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