Error: All dihedral coeffs are not set (dihedral.cpp:57)

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1

I am trying to use the class2 options in lammps-21Dec11 and receiving an error message that reads: All dihedral coeffs are not set. I received a similar message in the past for when I was adding angle_style class2 to my molecule, and I discovered that it was caused by missing parameters in my data.file. I had only specified the Angle Coeffs section, and neglected to include the BondBond and BondAngle sections. After I added these, even when all parameters for each type were set to 0.0, everything worked fine.

Now I am beginning to add in dihedral forces and I have specified the coefficients in the Dihedral Coeffs, EndBondTorsion Coeffs, MiddleBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, and BondBond13 sections all as 0.0. Somehow, I get a message specifying that I have not specified all dihedral coeffs in the data file. I have gone over this again and again and can’t seem to find the problem.

The manual indicates that this is the correct format for specifying dihedral coefficients, basically everything is included but the identifier (ex: “at”, “mbt”) for each section.

Below I have attached my data and input file.

Best,
Josh Deetz
PhD Candidate Student
Chemical Engineering
University of California, Davis

in.file:
units real
atom_style full

kspace_style ewald 0.0001
pair_style lj/class2/coul/long 10.0
bond_style class2
angle_style class2
dihedral_style class2

boundary p p p

read_data data.singleclass2

#special_bonds lj/coul 0.0 0.0 1.0 dihedral yes

neighbor 2.0 bin
neigh_modify delay 5

timestep 0.2

thermo_style multi
thermo 100

fix 1 all nvt temp 275.0 275.0 100.0

group tes type <= 7

dump 1 tes atom 100 dump.singleclass2

run 3000

data.file:
LAMMPS Description

26 atoms
25 bonds
45 angles
45 dihedrals
7 atom types
6 bond types
9 angle types
6 dihedral types

-10.000000 10.000000 xlo xhi
-10.000000 10.000000 ylo yhi
-10.000000 10.000000 zlo zhi

Masses

1 1.0080
2 28.0855
3 15.9990
4 12.0110
5 1.0080
6 12.0110
7 1.0080

Pair Coeffs

1 1 0.0230 2.878
2 2 0.1310 4.290
3 3 0.0800 3.300
4 4 0.0620 3.854
5 5 0.0230 2.878
6 6 0.0620 3.854
7 7 0.0230 2.878

Bond Coeffs

1 1.48361 202.7798 -305.3603 280.2685
2 1.64307 350.1232 -517.3424 673.7067
3 1.43051 400.3954 -835.1951 1313.0142
4 1.09797 345.0000 -691.8900 844.6000
5 1.51796 299.6700 -501.7700 679.8100
6 1.09392 345.0000 -691.8900 844.6000

Angle Coeffs

1 110.49 57.6643 -10.6506 4.6274
2 126.55 22.1227 -11.7128 -5.2257
3 109.89 58.5446 -10.8088 -12.4006
4 110.27 41.4530 -10.6040 5.1290
5 107.79 39.6410 -12.9210 -2.4318
6 110.42 41.4530 -10.6040 5.1290
7 108.52 39.6410 -12.9210 -2.4318
8 108.41 70.3069 -6.9375 0.0000
9 108.98 54.5381 -8.3642 -13.0838

Dihedral Coeffs

1 0.0000 0 0.000 0 -0.0100 0
2 0.0000 0 0.000 0 -0.0100 0
3 0.0000 0 0.000 0 -0.0100 0
4 -0.1435 0 0.235 0 -0.0905 0
5 -0.1432 0 0.617 0 -0.1530 0
6 -0.2250 0 0.000 0 -0.0100 0

BondBond Coeffs

1 11.6183 1.48361 1.64307
2 17.0006 1.64307 1.43051
3 23.1979 1.43051 1.09797
4 3.3872 1.09797 1.51796
5 5.3316 1.09797 1.09797
6 3.3872 1.51796 1.09392
7 5.3316 1.09392 1.09392
8 41.1143 1.64307 1.64307
9 11.4318 1.43051 1.51796

BondAngle Coeffs

1 6.4278 20.5669 1.48361 1.64307
2 12.9287 12.9287 1.64307 1.43051
3 55.3270 4.6189 1.43051 1.09797
4 11.4210 20.7540 1.09797 1.51796
5 18.1030 18.1030 1.09797 1.09797
6 20.7540 11.4210 1.51796 1.09392
7 18.1030 18.1030 1.09392 1.09392
8 23.4380 23.4380 1.64307 1.64307
9 20.4033 2.6868 1.43051 1.51796

MiddleBondTorsion Coeffs

1 0.0 0.0 0.0 0.0
2 0.0 0.0 0.0 0.0
3 0.0 0.0 0.0 0.0
4 0.0 0.0 0.0 0.0
5 0.0 0.0 0.0 0.0
6 0.0 0.0 0.0 0.0

EndBondTorsion Coeffs

1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

AngleTorsion Coeffs

1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

AngleAngleTorsion Coeffs

1 0.0 0.0 0.0
2 0.0 0.0 0.0
2 0.0 0.0 0.0
4 0.0 0.0 0.0
5 0.0 0.0 0.0
6 0.0 0.0 0.0

BondBond13 Coeffs

1 0.0 0.0 0.0
2 0.0 0.0 0.0
3 0.0 0.0 0.0
4 0.0 0.0 0.0
5 0.0 0.0 0.0
6 0.0 0.0 0.0

Atoms

1 1 1 -0.200 -0.02278 -0.00141 2.06796 0 0 0
2 1 2 0.995 -0.00541 -0.00487 0.58446 0 0 0
3 1 3 -0.530 0.85023 -1.28996 0.02257 0 0 0
4 1 3 -0.530 -1.53630 -0.09799 -0.00465 0 0 0
5 1 3 -0.530 0.68952 1.37048 0.01425 0 0 0
6 1 4 0.370 2.26342 -1.48558 0.12856 0 0 0
7 1 4 0.370 -2.42794 -1.21044 0.11200 0 0 0
8 1 4 0.370 0.15962 2.69576 0.11022 0 0 0
9 1 5 -0.030 2.78148 -0.66030 -0.37144 0 0 0
10 1 5 -0.030 2.56224 -1.47844 1.18498 0 0 0
11 1 5 -0.030 -2.55165 -1.48181 1.16873 0 0 0
12 1 5 -0.030 -1.99728 -2.07364 -0.40664 0 0 0
13 1 5 -0.030 -0.79735 2.74105 -0.42044 0 0 0
14 1 5 -0.030 -0.02793 2.94788 1.16226 0 0 0
15 1 6 -0.210 2.62677 -2.81255 -0.51278 0 0 0
16 1 6 -0.210 -3.76774 -0.83529 -0.49492 0 0 0
17 1 6 -0.210 1.15405 3.66998 -0.49493 0 0 0
18 1 7 0.055 2.32929 -2.82035 -1.56376 0 0 0
19 1 7 0.055 3.70600 -2.98167 -0.45517 0 0 0
20 1 7 0.055 2.11870 -3.63627 -0.00588 0 0 0
21 1 7 0.055 -3.64574 -0.56246 -1.54553 0 0 0
22 1 7 0.055 -4.46400 -1.67670 -0.43248 0 0 0
23 1 7 0.055 -4.20402 0.01614 0.03264 0 0 0
24 1 7 0.055 1.34145 3.42046 -1.54170 0 0 0
25 1 7 0.055 0.76623 4.69162 -0.44473 0 0 0
26 1 7 0.055 2.10448 3.63271 0.04253 0 0 0

Bonds

1 1 1 2
2 2 2 3
3 2 2 4
4 2 2 5
5 3 3 6
6 3 4 7
7 3 5 8
8 4 6 9
9 4 6 10
10 4 7 11
11 4 7 12
12 4 8 13
13 4 8 14
14 5 6 15
15 5 7 16
16 5 8 17
17 6 15 18
18 6 15 19
19 6 15 20
20 6 16 21
21 6 16 22
22 6 16 23
23 6 17 24
24 6 17 25
25 6 17 26

Angles

1 1 1 2 3
2 1 1 2 4
3 1 1 2 5
4 2 2 3 6
5 2 2 4 7
6 2 2 5 8
7 3 3 6 9
8 3 3 6 10
9 3 4 7 11
10 3 4 7 12
11 3 5 8 13
12 3 5 8 14
13 4 9 6 15
14 4 10 6 15
15 4 11 7 16
16 4 12 7 16
17 4 13 8 17
18 4 14 8 17
19 5 9 6 10
20 5 11 7 12
21 5 13 8 14
22 6 6 15 18
23 6 6 15 19
24 6 6 15 20
25 6 7 16 21
26 6 7 16 22
27 6 7 16 23
28 6 8 17 24
29 6 8 17 25
30 6 8 17 26
31 7 18 15 19
32 7 19 15 20
33 7 18 15 20
34 7 21 16 22
35 7 22 16 23
36 7 21 16 23
37 7 24 17 25
38 7 25 17 26
39 7 24 17 26
40 8 3 2 4
41 8 4 2 5
42 8 3 2 5
43 9 3 6 15
44 9 4 7 16
45 9 5 8 17

Dihedrals

1 1 1 2 3 6
2 1 1 2 4 7
3 1 1 2 5 8
4 2 2 3 6 9
5 2 2 3 6 10
6 2 2 4 7 11
7 2 2 4 7 12
8 2 2 5 8 13
9 2 2 5 8 14
10 3 2 3 6 15
11 3 2 4 7 16
12 3 2 5 8 17
13 4 3 6 15 18
14 4 3 6 15 19
15 4 3 6 15 20
16 4 4 7 16 21
17 4 4 7 16 22
18 4 4 7 16 23
19 4 5 8 17 24
20 4 5 8 17 25
21 4 5 8 17 26
22 5 9 6 15 18
23 5 9 6 15 19
24 5 9 6 15 20
25 5 10 6 15 18
26 5 10 6 15 19
27 5 10 6 15 20
28 5 11 7 16 21
29 5 11 7 16 22
30 5 11 7 16 23
31 5 12 7 16 21
32 5 12 7 16 22
33 5 12 7 16 23
34 5 13 8 17 24
35 5 13 8 17 25
36 5 13 8 17 26
37 5 14 8 17 24
38 5 14 8 17 25
39 5 14 8 17 26
40 6 3 2 4 7
41 6 3 2 5 8
42 6 4 2 3 6
43 6 4 2 5 8
44 6 5 2 3 6
45 6 5 2 4 7

2

I am trying to use the class2 options in lammps-21Dec11 and receiving an
error message that reads: All dihedral coeffs are not set. I received a
similar message in the past for when I was adding angle_style class2 to my
molecule, and I discovered that it was caused by missing parameters in my
data.file. I had only specified the Angle Coeffs section, and neglected to
include the BondBond and BondAngle sections. After I added these, even when
all parameters for each type were set to 0.0, everything worked fine.

Now I am beginning to add in dihedral forces and I have specified the
coefficients in the Dihedral Coeffs, EndBondTorsion Coeffs,
MiddleBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, and
BondBond13 sections all as 0.0. Somehow, I get a message specifying that I
have not specified all dihedral coeffs in the data file. I have gone over
this again and again and can't seem to find the problem.

...and guess what? LAMMPS is correct. :wink:

have a look at the AngleAngleTorsion Coeffs section.
you are setting the value for type 2 twice and don't set
the one for type 3. given the large number of entries,
this can happen... perhaps, there was a piece of dirt
on you screen or your glasses. :wink:

The manual indicates that this is the correct format for specifying dihedral
coefficients, basically everything is included but the identifier (ex: "at",
"mbt") for each section.

yes. the format is correct. if the format was wrong, you would
get a different error message. the error message you see originates
from dihedral.cpp and not dihedral_class2.cpp

cheers,
     axel.