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This is my input file for the lammps simulation.

variable x equal 47.59
variable y equal 41.2141489661
variable z equal 136.636
variable t equal 300.0

#Setup parameters
units real
atom_style atomic
read_data atomic_structure_atomic
mass 1 16.0 #O in Al2O3
mass 2 27.0 #Al in Al2O3
mass 3 12.0 #C within one graphene layer
mass 4 12.0 #C within another graphene layer
velocity all create $t 87287

pair_style hybrid/overlay lj/cut 10.0 morse 2.5 tersoff shift -0.0462 kolmogorov/crespi/z 20.0
pair_coeff 1 1 lj/cut 0.194633996 3.541
pair_coeff 1 2 lj/cut 0.31351524159 4.02
pair_coeff 2 2 lj/cut 0.50500834301 4.499
pair_coeff 2 3 morse 0.4691 1.738 2.246
pair_coeff 2 4 morse 0.4691 1.738 2.246
pair_coeff * * tersoff ./Copt.tersoff NULL NULL C NULL
pair_coeff * * kolmogorov/crespi/z /public23/home/a21000018/lammps/lammps-2Aug2023/potentials/CC.KC NULL NULL C C
pair_coeff * * tersoff ./Copt.tersoff NULL NULL NULL C

neighbor 0.3 bin
neigh_modify delay 0 every 1

#layers for heat flux
region hot block INF INF INF INF 28.69356 41.810616
region cold block INF INF INF INF 96.32838 97.01156
compute Thot all temp/region hot
compute Tcold all temp/region cold

#1st equilibirum run
fix 1 all nvt temp $t $t 1.0
thermo 1
run 1000000
velocity all scale $t
unfix 1

#2nd equilibrium run
fix 1 all nve
fix hot all heat 1 400.0 region hot
fix cold all heat 1 -400.0 region cold
thermo_style custom step temp c_Thot c_Tcold
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold
thermo 1000
run 10000

#thermal conductivity calculation
compute ke all ke/atom
variable temp atom c_ke/1.5
compute layers all chunk/atom bin/1d z lower 1.0 units box
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.heat
variable tdiff equal f_2[20][3]-f_2[36][3]
fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000

variable kappa equal (400.0/(lx*ly)/2.0)*(lz/2.0)/f_ave
thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold &
              colname v_tdiff dTemp_step colname f_ave dTemp

run 200000
print "Running average thermal conductivity: $(v_kappa:%.4f)"

After I launched the calculation, lammps responded to me with the following error message:

LAMMPS (2 Aug 2023 - Update 1)
Reading data file ...
  triclinic box = (0 0 0) to (47.59 41.214149 136.636) with tilt (-23.795 0 0)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:220)
  2 by 2 by 8 MPI processor grid
  reading atoms ...
  19600 atoms
  read_data CPU = 0.092 seconds
Reading kolmogorov/crespi/z potential file /public23/home/a21000018/lammps/lammps-2Aug2023/potentials/CC.KC with DATE: 2017-02-28
WARNING: Converting kolmogorov/crespi/z potential in metal units to real units (../potential_file_reader.cpp:289)
ERROR on proc 0: All pair coeffs are not set (../pair_hybrid.cpp:716)
Last command: run 1000000
...

I had already set up the pairwise potentials between O-O, O-Al, Al-C, C-C within the same graphene layer and C-C on a different graphene layer. I do not understand why the error message popped up.

Would anyone please give me some suggestions/comments on my input file?

Thank you in advance.

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  • $\begingroup$ Each potential needs to be defined for all atoms, no? you can have separate cutoffs for the lj/cut as you do for the atoms you need, but I think there needs to be a default something for every atom. So see if it helps to add pair_coeff * * lj/cut 1 1 1 and something similar for the morse before defining atom-specific pair_coeffs for each pair of atoms. Note the third argument to lj/cut creates a pair-specific cutoff, which at 1 Å would be intentionally too short to ever matter: it functions as a placeholder. $\endgroup$ Commented Apr 14 at 13:42
  • $\begingroup$ @Thank you for your suggestions. I will revise this part in the potential settings. $\endgroup$
    – Kieran
    Commented Apr 15 at 14:17

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