I am simulating the thermal conductance along the z axis for bilayer graphene sandwiched by Al2O3 system. This is my input setting.
variable x equal 47.59variable y equal 41.214148966101variable z equal 136.636variable t equal 300.0#Setup parametersunits realatom_style atomicread_data atomic_structure_atomicmass 1 16.0mass 2 27.0mass 3 12.0mass 4 12.0velocity all create $t 87287pair_style hybrid/overlay lj/cut 12.0 morse 6.287 tersoff shift -0.0462pair_coeff 1 1 lj/cut 0.194633996 3.541pair_coeff 1 2 lj/cut 0.31351524159 4.02pair_coeff 1 3 lj/cut 0.0 1pair_coeff 1 4 lj/cut 0.0 1pair_coeff 2 2 lj/cut 0.50500834301 4.499pair_coeff 2 3 morse 10.81786819 1.738 2.246pair_coeff 2 4 morse 10.81786819 1.738 2.246pair_coeff * * tersoff ./Copt.tersoff NULL NULL C 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 100.0thermo 1run 3000000velocity all scale $tunfix 1#2nd equilibrium runfix 1 all nvefix hot all heat 1 23.0609 region hotfix cold all heat 1 -23.0609 region coldthermo_style custom step temp c_Thot c_Tcoldthermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_coldthermo 10run 10000#thermal conductivity calculationcompute ke all ke/atomvariable temp atom c_ke/23.0609/1.5/8.617333262145e-5compute layers all chunk/atom bin/1d z lower 1.0 units reducedfix 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 23.0609/(lx*ly)*lz/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 3000000print "Running average thermal conductivity: $(v_kappa:%.4f)"This is the error message I received after I launched the calculation.
LAMMPS (2 Aug 2023 - Update 1)variable x equal 47.59variable y equal 41.214148966101variable z equal 136.636variable t equal 300.0#Setup parametersunits realatom_style atomicread_data atomic_structure_atomicReading 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 = 0.131 secondsmass 1 16.0mass 2 27.0mass 3 12.0mass 4 12.0velocity all create $t 87287velocity all create 300 87287#pair_style hybrid/overlay lj/cut 10.0 morse 6.287 tersoff shift -0.0462 kolmogorov/crespi/z 20.0pair_style hybrid/overlay lj/cut 12.0 morse 6.287 tersoff shift -0.0462pair_coeff 1 1 lj/cut 0.194633996 3.541pair_coeff 1 2 lj/cut 0.31351524159 4.02pair_coeff 1 3 lj/cut 0.0 1pair_coeff 1 4 lj/cut 0.0 1pair_coeff 2 2 lj/cut 0.50500834301 4.499pair_coeff 2 3 morse 10.81786819 1.738 2.246pair_coeff 2 4 morse 10.81786819 1.738 2.246pair_coeff * * tersoff ./Copt.tersoff NULL NULL C 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 100.0fix 1 all nvt temp 300 $t 100.0fix 1 all nvt temp 300 300 100.0thermo 1run 3000000Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.3 ghost atom cutoff = 12.3 binsize = 6.15, bins = 12 7 23 6 neighbor lists, perpetual/occasional/extra = 6 0 0 (1) pair lj/cut, perpetual, skip from (4) attributes: half, newton on pair build: skip stencil: none bin: none (2) pair morse, perpetual, skip from (5) attributes: half, newton on, cut 6.587 pair build: skip stencil: none bin: none (3) pair tersoff, perpetual, skip from (6) attributes: full, newton on, cut 2.4 pair build: skip stencil: none bin: none (4) neighbor class addition, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard (5) neighbor class addition, perpetual, trim from (4) attributes: half, newton on, cut 6.587 pair build: trim stencil: none bin: none (6) neighbor class addition, perpetual attributes: full, newton on, cut 2.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standardPer MPI rank memory allocation (min/avg/max) = 6.496 | 8.707 | 10.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 4.3067738e+08 0 4.306949e+08 4.4405907e+08 1 9.6397316e-73 2.5266396e+09 0 2.5266396e+09 2.5914761e+09ERROR: Lost atoms: original 19600 current 19595 (../thermo.cpp:488)Last command: run 3000000I checked the unit for the potential and energy settings. It is said that the metal units would be converted into real unit by LAMMPS for the tersoff potential automatically. I did not changed the tersoff potential and only change the unit for energy from eV to Kcal/mol in the lj and mose potential.
I think that the force was not that large to blow up some atoms out of the unit cell. I do not understand why I still receive this error message.
Would anyone please give me some suggestions/comments on the parameter settings in my input file?
Thank you in advance.