hello dear
this is my input script .should i use flux compensating. can anybody explain to me about flux compensator in my input script.i want to compute thermal conductivity and viscosity.
thankyou very much
variable T equal 298
variable V equal vol
variable dt equal .02 #.00000000002
variable x equal 23.41
variable y equal 23.41
variable rho equal 0.6
variable t equal 20
variable rc equal 2.5
variable p equal 200 # correlation length
variable s equal 2 # sample interval
variable d equal $p*$s # dump interval
convert from LAMMPS real units to SI
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23
variable atm2Pa equal 101325.0
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal {kCal2J}*{kCal2J}/{fs2s}/{A2m} #thermal conductivity
variable convert equal {atm2Pa}*{atm2Pa}{fs2s}*{A2m}{A2m}*{A2m} #*${kCal2J}
#set up problem
dimension 3
echo screen
boundary p p p
atom_style full
bond_style harmonic #hybrid harmonic
angle_style harmonic #hybrid harmonic
kspace_style pppm 1.0e-4
read_data water.data
group hydrogen type 1
group water type 1 2
group cu type 3
group oxygen type 2
lattice fcc 3.615 #Cu lattice constant
region Cu sphere 0 0 0 3 units box
create_atoms 3 region Cu
#set group oxygen charge -1.040 #???
#set group hydrogen charge .520 #???
#set group cu charge 0.000
pair_style hybrid lj/cut/coul/long 0.1521 3.157 eam lj/cut .583 #2.8 # 3.157 # 7.5 #@ 7
pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 #H-H epsilon sigm # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753 #O-H epsilon sigma
pair_coeff 1 3 lj/cut 0.6589 0.2117 #H-Cu epsilon sigma
pair_coeff 2 2 lj/cut/coul/long 0.1521 3.157 #O-O epsilon sigma # 0 0
pair_coeff 2 3 lj/cut 1.198 1.587 #O-Cu epsilon sigma
pair_coeff 3 3 eam cu.eam #Cu-Cu
for cu-cu bond sigma=.227 epsilon(Lj)=.583 ev # sigma=2.34 epsilon=9.4512 kcal/mol … cu eam cut off= 4.95 Ang
bond_coeff 1 450 0.9572 #O-H
angle_coeff 1 55 104.52 #H-O-H
++++++++++++++++setting+++++++++++++++++++++
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
min_modify dmax 0.01
minimize 1.0e-8 1.0e-5 1000 3000
timestep .00000000002 #${dt}
thermo $d
velocity all create 298 4928459 rot yes dist gaussian #23482341
fix 1 hydrogen shake 1e-6 500 0 m 1.0 a 1 #for hydrogen
fix 12 water npt temp 298 298 100.0 iso 0.0 0.0 1000.0
---------- Relaxation -----------------------------------------
minimization : avoid atoms overlapping
#min_style fire
#thermo_style custom step etotal enthalpy pe press ke
#thermo_modify flush yes
run 400
reset_timestep 0
#------------------------dump--------------------------------
#dump 1 all custom 10000 dump.equilibrium. id type x y z vx vy vz
settings
Green-Kubo viscosity calculation
Define distinct components of symmetric traceless stress tensor
variable pxy equal pxy
variable pxz equal pxz #-press
variable pyz equal pyz
fix SS all ave/correlate $s $p $d &
v_pxy v_pxz v_pyz type auto file S0St.dat ave running
v_pxy v_pxx type auto file profile.gk.3d ave running
Diagonal components of SS are larger by factor 2-2/d,
which is 4/3 for d=3, but 1 for d=2.
See Daivis and Evans, J.Chem.Phys, 100, 541-547 (1994)
#variable scale equal 1.0/$tvols*dt 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}
#*******************************#thermal conductivity
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom virial
compute flux all heat/flux myKE myPE myStress
variable Jx equal c_flux[1]/vol
variable Jy equal c_flux[2]/vol
variable Jz equal c_flux[3]/vol
fix JJ all ave/correlate $s $p d &
c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running
variable scale equal {convert}/${kB}/$T/$T/$Vs*{dt}
variable k11 equal trap(f_JJ[3]){scale}
variable k22 equal trap(f_JJ[4])*{scale}
variable k33 equal trap(f_JJ[5])${scale}
thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 # etotal enthalpy pe press ke # v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
thermo_modify flush yes
run 40000
variable k equal (v_k11+v_k22+v_k33)/3.0
variable ndens equal count(all)/vol
print “average conductivity: $k[W/mK] @ T K, {ndens} /A^3”
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”