0

Dihedrals

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

Improper Coeffs

1 1.1000 -1 2
2 1.1000 -1 2
3 1.0000 -1 2

Impropers

1 1 6 1 2 10
2 1 5 1 2 10
3 1 4 3 2 10
4 1 8 1 2 10
5 2 2 3 4 11
6 2 8 3 4 11
7 2 1 5 4 11
8 2 9 5 4 11
9 2 2 1 5 9
10 2 6 1 5 9
11 2 3 4 5 9
12 3 17 7 6 1
13 3 18 7 6 1
14 3 19 7 6 1

Pair Coeffs

1 0.1700 3.2500
2 0.0860 3.3997
3 0.0860 3.3997
4 0.1094 3.3997
5 0.0150 2.5106
6 0.0150 2.4215
7 0.0157 2.4714
8 0.0157 2.6495
9 0.0950 3.5814
10 0.0610 3.1181

Axel Kohlmeyer wrote:

4

Hi Axel,

Thank you very much for your prompt reply.
I have already tried examples, and I could run them.
I got 'nan' with my input script which I created....
The following is my input script and data file.
Actually I am not sure what I need to select for "fix" command, but,
I get 'nan' at the first step, so I thought something is wrong with my
initial settings...
Thank you very much.

Best regards,
Nanako Takahashi

* input script*-----------------------

units real
atom_style full
bond_style harmonic
special_bonds amber
angle_style harmonic
dihedral_style charmm
improper_style cvff
pair_style lj/cut/coul/cut 200.0

your cutoff is much larger than your box.

read_data data.EMI_BF4

neighbor 17. bin

# Temperature T=300 K
velocity all create 300.00 376847
minimize 1.0e-4 1.0e-6 100 10000

fix 1nn all nvt 300.0 300.0 3000.0

i would try running with nve first. that is more stable.

also, you have to find a way to verify that all bonds
and so on are assigned properly. you could try the converter
scripts to VMD for example...

cheers,
   axel.

5

If you get a NaN in the thermo output, something is wrong
with your simulation. If it happens at time 0, your
initial config is bad.

Steve