LAMMPS (24 Dec 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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -47.363434 0.0000000) to (33.488452 47.363434 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2304096 6.0576517 5.1069410 Created 693 atoms create_atoms CPU = 0.001 seconds 693 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2304096 6.0576517 5.1069410 Created 693 atoms create_atoms CPU = 0.001 seconds 693 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 13 36 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 13 atoms, new total = 1373 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 13 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.422 | 5.422 | 5.422 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5734.7433 0 -5734.7433 17432.391 47 0 -5812.8594 0 -5812.8594 2706.9344 Loop time of 7.34371 on 1 procs for 47 steps with 1373 atoms 40.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5734.74328210755 -5812.85400752129 -5812.85937440108 Force two-norm initial, final = 75.609628 0.29630687 Force max component initial, final = 12.598001 0.054717757 Final line search alpha, max atom move = 1.0000000 0.054717757 Iterations, force evaluations = 47 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2858 | 7.2858 | 7.2858 | 0.0 | 99.21 Neigh | 0.031735 | 0.031735 | 0.031735 | 0.0 | 0.43 Comm | 0.02335 | 0.02335 | 0.02335 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00283 | | | 0.04 Nlocal: 1373.00 ave 1373 max 1373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5164.00 ave 5164 max 5164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74096.0 ave 74096 max 74096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74096 Ave neighs/atom = 53.966497 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.422 | 5.422 | 5.422 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -5812.8594 0 -5812.8594 2706.9344 16200.525 49 0 -5812.8751 0 -5812.8751 678.29312 16220.574 Loop time of 0.406153 on 1 procs for 2 steps with 1373 atoms 39.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5812.85937440106 -5812.87497951609 -5812.87507214011 Force two-norm initial, final = 34.963163 0.30330572 Force max component initial, final = 28.133547 0.060643809 Final line search alpha, max atom move = 0.00071733334 4.3501826e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40545 | 0.40545 | 0.40545 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001721 | 0.0001721 | 0.0001721 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005299 | | | 0.13 Nlocal: 1373.00 ave 1373 max 1373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5164.00 ave 5164 max 5164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74068.0 ave 74068 max 74068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74068 Ave neighs/atom = 53.946103 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.559 | 5.559 | 5.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5812.8751 0 -5812.8751 678.29312 Loop time of 2.1e-06 on 1 procs for 0 steps with 1373 atoms 142.9% 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 | | 2.1e-06 | | |100.00 Nlocal: 1373.00 ave 1373 max 1373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5164.00 ave 5164 max 5164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74068.0 ave 74068 max 74068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74068 Ave neighs/atom = 53.946103 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) = 5.559 | 5.559 | 5.559 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 -5812.8751 -5812.8751 33.514687 94.726868 5.1092584 678.29312 678.29312 -5.994745 2040.228 0.64608686 2.3249827 498.91534 Loop time of 2.1e-06 on 1 procs for 0 steps with 1373 atoms 190.5% 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 | | 2.1e-06 | | |100.00 Nlocal: 1373.00 ave 1373 max 1373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5164.00 ave 5164 max 5164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37034.0 ave 37034 max 37034 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74068.0 ave 74068 max 74068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74068 Ave neighs/atom = 53.946103 Neighbor list builds = 0 Dangerous builds = 0 1373 -5812.87507214011 eV 2.32498271180618 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08