This is my input file for the lammps simulation.
variable x equal 47.59variable y equal 41.2141489661variable z equal 136.636variable t equal 300.0#Setup parametersunits realatom_style atomicread_data atomic_structure_atomicmass 1 16.0 #O in Al2O3mass 2 27.0 #Al in Al2O3mass 3 12.0 #C within one graphene layermass 4 12.0 #C within another graphene layervelocity all create $t 87287pair_style hybrid/overlay lj/cut 10.0 morse 2.5 tersoff shift -0.0462 kolmogorov/crespi/z 20.0pair_coeff 1 1 lj/cut 0.194633996 3.541pair_coeff 1 2 lj/cut 0.31351524159 4.02pair_coeff 2 2 lj/cut 0.50500834301 4.499pair_coeff 2 3 morse 0.4691 1.738 2.246pair_coeff 2 4 morse 0.4691 1.738 2.246pair_coeff * * tersoff ./Copt.tersoff NULL NULL C NULLpair_coeff * * kolmogorov/crespi/z /public23/home/a21000018/lammps/lammps-2Aug2023/potentials/CC.KC NULL NULL C Cpair_coeff * * tersoff ./Copt.tersoff NULL NULL NULL Cneighbor 0.3 binneigh_modify delay 0 every 1#layers for heat fluxregion hot block INF INF INF INF 28.69356 41.810616region cold block INF INF INF INF 96.32838 97.01156compute Thot all temp/region hotcompute Tcold all temp/region cold#1st equilibirum runfix 1 all nvt temp $t $t 1.0thermo 1run 1000000velocity all scale $tunfix 1#2nd equilibrium runfix 1 all nvefix hot all heat 1 400.0 region hotfix cold all heat 1 -400.0 region coldthermo_style custom step temp c_Thot c_Tcoldthermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_coldthermo 1000run 10000#thermal conductivity calculationcompute ke all ke/atomvariable temp atom c_ke/1.5compute layers all chunk/atom bin/1d z lower 1.0 units boxfix 2 all ave/chunk 10 100 1000 layers v_temp file profile.heatvariable tdiff equal f_2[20][3]-f_2[36][3]fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000variable kappa equal (400.0/(lx*ly)/2.0)*(lz/2.0)/f_avethermo_style custom step temp c_Thot c_Tcold v_tdiff f_avethermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold & colname v_tdiff dTemp_step colname f_ave dTemprun 200000print "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 secondsReading kolmogorov/crespi/z potential file /public23/home/a21000018/lammps/lammps-2Aug2023/potentials/CC.KC with DATE: 2017-02-28WARNING: 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.
