LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] msd calculation for WATER(SPC) Model
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] msd calculation for WATER(SPC) Model


From: "Chowdhury, Sanjib Chandra" <sanjib@...2437...>
Date: Fri, 6 Oct 2017 19:07:38 +0000

Why are you using ‘fix deform’ for MSD?

 

200 ps may be small. You could run for longer time even few ns.

 

From: sungpar@...4084... [mailto:sungpar@...4084...]
Sent: Friday, October 06, 2017 2:23 PM
To: lammps-users@lists.sourceforge.net <lammps-users@lists.sourceforge.net>
Subject: [lammps-users] msd calculation for WATER(SPC) Model

 

Dear all,

 

I want to calculate self diffusion coefficient for water model(SPC) it has 300 water molecule.

I know that I can calculate the diffusion coefficient by using Einstein relationship with MSD.

 

Experiment result is 2.3 E-09 m2/s (roughly), but my result is about 1/100 of the expected result.

 

I ran this model 100ps in npt to get equilibrium(save as write_restart) and ran 200ps more in nvt with read_restart command.

 

### Units

units                      real

### Resion

boundary                 p p p

### Force type

atom_style               full              

pair_style                 lj/cut/coul/cut 9 9

bond_style              harmonic

angle_style              harmonic

### Atom definition

read_data                data_300W.txt

velocity                   all create 300 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

fix                         1 all shake 1.0e-4 10 0 b 1 a 1

### Dynamic type

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

### Start running

run               100000

### Save the restart file

write_restart restart300W.txt

 

 

 

 

### Units

units                      real

### Resion

boundary                 p p p

### Force type

atom_style               full              

pair_style                 lj/cut/coul/cut 9 9

bond_style              harmonic

angle_style              harmonic

### Atom definition

read_restart              restart300W.txt

### 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

### Timestep

timestep                 1

### Fix molecular

fix                         1 all shake 1.0e-4 10 0 b 1 a 1

### Dynamic type

fix                         2 all deform 1 x final 0.0 20.992339 y final 0.0 20.992339 z final 0.0 20.992339

#fix                        3 all npt temp 298.15 298.15 100 iso 1 1 100

fix                          3 all nvt temp 298.15 298.15 100

#fix                        3 all nve

### Group

group                    ox type 1

### Compute

compute                  1 ox msd

#compute               2 all rdf 1000 1 1  # O-O

#compute               3 all rdf 1000 2 2  # O-H

#compute               4 all rdf 1000 1 2  # H-H

### Variable

variable  msd            equal c_1[4]

variable  fs               equal 1*step

variable  Temp          equal "temp"

variable  Vol              equal "vol"

variable  density         equal "density"

### Print results and make files

fix          7  all print 10  "${fs} ${msd}"        file water.msd      screen no

### Run a simulation

run               200000

 

 

 

 

Above are input file and result, MSD is too small than I expect. Can I have any suggestion ?

 

Thanks,