LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -49.504352 0.0000000) to (11.668288 49.504352 4.9753746) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3037672 6.0005275 4.9753746 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -49.504352 0.0000000) to (11.668288 49.504352 4.9753746) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3037672 6.0005275 4.9753746 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -49.504352 0.0000000) to (11.668288 49.504352 4.9753746) create_atoms CPU = 0.001 seconds 266 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 21 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 524 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_149104665840_005#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2225.1581 0 -2225.1581 38056.402 79 0 -2289.8357 0 -2289.8357 -5839.7454 Loop time of 1.72159 on 1 procs for 79 steps with 524 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2225.15805895546 -2289.83409322143 -2289.83573895605 Force two-norm initial, final = 205.02609 0.12862792 Force max component initial, final = 71.394429 0.025035922 Final line search alpha, max atom move = 1.0000000 0.025035922 Iterations, force evaluations = 79 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6913 | 1.6913 | 1.6913 | 0.0 | 98.24 Neigh | 0.013271 | 0.013271 | 0.013271 | 0.0 | 0.77 Comm | 0.010669 | 0.010669 | 0.010669 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006312 | | | 0.37 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7290.00 ave 7290 max 7290 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: 171124.0 ave 171124 max 171124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171124 Ave neighs/atom = 326.57252 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -2289.8357 0 -2289.8357 -5839.7454 5747.8615 84 0 -2289.9349 0 -2289.9349 -203.64439 5728.6736 Loop time of 0.0739515 on 1 procs for 5 steps with 524 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 = -2289.83573895602 -2289.93400581829 -2289.93491453726 Force two-norm initial, final = 48.480083 1.4234353 Force max component initial, final = 47.033725 1.0555786 Final line search alpha, max atom move = 0.00037509370 0.00039594089 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072214 | 0.072214 | 0.072214 | 0.0 | 97.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035685 | 0.00035685 | 0.00035685 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001381 | | | 1.87 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7260.00 ave 7260 max 7260 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: 168952.0 ave 168952 max 168952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168952 Ave neighs/atom = 322.42748 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2289.9349 0 -2289.9349 -203.64439 Loop time of 1.873e-06 on 1 procs for 0 steps with 524 atoms 106.8% 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 | | 1.873e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7260.00 ave 7260 max 7260 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: 169292.0 ave 169292 max 169292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169292 Ave neighs/atom = 323.07634 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.125 | 5.125 | 5.125 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 -2289.9349 -2289.9349 11.672568 98.584434 4.9782802 -203.64439 -203.64439 -64.869801 -250.67022 -295.39315 2.2497062 248.02326 Loop time of 2.335e-06 on 1 procs for 0 steps with 524 atoms 171.3% 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 | | 2.335e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7260.00 ave 7260 max 7260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84646.0 ave 84646 max 84646 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 169292.0 ave 169292 max 169292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169292 Ave neighs/atom = 323.07634 Neighbor list builds = 0 Dangerous builds = 0 524 -2289.93491453726 eV 2.24970619609851 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03