hi
i am a newcomer and run lammps on a windows machine.
i have been trying to conduct a simulation of water molecules movement in scnt.
So far i have exported the phisical model from MS via msi2lmp.exe.
I came across this problem "Bond/angle/dihedral extent > half of periodic box length ", i reset a smaller timestep .
But later i came across another error“ Bond atoms 53 54 missing on pro at step 6427”.
can u help me with that? i have been working on this problem for several days but i didn’t work.
in and data profiles are attached.
best wishes!
stephen
Chongqing university
Chongqing,China.
IN profile
units real
timestep 0.01
atom_style full
dimension 3
boundary p p p
read_data Layer_dis1712.data
pair_style lj/cut/coul/long 10 8
bond_style hybrid harmonic morse
angle_style hybrid harmonic cosine/squared
dihedral_style harmonic
pair_coeff 1 1 0.1051 3.851
pair_coeff 1 2 0.1051 3.851
pair_coeff 1 3 0.0749 0.3190
pair_coeff 2 2 0.1051 3.851
pair_coeff 2 3 0.0749 0.3190
pair_coeff 3 3 0.1554 3.166
pair_coeff * 3 0 0
pair_coeff * 4 0 0
#pair_coeff 1 2 0.07958 -0.8476 0.4238
bond_coeff * morse 114.46 2.1867 1.418
bond_coeff 4 harmonic 0.0 1.0
#special_bonds lj 0 0 0
angle_coeff * cosine/squared 67.2 120
angle_coeff 4 harmonic 0.0 109.47
dihedral_coeff * 3 -1 2
pair_modify tail yes
kspace_style pppm 1.0e-4
neighbor 3.0 bin
neigh_modify delay 0 every 1 check yes
group rightgra id <> 1 200
group leftgra id <> 1521 1720
group cnt id <> 201 1520
group water type 3 4
thermo 10
thermo_style custom temp press
dump 1 all atom 100 scnt.lammpstrj
dump 2 water atom 100 water.lammpstrj
dump 3 cnt atom 100 cnt.lammpstri
dump 4 rightgra atom 100 rightgra.lammpstrj
dump 5 cnt custom 1000 cnt.lammpstrj id type x y z vx vy vz
velocity cnt create 100.0 4928459 rot yes dist gaussian
#fix 1 cnt momentum 1 linear 1 1 1 # 保持碳管整体不动
velocity cnt set 0.0 0.0 0.0
fix 1 cnt setforce 0.0 0.0 0.0
fix 2 rightgra move linear 0 0 0.2 units box # 右边的向左运动
fix 3 leftgra momentum 1 linear 1 1 1 # 左边的不动
fix 4 cnt nvt temp 100. 100. 0.1 # 温度100K
fix 5 rightgra nve
#The atoms affected by this fix should not normally be time
#integrated by other fixes (e.g. fix nve, fix nvt), since that will change their positions and velocities twice.
fix 6 leftgra nve
run 50000
unfix 2
unfix 3
unfix 4
unfix 5
unfix 6
velocity cnt create 10.0 4928459 rot yes dist gaussian
fix 4 cnt nvt temp 100. 100. 0.01
run 100000 # done !
#碳管
thermo 1000
dump 6 cnt atom 100 cnt.lammpstrj
data profile
(too big to attched)
LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for Layer_dis1712
6856 atoms
5984 bonds
6792 angles
10100 dihedrals
1680 impropers
4 atom types
4 bond types
4 angle types
5 dihedral types
2 improper types
0.029941553 24.629941553 xlo xhi
-0.098447161 24.501552839 ylo yhi
0.393039334 108.873039334 zlo zhi
Masses
1 12.011150 # cp
2 12.011150 # c
3 15.999400 # o*
4 1.007970 # h*
Atoms
1 1 1 0.000000 24.600000000 0.000000000 2.046014978 -1 0 0 # cp
2 1 1 0.000000 0.819999640 1.639999280 2.046014978 0 0 0 # cp
3 1 1 0.000000 2.459998920 0.000000000 2.046014978 0 0 0 # cp
4 1 1 0.000000 3.279998560 1.639999280 2.046014978 0 0 0 # cp
5 1 1 0.000000 4.919997841 0.000000000 2.046014978 0 0 0 # cp
6 1 1 0.000000 5.739997481 1.639999280 2.046014978 0 0 0 # cp
7 1 1 0.000000 7.379996761 0.000000000 2.046014978 0 0 0 # cp
8 1 1 0.000000 8.199996401 1.639999280 2.046014978 0 0 0 # cp
9 1 1 0.000000 9.839995681 0.000000000 2.046014978 0 0 0 # cp
10 1 1 0.000000 10.659995322 1.639999280 2.046014978 0 0 0 # cp
11 1 1 0.000000 12.299994602 0.000000000 2.046014978 0 0 0 # cp
12 1 1 0.000000 13.119994242 1.639999280 2.046014978 0 0 0 # cp
13 1 1 0.000000 14.759993522 0.000000000 2.046014978 0 0 0 # cp
14 1 1 0.000000 15.579993162 1.639999280 2.046014978 0 0 0 # cp
15 1 1 0.000000 17.219992443 0.000000000 2.046014978 0 0 0 # cp
16 1 1 0.000000 18.039992083 1.639999280 2.046014978 0 0 0 # cp
…