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 = 3.52043 3.52043 3.52043 Created orthogonal box = (0 -35.905 0) to (31.0916 35.905 6.09756) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.58054 5.5233 6.09756 Created 629 atoms create_atoms CPU = 0.000577927 secs 629 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.58054 5.5233 6.09756 Created 628 atoms create_atoms CPU = 0.000454903 secs 628 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 11 25 3 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 1234 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7056.5776 0 -7056.5776 561.11697 59 0 -7102.2787 0 -7102.2787 -8833.6517 Loop time of 21.0714 on 1 procs for 59 steps with 1234 atoms 87.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7056.57763991 -7102.27215327 -7102.27871393 Force two-norm initial, final = 44.259 0.274876 Force max component initial, final = 6.95712 0.0579416 Final line search alpha, max atom move = 1 0.0579416 Iterations, force evaluations = 59 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.061 | 21.061 | 21.061 | 0.0 | 99.95 Neigh | 0.0024281 | 0.0024281 | 0.0024281 | 0.0 | 0.01 Comm | 0.0038455 | 0.0038455 | 0.0038455 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003819 | | | 0.02 Nlocal: 1234 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4594 ave 4594 max 4594 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: 95264 ave 95264 max 95264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95264 Ave neighs/atom = 77.1994 Neighbor list builds = 1 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -7102.2787 0 -7102.2787 -8833.6517 13613.907 62 0 -7102.365 0 -7102.365 -3897.9325 13579.819 Loop time of 0.894088 on 1 procs for 3 steps with 1234 atoms 97.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7102.27871393 -7102.36335213 -7102.36504962 Force two-norm initial, final = 78.9513 1.8888 Force max component initial, final = 72.5296 1.63628 Final line search alpha, max atom move = 0.000131075 0.000214475 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89339 | 0.89339 | 0.89339 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013065 | 0.00013065 | 0.00013065 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005684 | | | 0.06 Nlocal: 1234 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4305 ave 4305 max 4305 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: 95200 ave 95200 max 95200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95200 Ave neighs/atom = 77.1475 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.774 | 4.774 | 4.774 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7102.365 0 -7102.365 -3897.9325 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1234 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: 1234 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4391 ave 4391 max 4391 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: 95208 ave 95208 max 95208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95208 Ave neighs/atom = 77.154 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) = 4.774 | 4.774 | 4.774 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 -7102.365 -7102.365 31.081551 71.809921 6.0842472 -3897.9325 -3897.9325 -105.11407 -11396.053 -192.63001 2.291817 918.01749 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1234 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 1234 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4391 ave 4391 max 4391 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47604 ave 47604 max 47604 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95208 ave 95208 max 95208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95208 Ave neighs/atom = 77.154 Neighbor list builds = 0 Dangerous builds = 0 1234 -2987.22006823696 eV 2.29181704579168 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22