ERROR: All angle coeffs are not set

Hi,

I’m Ashok Kumar Bevara, working on Nanoindentation of reinforced CNT.

please help me with ERROR : All angle coeffs are not set

i did check mailing list, but unable to clear this error.

My restart file:

#indentation of a CNT POLYMER by a virtual spherical indenter with Mishin potential - molecular dynamics

echo both

read_restart restart.200000
neighbor 2.0 bin
neigh_modify delay 1

#potentials
pair_style lj/class2 10.0
bond_style class2
angle_style class2
dihedral_style class2
pair_modify mix sixthpower
special_bonds lj/coul 0 1 1 extra 2000

pair_coeff 1 1 0.24 3.32 15 #o_2
pair_coeff 2 2 0.068 3.915 15 #c3a
pair_coeff 3 3 0.023 2.878 15 #h1
pair_coeff 4 4 0.054 4.01 15 #c
pair_coeff 5 5 0.02 2.995 15 #h
pair_coeff 6 6 0.096 3.32 15 #n2
pair_coeff 7 7 0.062 3.854 15 #c4
pair_coeff 8 8 0.096 3.32 15 #n2
pair_coeff 9 9 0.096 3.32 15 #n2

#read_data angle_coeff.txt

bond_coeff 1 1.4098 387.912 -715.919 660.244 #o_2-cp
bond_coeff 2 1.4457 326.727 -608.531 689.033 #o_2-c
bond_coeff 3 1.4170 470.836 -627.618 1327.63 #c3a-c3a
bond_coeff 4 1.0982 327.825 -803.453 894.317 #c3a-h1
bond_coeff 5 1.5010 321.902 -521.821 572.163 #c3a-c4
bond_coeff 6 1.1010 345.000 -691.890 844.600 #c4-h1
bond_coeff 7 1.1010 345.000 -691.890 844.600 #c4-h1
bond_coeff 8 1.4098 387.912 -715.919 660.244 #o_2-cp
bond_coeff 9 1.5300 299.670 -501.770 679.810 #c4-c4
bond_coeff 10 1.4457 326.727 -608.531 689.033 #0_2-c
bond_coeff 11 0.9520 534.299 -1287.19 1889.14 #o_2-h1
bond_coeff 12 1.4000 350.000 0.0000 0.0000 #c3a-n2
bond_coeff 13 1.0310 540.112 -1500.3 2431.01 #h1-n2
bond_coeff 14 1.4457 326.727 -608.531 689.033 #same as 10 used for bond break
bond_coeff 15 1.474 337.060 -147.370 213.633 #bond creation c4-n2
bond_coeff 16 0.9520 534.299 -1287.19 1889.14 #bond creation o_2-h1

angle_coeff 1 113.07 47.1131 -32.5592 13.1257 #c_1-o_2-cp
angle_coeff 2 117.14 33.0391 -14.7808 3.8573 #o_2-cp-cp
angle_coeff 3 118.90 61.0226 -34.9931 0.0000 #c3a-c3a-c3a
angle_coeff 4 117.94 35.1558 -12.46.82 0.000 #c3a-c3a-h1
angle_coeff 5 120.05 44.7148 -22.7352 0.0000 #c3a-c3a-c4
angle_coeff 6 111.00 44.3234 -9.44554 0.0000 #c3a-c4-c3a
angle_coeff 7 108.40 43.9594 -8.39240 -9.3379 #c3a-c4-c4
angle_coeff 8 107.66 39.6410 -12.9210 -2.4318 #h1-c4-h1
angle_coeff 9 120.05 44.7148 -22.7352 0.0000 #c3a-c3a-c4
angle_coeff 10 117.14 33.0391 -14.7808 3.8573 #o_2-cp-cp
angle_coeff 11 107.41 63.3907 -13.4513 1.665 #o_2-c-c
angle_coeff 12 107.688 65.4801 -10.3498 5.8866 #o_2-c-h
angle_coeff 13 110.77 41.4530 -10.6040 5.1290 #c4-c4-h1
angle_coeff 14 112.67 39.516 -7.443 -9.5583 #c4-c4-c4
angle_coeff 15 107.41 63.3907 -13.4517 1.665 #0_2-c-c
angle_coeff 16 112.874 53.2512 -14.9979 2.464 #c_1-o_2-h1
angle_coeff 17 117.317 55.242 0.000 0.0000 #c4-c4-n2
angle_coeff 18 117.200 37.262 0.000 0.0000 #c4-n2-h1
angle_coeff 19 110.91 31.0910 0.000 0.0000 #h1-n2-h1
angle_coeff 20 108.4 43.9594 -8.3924 -9.3379 #c3a-c4-c4
angle_coeff 21 107.499 62.731 0.000 0.000 #h1-c4-n2

dihedral_coeff 1 -1.1077 0.0 2.0082 0.0 0.000 0.0 #cp-c_1-o_2-c
dihedral_coeff 2 0.0000 0.0 0.0000 0.0 -0.1932 0.0 #c_1-o_2-c-c
dihedral_coeff 3 0.0000 0.0 0.0000 0.0 -0.1932 0.0 #c_1-o_2-c-h
dihedral_coeff 4 0.0000 0.0 2.5372 0.0 0.0000 0.0 #o_2-cp-cp-cp
dihedral_coeff 5 0.0000 0.0 2.167 0.0 0.0000 0.0 #o_2-cp-cp-h
dihedral_coeff 6 8.3667 0.0 1.200 0.0 0.0000 0.0 #c3a-c3a-c3a-c3a
dihedral_coeff 7 0.0000 0.0 3.9661 0.0 0.000 0.0 #c3a-c3a-c3a-h1
dihedral_coeff 8 0.0000 0.0 3.9661 0.0 0.000 0.0 #h1-c3a-c3a-c3a
dihedral_coeff 9 0.0000 0.0 2.3500 0.0 0.000 0.0 #h1-c3a-c3a-h1
dihedral_coeff 10 0.000 0.0 4.4072 0.0 0.000 0.0 #c3a-c3a-c3a-c4
dihedral_coeff 11 0.000 0.0 1.5590 0.0 0.000 0.0 #c4-c3a-c3a-h1
dihedral_coeff 12 0.000 0.0 4.4072 0.0 0.000 0.0 #c4-c3a-c3a-c3a
dihedral_coeff 13 0.000 0.0 1.5590 0.0 0.000 0.0 #c4-c3a-c3a-h1
dihedral_coeff 14 -0.2808 0.0 -0.0678 0.0 -0.0122 0.0 #c3a-c3a-c4-c3a
dihedral_coeff 15 -0.2808 0.0 -0.0678 0.0 -0.0122 0.0 #c3a-c3a-c4-h1
dihedral_coeff 16 -0.2808 0.0 -0.0678 0.0 -0.0122 0.0 #c3a-c3a-c4-c3a
dihedral_coeff 17 -0.2808 0.0 -0.0678 0.0 -0.0122 0.0 #c3a-c3a-c4-h1
dihedral_coeff 18 0.0000 0.0 2.5372 0.0 0.000 0.0 #o_2-cp-cp-cp
dihedral_coeff 19 0.0000 0.0 2.1670 0.0 0.000 0.0 #h-cp-cp-o_2
dihedral_coeff 20 0.0000 0.0 0.000 0.0 0.000 0.0 #not used
dihedral_coeff 21 0.0000 0.0 0.000 0.0 -0.250 0.0 #o_2-c-c-c
dihedral_coeff 22 0.0000 0.0 0.000 0.0 0.000 0.0 #OHp-CT-CT-OS, not found
dihedral_coeff 23 0.0000 0.0 0.000 0.0 -0.25 0.0 #o_2-c-c-h
dihedral_coeff 24 0.0000 0.0 0.0316 0.0 -0.1681 0.0 #c4-c4-c4-h1
dihedral_coeff 25 0.0000 0.0 0.0000 0.0 -0.250 0.0 #o_2-c-c-h
dihedral_coeff 26 -0.1432 0.0 0.0617 0.0 -0.153 0.0 #h1-c4-c4-h1
dihedral_coeff 27 0.0000 0.0 0.0316 0.0 -0.1681 0.0 #c4-c4-c4-h1
dihedral_coeff 28 -1.1077 0.0 2.0082 0.0 0.0000 0.0 #cp-c_1-o_2-h1
dihedral_coeff 29 0.0000 0.0 0.0000 0.0 0.0000 0.0 #HO-OS-CT-HC~1, not found
dihedral_coeff 30 0.0970 0.0 0.072 0.0 -0.258 0.0 #c4-c4-c4-n2
dihedral_coeff 31 0.0970 0.0 0.072 0.0 -0.258 0.0 #c4-c4-c4-n2
dihedral_coeff 32 0.0970 0.0 0.072 0.0 -0.258 0.0 #c4-c4-c4-n2
dihedral_coeff 33 0.0970 0.0 0.072 0.0 -0.258 0.0 #c4-c4-c4-n2
dihedral_coeff 34 0.0000 0.0 1.000 0.0 0.0000 0.0 #-c3a-n2-
dihedral_coeff 35 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 #c3a-c3a-c4-c4
dihedral_coeff 36 -0.0228 0.0 0.028 0.0 -0.1863 0.0 #c3a-c-c-h1
dihedral_coeff 37 -0.151 0.0 0.001 0.0 -0.186 0.0 #h1=c4-c4-n2
dihedral_coeff 38 0.0 0.0 0.0 0.0 0.0 0.0 #n2-c4-c4-

#Shrinking the box before curing polymer
compute new all temp/com
velocity all create 600.0 862075 temp new
thermo 1000
thermo_modify temp new

min_style cg

#Output
#dump 1 all cfg 1 Dump_*.txt mass type xs ys zs
#minimize 1.0e-5 1.0e-7 1000 1000
#undump 1

#seperate group for polymer molecules during box change
group 1 molecule 1:1668

restart 10000 restart.*

#setting up force field to keep polymer from running into CNT

fix 11 1 indent 50.0 cylinder z 0.0 0.0 11.0

timestep 0.05

fix 7 all nvt temp 300.0 300.0 0.05

reset_timestep 0

fix 2 all deform 10 x final -140.0 140.0 y final -140.0 140.0 units box
minimize 1.0e-5 1.0e-7 1000 1000
run 6670000
unfix 2

reset_timestep 100

fix 9 all deform 11 x final -130.0 130.0 y final -130.0 130.0 units box
minimize 1.0e-5 1.0e-7 1000 1000
run 7140000
unfix 9

reset_timestep 1000

fix 20 all deform 10 x final -120.0 120.0 y final -120.0 120.0 units box
minimize 1.0e-5 1.0e-7 1000 1000
run 7690000
unfix 20

reset_timestep 10000

fix 90 all deform 11 x final -110.0 110.0 y final -110.0 110.0 units box
minimize 1.0e-5 1.0e-7 1000 1000
run 8330000
unfix 90

reset_timestep 10000

fix 21 all deform 11 x final -100.0 100.0 y final -100.0 100.0 units box
minimize 1.0e-5 1.0e-7 1000 1000
run 9090000
unfix 21

rest_timestep 100000

fix 91 all deform 11 x final -90.0 90.0 y final -90.0 90.0 units box
minimize 1.0e-5 1.0e-7 1000 1000
run 10000000
unfix 91

reset_timestep 1000000

fix 22 all deform 10 x final -80.0 80.0 y final -80.0 80.0 units box
minimize 1.0e-5 1.0e-7 1000 1000
run 11100000
unfix 22

reset_timestep 10000000

fix 92 all deform 11 x final -75.0 75.0 y final -75.0 75.0 units box
minimize 1.0e-5 1.0e-7 1000 1000
run 6250000
unfix 92

#regions for pull out
region 2 block INF INF INF -30 INF INF
group frozen region 2
group mobile subtract all frozen

#Bond creation
#velocities
compute new mobile temp/com
velocity all create 1200.0 862075 temp new
reset_timestep 0

timestep 0.0005
thermo 1000
thermo_modify temp new

fix 1 all nvt temp 600.0 600.0 0.05 drag 1.5

fix 4 all bond/create 100 9 7 3.0 15
fix 5 all bond/create 100 6 7 3.0 15
fix 6 all bond/create 100 1 5 2.5 16 prob 0.5 12374

restart 10000 restart

run 2000

unfix 1
unfix 4
unfix 5
unfix 6

#Nanoindentation

#initial
fix 1 frozen setforce 0.0 0.0 0.0

thermo 1000

compute 30 all ke/atom
compute 40 all pe/atom pair

#energy minimization

write_restart restart.relax

#velocities
velocity mobile create 300.0 482748 temp new
reset_timestep 0

thermo_modify temp new

fix 5 all nvt temp 300.0 300.0 0.05

variable y equal 91-0.01dtstep
fix 3 all indent 10 sphere 0 v_y 0 50 units box
compute stress mobile stress/atom NULL ke pair

fix dump mobile ave/spatial 5000 1 5000 y lower 70 c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] file stress.dat units lattice

dump 1 all cfg 10000 dump_centro_.txt mass type xs ys zs c_30 c_40
dump 2 all cfg 10000 dump_stress_
.txt mass type xs ys zs c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
restart 100000 restart

#deformation
run 3000000

Thanks in advance

Ashok Kumar Bevara

Hi,

I'm Ashok Kumar Bevara, working on Nanoindentation of reinforced CNT.
please help me with ERROR : All angle coeffs are not set
i did check mailing list, but unable to clear this error.

with class2 angles and dihedrals you need to provide three sets of
coefficients for angles and six sets for dihedrals:

you only have one set for each in your input below. please check out
the documentation of them (again).

http://lammps.sandia.gov/doc/angle_class2.html
http://lammps.sandia.gov/doc/dihedral_class2.html

Hi everyone,

Greetings!

First, thanks to Mr. Kohlmeyer for last mail reply.

(for the same file which i copied in above mail)

I have been trying to keep final temperature between 0 t0 300, but its varying between 0 to 1000 few times little above the 1000
I tried several ways by varying drag coefficient and damping parameter ( temperature) but getting same values.
Plz help me with this

Thanks in advance,

Ashok Kumar Bevara

Hi everyone,

Greetings!

First, thanks to Mr. Kohlmeyer for last mail reply.

(for the same file which i copied in above mail)
I have been trying to keep final temperature between 0 t0 300, but its
varying between 0 to 1000 few times little above the 1000
I tried several ways by varying drag coefficient and damping parameter (
temperature) but getting same values.

this is likely due to bad parameters, bad input, or a bad model or a
combination of it.
your input is horribly complex and quite a bit of it doesn't make too
much sense without context.

i would suggest to start with constructing a simple system and without
any of the manipulations and see, if you can get a meaningful
simulation going.

axel.