Dear All,
I have lammps 29Sep21 installed.
I’m trying to calculate the thermal conductivity of my nanofluid using Green-Kubo method.
When I run my script I get this error “ERROR: Fix in variable not computed at compatible time (…/variable.cpp:4128)”.
I understand that this error has to do with frequency of output mismatch.
In my input script this is has to do with the dt and s variables.
If I do dt=10 and s=1 my simulation runs and I get rid from this error. However, it screws up my simulation because my time step needs to be 0.04
Do you know a work around or how I can fix this without changing my time step?
My input script looks like this:
------------------------ INITIALIZATION ----------------------------
units real
dimension 3
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
variable latparam equal 5.0553
variable T equal 300
variable V equal vol
variable dt equal 0.04
variable p equal 200 # correlation length
variable s equal 1 # sample interval
variable d equal $p*s # dump interval
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal {kCal2J}*{kCal2J}/{fs2s}/${A2m}
----------------------- ATOM DEFINITION ----------------------------
region whole block -50 50 -50 50 -50 50 units lattice
create_box 4 whole bond/types 9 angle/types 14 extra/bond/per/atom 9 extra/angle/per/atom 14 extra/special/per/atom 10
lattice fcc ${latparam} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
molecule ethylene_glycol lammps.data
create_atoms 0 region whole mol ethylene_glycol 52874 ratio 0.035 74637
region nanoparticle sphere 0 0 0 3.5 units lattice
lattice fcc ${latparam} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
create_atoms 4 region nanoparticle
mass 1 12.011 #O
mass 2 15.999 #C
mass 3 1.008 #H
mass 4 63.546 #Cu
------------------------ FORCE FIELDS ------------------------------
#pair_style hybrid eam/fs lj/cut 2.5
pair_style eam/fs
pair_coeff * * Mendelev_Cu2_2012.eam.fs NULL NULL NULL Cu
pair_style lj/cut 2.5
#pair_coef type_i type_j epsilon sigma rcut
pair_coeff * * 0.030 2.5 2.5 #all
pair_coeff 2 3 0.030 2.5 2.5 #H-C
pair_coeff 2 2 0.066 3.5 2.5 #C-C
pair_coeff 1 3 0.170 3.07 2.5 #O-H
pair_coeff 3 4 0.03396 1.335 2.5 #H-Cu
pair_coeff 1 4 0.06387 2.7172 2.5 #O-Cu
bond_coeff 1 268.0000 1.5290
bond_coeff 2 320.0000 1.4100
bond_coeff 3 320.0000 1.4100
bond_coeff 4 340.0000 1.0900
bond_coeff 5 340.0000 1.0900
bond_coeff 6 340.0000 1.0900
bond_coeff 7 340.0000 1.0900
bond_coeff 8 553.0000 0.9450
bond_coeff 9 553.0000 0.9450
angle_coeff 1 50.000 109.500
angle_coeff 2 50.000 109.500
angle_coeff 3 37.500 110.700
angle_coeff 4 37.500 110.700
angle_coeff 5 37.500 110.700
angle_coeff 6 37.500 110.700
angle_coeff 7 55.000 108.500
angle_coeff 8 55.000 108.500
angle_coeff 9 35.000 109.500
angle_coeff 10 33.000 107.800
angle_coeff 11 35.000 109.500
angle_coeff 12 35.000 109.500
angle_coeff 13 35.000 109.500
angle_coeff 14 33.000 107.800
info system
print “Finished INFO”
---------------------Minimization---------------------------
reset_timestep 0
minimize 1.0e-13 1.0e-12 1000 10000
print “Finished Minimizing”
---------------------EQUILIBRATION--------------------------
reset_timestep 0
timestep ${dt}
velocity all create 300.0 97563 mom yes rot no
fix 1 all nvt temp 300.0 300.0 $(100.0*dt) tchain 1
Set thermo output
thermo 1
thermo_style custom step lx ly lz press pxx pyy pzz pe temp
run 10
unfix 1
---------------------Production-----------------------------
reset_timestep 0
timestep ${dt}
velocity all create 300.0 54664 mom yes rot no
fix 1 all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0
Set thermo output
thermo 1
thermo_style custom step lx ly lz press pxx pyy pzz pe temp
run 10
unfix 1
------------Thermal_Conductivity_Calculation----------------
variable dt equal 10
reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom NULL 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 1
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
Run for at least 100 picosecond (assuming 0.04 fs timestep)
dump 1 all custom 1 dump.comp_*.dump mass type x y z
run 10
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”
