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[lammps-users] Benzene fix rigid
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[lammps-users] Benzene fix rigid


From: <sungpar@...4084...>
Date: Mon, 9 Oct 2017 13:39:57 -0400

Dear lammps users,

 

I am trying to simulate Benzene molecule (only one).

I know that I can use ‘fix shake’ command for molecule within 4 atoms.

So, I am trying to use ‘fix rigid’ command to fix atoms of benzene.

But, I cant hold benzene ( it moves differently, not together).

Any suggesiton ?

 

Thanks,

 

### Units

 

units                    real

 

### Resion

 

boundary              p p p

 

### Force type

 

atom_style            full              

pair_style              lj/cut/coul/cut 9 12

bond_style              harmonic

angle_style              harmonic

dihedral_style          harmonic

improper_style         cvff

 

### Atom definition

 

read_data              data_1Benzene.txt

velocity                all create 298.15 8343 dist gaussian units box

 

### Neighbor list

 

neighbor               2.0 bin

neigh_modify          every 10 delay 0 check yes

 

### Calculation

 

thermo_style          custom step pe ke etotal temp press vol density

thermo                  10

 

### Minimization

 

minimize               1.0e-5 1.0e-7 1000 100000

 

### Timestep

 

timestep                1

 

### Fix molecular

 

group  Benzene  type 1 2

fix                         1 Benzene rigid molecule

 

### Dynamic type

 

fix                       2 all npt temp 298.15 298.15 100 iso 1 1 100

 

### Variable

 

variable fs equal 1*step

variable density equal "density"

variable vol equal "vol"

 

### Print density

 

fix                         3 all print 10 "${fs} ${density}"    file fsDensity.txt         screen no

fix                         4 all print 10 "${fs} ${vol}"    file fsVol.txt         screen no

 

### Dump

 

dump               1 all xyz 10 dump.xyz

dump_modify    1 element C H

 

### Start running

 

run              10000

 

### Save the restart file

 

write_restart restart1Benzene.txt