LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.52733 3.52733 3.52733 Created orthogonal box = (0 -39.9107 0) to (17.2803 39.9107 6.10951) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7601 4.9884 6.10951 Created 396 atoms create_atoms CPU = 0.000596046 secs 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7601 4.9884 6.10951 Created 396 atoms create_atoms CPU = 0.000386953 secs 396 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 4 16 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 10.1329 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 752 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 4 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.456 | 5.456 | 5.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3092.4627 0 -3092.4627 -1338.1607 62 0 -3133.0917 0 -3133.0917 -30523.71 Loop time of 1.0037 on 1 procs for 62 steps with 752 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3092.46272607 -3133.08891061 -3133.09173596 Force two-norm initial, final = 21.7819 0.215236 Force max component initial, final = 3.71386 0.0188537 Final line search alpha, max atom move = 1 0.0188537 Iterations, force evaluations = 62 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9931 | 0.9931 | 0.9931 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0074508 | 0.0074508 | 0.0074508 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003152 | | | 0.31 Nlocal: 752 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8361 ave 8361 max 8361 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 281856 ave 281856 max 281856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281856 Ave neighs/atom = 374.809 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.456 | 5.456 | 5.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -3133.0917 0 -3133.0917 -30523.71 8427.0907 72 0 -3133.7752 0 -3133.7752 -17610.3 8364.7055 Loop time of 0.142601 on 1 procs for 10 steps with 752 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3133.09173596 -3133.77515198 -3133.77520122 Force two-norm initial, final = 152.593 0.489184 Force max component initial, final = 152.562 0.151602 Final line search alpha, max atom move = 0.000801026 0.000121437 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13877 | 0.13877 | 0.13877 | 0.0 | 97.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089049 | 0.00089049 | 0.00089049 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002945 | | | 2.07 Nlocal: 752 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8199 ave 8199 max 8199 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 284720 ave 284720 max 284720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284720 Ave neighs/atom = 378.617 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 4 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.593 | 5.593 | 5.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3133.7752 0 -3133.7752 -17610.3 Loop time of 9.53674e-07 on 1 procs for 0 steps with 752 atoms 314.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 752 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8253 ave 8253 max 8253 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 285328 ave 285328 max 285328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 285328 Ave neighs/atom = 379.426 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.593 | 5.593 | 5.593 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -3133.7752 -3133.7752 17.126554 79.821408 6.11873 -17610.3 -17610.3 -15.219737 -52786.6 -29.081577 2.3600217 511.6008 Loop time of 1.90735e-06 on 1 procs for 0 steps with 752 atoms 157.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.907e-06 | | |100.00 Nlocal: 752 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8253 ave 8253 max 8253 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 142664 ave 142664 max 142664 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 285328 ave 285328 max 285328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 285328 Ave neighs/atom = 379.426 Neighbor list builds = 0 Dangerous builds = 0 752 -3133.77520121701 eV 2.36002174383397 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01