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 = 3.52152 3.52152 3.52152 Created orthogonal box = (0 -42.2618 0) to (14.9406 42.2618 4.98018) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.98018 5.8692 4.98018 Created 292 atoms create_atoms CPU = 0.000344992 secs 292 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.98018 5.8692 4.98018 Created 292 atoms create_atoms CPU = 0.000189066 secs 292 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 28 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 572 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.512 | 4.512 | 4.512 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3258.1424 0 -3258.1424 14887.485 53 0 -3296.0864 0 -3296.0864 -5385.0756 Loop time of 33.177 on 1 procs for 53 steps with 572 atoms 72.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3258.14236832 -3296.08423819 -3296.08639379 Force two-norm initial, final = 48.5527 0.136354 Force max component initial, final = 12.546 0.0209038 Final line search alpha, max atom move = 1 0.0209038 Iterations, force evaluations = 53 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.172 | 33.172 | 33.172 | 0.0 | 99.98 Neigh | 0.0011411 | 0.0011411 | 0.0011411 | 0.0 | 0.00 Comm | 0.0025415 | 0.0025415 | 0.0025415 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001571 | | | 0.00 Nlocal: 572 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3614 ave 3614 max 3614 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: 46824 ave 46824 max 46824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46824 Ave neighs/atom = 81.8601 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.512 | 4.512 | 4.512 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -3296.0864 0 -3296.0864 -5385.0756 6289.1189 55 0 -3296.1115 0 -3296.1115 -625.54749 6274.5292 Loop time of 1.47659 on 1 procs for 2 steps with 572 atoms 69.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3296.08639379 -3296.11082099 -3296.11153616 Force two-norm initial, final = 30.9056 1.417 Force max component initial, final = 22.5062 1.29078 Final line search alpha, max atom move = 0.000221006 0.000285271 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4762 | 1.4762 | 1.4762 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002913 | | | 0.02 Nlocal: 572 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3593 ave 3593 max 3593 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: 46408 ave 46408 max 46408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46408 Ave neighs/atom = 81.1329 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.649 | 4.649 | 4.649 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3296.1115 0 -3296.1115 -625.54749 Loop time of 2.14577e-06 on 1 procs for 0 steps with 572 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 | | 2.146e-06 | | |100.00 Nlocal: 572 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3593 ave 3593 max 3593 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: 47376 ave 47376 max 47376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47376 Ave neighs/atom = 82.8252 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) = 4.649 | 4.649 | 4.649 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 -3296.1115 -3296.1115 14.921645 84.523565 4.974926 -625.54749 -625.54749 -144.62623 -2061.2647 329.24846 2.2949124 304.08673 Loop time of 9.53674e-07 on 1 procs for 0 steps with 572 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: 572 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3593 ave 3593 max 3593 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23688 ave 23688 max 23688 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47376 ave 47376 max 47376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47376 Ave neighs/atom = 82.8252 Neighbor list builds = 0 Dangerous builds = 0 572 -1640.99356468456 eV 2.2949124359616 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:36