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[lammps-users] problem with calculating viscousity
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[lammps-users] problem with calculating viscousity

From: ‪Alireza Shadloo‬ ‪ <alirezashadloo@...16...>
Date: Sun, 20 May 2018 16:13:20 +0000 (UTC)

dear all
I am new in lammps and i try to calculate the viscousity of water molecular (spce) confined between two harmonic walls. in lammps manual,  a Sample LAMMPS input script has been written for viscosity of liquid Ar. so i tried to modify this code for my simulation. so my lammps input script is:

variable  T equal 300
variable  V equal vol
variable  dt equal 1
variable  p equal  400
variable  s equal  5
variable  d equal $p*$s

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

variable   A2m equal 1.0e-10
variable   fs2s equal 1.0e-15
variable  atm2Pa equal 101325.0
variable   convert2 equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}
dimension    3


 velocity    all  create  $T 34387 rot yes dist gaussian
fix         55 up-wall nvt temp $T $T 10
fix         5 down-wall nvt temp $T $T 10
fix         4 spce nve
fix         7 spce temp/rescale 100 $T $T 0.02 1.0
fix         77
up-wall temp/rescale 100 $T $T 0.02 1.0
fix         777
down-wall temp/rescale 100 $T $T 0.02 1.0  
timestep    ${dt}

thermo        $d
thermo_style custom step temp pe  ke etotal enthalpy press vol ebond  ecoul eangle
 run        20000

variable  pxy equal pxy

variable   pxz equal pxz

variable   pyz equal pyz

fix    SS spce ave/correlate $s $p $d  v_pxy v_pxz v_pyz type auto file S0St.dat ave running

variable   scale2 equal ${convert2}/(${kB}*$T)*$V*$s*${dt}

variable  v11 equal trap(f_SS[3])*${scale2}

variable   v22 equal trap(f_SS[4])*${scale2}

variable    v33 equal trap(f_SS[5])*${scale2}

thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
run   10000

variable   v equal (v_v11+v_v22+v_v33)/3.0
variable  ndens equal count(spce)/vol

variable  k equal (v_k11+v_k22+v_k33)/3.0

variable   ndens equal count(spce)/vol

print  "average viscosity: $v [Pa.s/ @ $T K, ${ndens2} /A^3"

my problem is pxy,pxz and pyz. because i think these values are for all atoms (both wall and water molecules) and i just want to calculate the viscousity of water molecule (no walls).
how can i calculate the pxy pxz and pyz just for water (no water+wall)??

can i use compute stress/atom command instead?? if yes how should i modify the fix ave/correlate???
can i use the flowing code??
compute mystress spce stress/atom

fix    SS spce ave/correlate $s $p $d  c_mysterss[4]  c_mysterss[5]  c_mysterss[6]  type auto file S0St.dat ave running