I followed the tutorial (https://github.com/lammps/lammps/blob/develop/examples/KAPPA/in.heat) to compute the thermal conductance of bilayer graphene sandwiched by Al2O3 on both sides along the z axis.Here is my input file.
variable x equal 47.59variable y equal 41.214148966101variable z equal 136.636variable t equal 300.0#Setup parametersunits metalatom_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 0.00844 3.541pair_coeff 1 2 lj/cut 0.0135951 4.02pair_coeff 1 3 lj/cut 0.0 1.0pair_coeff 1 4 lj/cut 0.0 1.0pair_coeff 2 2 lj/cut 0.0218989 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 Cneighbor 0.3 binneigh_modify delay 0 every 1#energy minimizationfix 5 all box/relax iso 0.0 vmax 0.001minimize 1.0e-4 1.0e-6 1000 100000unfix 5#layers for heat fluxregion hot block INF INF INF INF 28.69356 42.12042884region cold block INF INF INF INF 98.51465116 111.50565116compute Thot all temp/region hotcompute Tcold all temp/region cold#1st equilibirum runfix 1 all nvt temp $t $t 100.0thermo 10run 100000velocity all scale $tunfix 1#2nd equilibrium runfix 1 all nvefix hot all heat 1 1.0 region hotfix cold all heat 1 -1.0 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/1.5/8.617333262145e-5compute layers all chunk/atom bin/1d z lower 0.02 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 10 100 1000 v_tdiff ave running start 13000variable kappa equal 1.0/(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 200000print "Running average thermal conductivity: $(v_kappa:%.4f)"
I received the following error message after I launched the calculation.
LAMMPS (2 Aug 2023)variable x equal 47.59variable y equal 41.214148966101variable z equal 136.636variable t equal 300.0#Setup parametersunits metalatom_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) 1 by 1 by 1 MPI processor grid reading atoms ... 19600 atoms read_data CPU = 0.199 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 0.00844 3.541pair_coeff 1 2 lj/cut 0.0135951 4.02pair_coeff 1 3 lj/cut 0.0 1.0pair_coeff 1 4 lj/cut 0.0 1.0pair_coeff 2 2 lj/cut 0.0218989 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 Cneighbor 0.3 binneigh_modify delay 0 every 1#energy minimizationfix 5 all box/relax iso 0.0 vmax 0.001minimize 1.0e-4 1.0e-6 1000 100000Neighbor 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: standardWARNING: Energy due to 1 extra global DOFs will be included in minimizer energies (../min.cpp:225)Per MPI rank memory allocation (min/avg/max) = 87.58 | 87.58 | 87.58 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 18675574 0 18676334 4.5038706e+08 267995.3 1000 300 355.71228 0 1115.7232 7818.4545 2143962.4 Loop time of 192.986 on 1 procs for 1000 steps with 19600 atoms99.8% CPU use with 1 MPI tasks x no OpenMP threadsMinimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = 18675574.3392642 370.713719775112 355.712282174799 Force two-norm initial, final = 2.2600666e+08 14933.478 Force max component initial, final = 2.2600657e+08 14933.459 Final line search alpha, max atom move = 6.6359114e-08 0.00099097112 Iterations, force evaluations = 1000 1000MPI task timing breakdown:Section | min time | avg time | max time |%varavg| %total---------------------------------------------------------------Pair | 81.011 | 81.011 | 81.011 | 0.0 | 41.98Neigh | 109.55 | 109.55 | 109.55 | 0.0 | 56.77Comm | 0.48548 | 0.48548 | 0.48548 | 0.0 | 0.25Output | 0.00010763 | 0.00010763 | 0.00010763 | 0.0 | 0.00Modify | 0 | 0 | 0 | 0.0 | 0.00Other | | 1.938 | | | 1.00Nlocal: 19600 ave 19600 max 19600 minHistogram: 1 0 0 0 0 0 0 0 0 0Nghost: 13422 ave 13422 max 13422 minHistogram: 1 0 0 0 0 0 0 0 0 0Neighs: 0 ave 0 max 0 minHistogram: 1 0 0 0 0 0 0 0 0 0Total # of neighbors = 0Ave neighs/atom = 0Neighbor list builds = 539Dangerous builds = 78unfix 5#layers for heat fluxregion hot block INF INF INF INF 28.69356 42.12042884region cold block INF INF INF INF 98.51465116 111.50565116compute 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 10run 100000Per MPI rank memory allocation (min/avg/max) = 95.1 | 95.1 | 95.1 Mbytes Step Temp E_pair E_mol TotEng Press 1000 300 355.71228 0 1115.7232 7818.4545 1010 289.14242 383.22878 0 1115.7334 7898.4387 1020 262.83777 449.97678 0 1115.842 8094.8676...... 110980 1884.322 1864.0873 1986.5247 110990 1881.9124 1881.575 1937.1548 111000 1882.1765 1886.5183 1926.9182 Loop time of 490.656 on 1 procs for 10000 steps with 19600 atomsPerformance: 1.761 ns/day, 13.629 hours/ns, 20.381 timesteps/s, 399.465 katom-step/s100.0% CPU use with 1 MPI tasks x no OpenMP threadsMPI task timing breakdown:Section | min time | avg time | max time |%varavg| %total---------------------------------------------------------------Pair | 119.07 | 119.07 | 119.07 | 0.0 | 24.27Neigh | 350.79 | 350.79 | 350.79 | 0.0 | 71.49Comm | 4.3024 | 4.3024 | 4.3024 | 0.0 | 0.88Output | 0.41462 | 0.41462 | 0.41462 | 0.0 | 0.08Modify | 13.986 | 13.986 | 13.986 | 0.0 | 2.85Other | | 2.1 | | | 0.43Nlocal: 19600 ave 19600 max 19600 minHistogram: 1 0 0 0 0 0 0 0 0 0Nghost: 16269 ave 16269 max 16269 minHistogram: 1 0 0 0 0 0 0 0 0 0Neighs: 0 ave 0 max 0 minHistogram: 1 0 0 0 0 0 0 0 0 0Total # of neighbors = 0Ave neighs/atom = 0Neighbor list builds = 4670Dangerous builds = 2#thermal conductivity calculationcompute ke all ke/atomvariable temp atom c_ke/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 10 100 1000 v_tdiff ave running start 13000variable kappa equal 1.0/(lx*ly)*lz/f_avethermo_style custom step temp c_Thot c_Tcold v_tdiff f_aveWARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:903)thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold colname v_tdiff dTemp_step colname f_ave dTemprun 3000000ERROR: Thermo and fix ave not computed at compatible times (../thermo.cpp:301)Last command: run 3000000
I ran the tutorial and the calculation could be done successfully.
Would anyone please tell me why the 'Thermo' and 'fix ave' command conflicts in my case? Thank you in advance.