Re: [lammps-users] Green-Kubo method for calculating viscosity

Dear Smith,

Thanks for your answer.

It seems that the calculated viscosity is quite dependent on the value of correlation length. Of course, correlation length should affect convergence of the computed viscosity. But I think that it's effect on my results is abnormal. for example, if I reduce correlation length from 400 to 100, the calculated viscosity reduces from about 0.00082 pa.s to about 0.00037 pa.s. It is while the correlation values obtained for off-diagonal elements of the stress tensor do not show a significant change. Is it normal?

It should be noted that I have reduced my time step to 2.0 fs now, that is the appropriate time step in presence of water molecules.

Best,

Majid

From: "Smith, Micholas D." <smithmd@...79...>
To: "majid-rezaei" <majid-rezaei@...3054...>, "lammps-users" <lammps-users@lists.sourceforge.net>
Sent: Monday, June 19, 2017 2:06:06 PM
Subject: Re: Green-Kubo method for calculating viscosity

Viscosity estimates are known to have difficulty converging. You may need to run multiple short runs once the system is at equilibrium and compute the average viscosity from these instead of a single correlation measurement.

See:

Yong Zhang, Akihito Otani, and Edward J. Maginn. "Reliable Viscosity Calculation from Equilibrium Molecular Dynamics Simulations: A Time Decomposition Method" JCTC

for suggested best-practicies

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: Majid Rezaei <majid-rezaei@...12...3054...>
Sent: Monday, June 19, 2017 6:45 AM
To: lammps-users@lists.sourceforge.net
Subject: [lammps-users] Green-Kubo method for calculating viscosity

Dear all,

I use the following Green-Kubo formulation to calculate viscosity of water and NaCl. It seems that it works good. However, when I run the job twice, I obtain different viscosities (the difference is in order of 0.00007 Pa.s which is not negligible). I checked my results and found that this conflict comes from the difference appeared in variable V11 (the other variables are almost the same).

Could you please help me to find the problem?

Best,

Majid

units real

variable T equal 300

variable V equal vol

variable dt equal 4.0

variable p equal 400 # correlation length

variable s equal 5 # sample interval

variable d equal $p*$s # dump interval

variable kB equal 1.3806504e-23 # [J/K/** Boltzmann

variable atm2Pa equal 101325.0

variable A2m equal 1.0e-10

variable fs2s equal 1.0e-15

variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}

dimension 3

boundary p p p

atom_style full

bond_style harmonic

angle_style harmonic

pair_style lj/cut/coul/long 11.0

kspace_style pppm 1e-4

read_data data.1

pair_coeff 1 1 0.0 0.0

pair_coeff 2 2 0.155 3.17

pair_coeff 3 3 0.106 4.45

pair_coeff 4 4 0.0148 2.58

pair_modify mix geometric

bond_coeff 1 1000.0 1.0

angle_coeff 1 100.0 109.47

special_bonds lj/coul 0.0 0.0 0.5

min_style cg

minimize 0 1.0e-6 100 1000

timestep ${dt}

thermo $d

velocity all create $T 102486 mom yes rot yes dist gaussian

fix NVT all nvt temp $T $T 10 drag 0.2

fix 66 all shake 0.0001 20 0 b 1 a 1

run 1000000

reset_timestep 0

variable pxy equal pxy

variable pxz equal pxz

variable pyz equal pyz

fix SS all ave/correlate $s $p $d &

v_pxy v_pxz v_pyz type auto file S0St.dat ave running

variable scale equal ${convert}/(${kB}*$T)*$V*$s*${dt}

variable v11 equal trap(f_SS[3])*${scale}

variable v22 equal trap(f_SS[4])*${scale}

variable v33 equal trap(f_SS[5])*${scale}

thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33

run 5000000

variable v equal (v_v11+v_v22+v_v33)/3.0

variable ndens equal count(all)/vol

print "average viscosity: $v [Pa.s] @ $T K, ${ndens} /A^3"

From:	Majid Rezaei <majid-rezaei@...3054...>
Date:	Tue, 20 Jun 2017 19:27:02 +0430 (IRDT)