A strange phenomena simulated in an equilibrium system

LAMMPS LAMMPS General Discussion
1

Hi, all,

I am simulating an equilibrium system of high-density polymers. The simulation involves an initial relaxation in the NPT ensemble, followed by running it in the NVT ensemble. However, when I utilize the visualization software, I observe an unusual directional flow trend among the atoms. Could you please tell me how can I solve this problem or what might be causing the problem? Attached below is the code from my input file:


dimension          3
boundary           p p p
atom_style         full
atom_modify        map array  
units              lj
read_data          D11N1000l16.data

# potentials
pair_style        lj/cut 2.5 
pair_coeff        * * 1.0 1.0 2.5
bond_style        fene 
bond_coeff        1 30.0 1.5 1.0 1.0
special_bonds     fene 
angle_style       cosine 
angle_coeff       1 0.75

# define groups
group             seg type 1
group             nr type 2
fix               777 nr setforce 0.0 0.0 0.0
minimize          1e-10 1e-10 10000 10000
reset_timestep    0
neighbor          0.3 bin
neigh_modify      every 1 delay 0 check yes
unfix             777
velocity          all create 1.0 4928459  mom yes rot yes dist gaussian
fix               1 nr rigid single
fix               2 seg npt temp 1.0 1.0 10 iso 0.0 0.0 100

# Run
thermo		       100
timestep          0.01
run               1000000

unfix              2    
fix               4 seg nvt temp 1.0 1.0  10
dump            	1 all atom 500000 long.xyz
timestep          0.01
run              100000000

Thanks,
Jessica

2

Could you post some snapshots of your system? It’s hard to know what’s going on from just the input script.

3

Sounds like the flying ice cube effect.

1 Like
4

As an initial observation your NPT time constants seem a bit too large for comfort. You can often start with temperature time constant at 100x the timestep and barostat time constant at 1000x. Your values are ten times larger.

5

图片1

The trajectory line is shown in the figure, where periodic boundary conditions are used.

6

The question had never been thought of before. If so, how can I solve this problem? Really appreciate the help!

7

Thank you for your reply.

I have changed NPT time constants before, but it doesn’t seem to work.