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


From: Stefan Paquay <stefanpaquay@...24...>
Date: Mon, 9 Oct 2017 13:47:26 -0400

You cannot minimize rigid objects with minimize. It will not respect the constraints and the atoms can freely move away from each other. If you need to minimize, you can use bond and angle potentials to keep them in place.

On Mon, Oct 9, 2017 at 1:39 PM, <sungpar@...4084...> wrote:

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

 

 

 

 

 


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