Dear lammps user’s
i try to compute thermal conductivity of ZnO system using the ReaxFF potential included in lammps distribution and i have used the script giving in the lammps manuals for Ar with some modifications:
the input file is the next:
units real
variable V equal vol
variable T equal 300
variable dt equal 0.5
variable p equal 200 # correlation length
variable s equal 10 # 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 A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal {kCal2J}*{kCal2J}/{fs2s}/{A2m}
setup problem
dimension 3
boundary p p p
atom_style charge
read_data data.ZnOH2
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.ZnOH O Zn
neighbor 0.5 bin
neigh_modify every 1 delay 0 check no
#timestep 0.5
timestep ${dt}
thermo 10
equilibration and thermalization
velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 60 drag 0.0
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c #param.qeq
run 2000
thermal conductivity calculation, switch to NVE if desired
#unfix NVT
#fix NVE all nve
reset_timestep 0
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/$V*s*{dt}
variable k11 equal trap(f_JJ[3]){scale}
variable k22 equal trap(f_JJ[4])*{scale}
variable k33 equal trap(f_JJ[5])${scale}
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 400000
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”
for equilibration part thereis no problem and the code run just fine however for the second part which is reserved to thermal conductivity computing the run stop with the next message:
ERROR: fix in variable not computed at compatible time (…/variable.cpp/3173)
so please if any one has a solution let me know
best regards