LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.52221 3.52221 3.52221 Created orthogonal box = (0 -37.4451 0) to (37.4416 37.4451 3.52221) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.97013 4.97013 3.52221 Created 454 atoms create_atoms CPU = 0.000272989 secs 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.97013 4.97013 3.52221 Created 454 atoms create_atoms CPU = 0.000145912 secs 454 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 23 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 900 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.953 | 4.953 | 4.953 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5148.4648 0 -5148.4648 12678.201 82 0 -5190.9851 0 -5190.9851 -1615.4687 Loop time of 35.5013 on 1 procs for 82 steps with 900 atoms 77.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5148.46483639 -5190.98086441 -5190.98511239 Force two-norm initial, final = 21.1451 0.171231 Force max component initial, final = 4.58913 0.0138588 Final line search alpha, max atom move = 1 0.0138588 Iterations, force evaluations = 82 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 35.491 | 35.491 | 35.491 | 0.0 | 99.97 Neigh | 0.00225 | 0.00225 | 0.00225 | 0.0 | 0.01 Comm | 0.0050859 | 0.0050859 | 0.0050859 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003084 | | | 0.01 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6220 ave 6220 max 6220 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: 103232 ave 103232 max 103232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103232 Ave neighs/atom = 114.702 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.953 | 4.953 | 4.953 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -5190.9851 0 -5190.9851 -1615.4687 9876.3237 85 0 -5191.0112 0 -5191.0112 -875.84654 9872.4033 Loop time of 1.387 on 1 procs for 3 steps with 900 atoms 81.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5190.98511239 -5191.01066403 -5191.01115806 Force two-norm initial, final = 24.6273 1.76209 Force max component initial, final = 23.4878 1.74641 Final line search alpha, max atom move = 0.000211889 0.000370045 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3863 | 1.3863 | 1.3863 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017214 | 0.00017214 | 0.00017214 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005291 | | | 0.04 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6225 ave 6225 max 6225 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: 101912 ave 101912 max 101912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101912 Ave neighs/atom = 113.236 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.091 | 5.091 | 5.091 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5191.0112 0 -5191.0112 -875.84654 Loop time of 9.53674e-07 on 1 procs for 0 steps with 900 atoms 0.0% 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: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6235 ave 6235 max 6235 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: 102108 ave 102108 max 102108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102108 Ave neighs/atom = 113.453 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) = 5.091 | 5.091 | 5.091 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 -5191.0112 -5191.0112 37.378201 74.890273 3.5267858 -875.84654 -875.84654 -24.291516 -2887.0389 283.79081 2.2361692 133.04245 Loop time of 1.90735e-06 on 1 procs for 0 steps with 900 atoms 0.0% 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: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6235 ave 6235 max 6235 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51054 ave 51054 max 51054 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102108 ave 102108 max 102108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102108 Ave neighs/atom = 113.453 Neighbor list builds = 0 Dangerous builds = 0 900 -2552.51439797048 eV 2.23616924715958 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:38