Here is my Lammps Data file.
LAMMPS Description
3 atoms
2 bonds
0 angles
0 dihedrals
0 impropers
1 atom types
1 bond types
-250.0 250.0 xlo xhi
-250.0 250.0 ylo yhi
-250.0 250.0 zlo zhi
Masses
1 116.0
Atoms
1 1 1 0.0 0.0 0.0 0.0
2 1 1 0.0 3.0 0.0 0.0
3 1 1 0.0 2.0 3.0 0.0
Bonds
1 1 1 2
2 1 2 3
So as you can see I have two bonds between 1-2 and 2-3. So 1-3 must be treated as a pair not a bond.
My Forcefield file is:
pair_style lj/cut 10.5
pair_coeff 1 1 0.6 3.8 10.5
bond_style harmonic
bond_coeff 1 10.0 3.8
So before simulation has been started, the total bond energy ebond will be 10.466898. And total pair energy evdwl has to be (from 1-3 contribution only) 1.2185494.
Here is the glimpse of my lammps input file:
units real
atom_style full
dimension 3
boundary p p p
read_data lmpsIPdata.data
include fffile.input
#minimize 1e-12 1e-10 1000 100000
neighbor 3.5 bin
neigh_modify every 10 delay 0 check yes
#define initial velocities
velocity all create 84 8728756
#thermo
thermo_style custom step temp ebond evdwl pe ke etotal lx ly lz
thermo 10000
Define fixes
fix 1 all nve
fix 2 all langevin 300 300 50000.0 548669595
Output settings
dump 1 all custom 1000 polysimu.lammpstrj id type xu yu zu
dump_modify 1 sort id
timestep 10
run 500000
But as I can see no pair calculation is being done. Total potential energy is just the bond energy. What may be the problem?
the glimpse of the log file is as follows:
…
…
timestep 10
run 500000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info …
update: every = 10 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5
ghost atom cutoff = 11.5
binsize = 5.75, bins = 87 87 87
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.156 | 9.156 | 9.156 Mbytes
Step Temp E_bond E_vdwl PotEng KinEng TotEng Lx Ly Lz
0 84 10.466898 0 10.466898 0.50077609 10.967674 500 500 500
10000 129.89372 0.18859904 0 0.18859904 0.77437703 0.96297607 500 500 500
Please correct me.