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 = 3.6149602 3.6149602 3.6149602 Created orthogonal box = (0.0000000 -39.599905 0.0000000) to (8.0832967 39.599905 8.8548078) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8499780 5.2799873 5.9032052 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.599905 0.0000000) to (8.0832967 39.599905 8.8548078) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8499780 5.2799873 5.9032052 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.599905 0.0000000) to (8.0832967 39.599905 8.8548078) create_atoms CPU = 0.000 seconds 242 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 19 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 8.395337773223552 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 476 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_950828638160_000#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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1614.2604 0 -1614.2604 26275.131 120 0 -1678.6527 0 -1678.6527 1192.5476 Loop time of 1.30571 on 1 procs for 120 steps with 476 atoms 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1614.26044174549 -1678.65134772409 -1678.65271707012 Force two-norm initial, final = 156.26071 0.10847206 Force max component initial, final = 54.911605 0.028238615 Final line search alpha, max atom move = 1.0000000 0.028238615 Iterations, force evaluations = 120 227 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2679 | 1.2679 | 1.2679 | 0.0 | 97.10 Neigh | 0.020243 | 0.020243 | 0.020243 | 0.0 | 1.55 Comm | 0.010068 | 0.010068 | 0.010068 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007527 | | | 0.58 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4738.00 ave 4738 max 4738 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: 95220.0 ave 95220 max 95220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95220 Ave neighs/atom = 200.04202 Neighbor list builds = 3 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 120 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press Volume 120 0 -1678.6527 0 -1678.6527 1192.5476 5668.8086 126 0 -1678.7251 0 -1678.7251 40.886776 5673.8398 Loop time of 0.0467194 on 1 procs for 6 steps with 476 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1678.65271707012 -1678.72382068274 -1678.72512347139 Force two-norm initial, final = 22.942471 0.40501292 Force max component initial, final = 21.789264 0.26139542 Final line search alpha, max atom move = 0.00046012314 0.00012027408 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044901 | 0.044901 | 0.044901 | 0.0 | 96.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031262 | 0.00031262 | 0.00031262 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001506 | | | 3.22 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4441.00 ave 4441 max 4441 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: 95120.0 ave 95120 max 95120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95120 Ave neighs/atom = 199.83193 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 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) = 4.728 | 4.728 | 4.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1678.7251 0 -1678.7251 40.886776 Loop time of 2.281e-06 on 1 procs for 0 steps with 476 atoms 131.5% 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 | | 2.281e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4462.00 ave 4462 max 4462 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: 95048.0 ave 95048 max 95048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95048 Ave neighs/atom = 199.68067 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 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) = 4.728 | 4.728 | 4.728 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 -1678.7251 -1678.7251 8.0636276 79.65399 8.8336274 40.886776 40.886776 22.820922 26.203237 73.63617 2.2924495 315.567 Loop time of 2.508e-06 on 1 procs for 0 steps with 476 atoms 239.2% 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 | | 2.508e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4462.00 ave 4462 max 4462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47524.0 ave 47524 max 47524 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95048.0 ave 95048 max 95048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95048 Ave neighs/atom = 199.68067 Neighbor list builds = 0 Dangerous builds = 0 476 -1678.72512347139 eV 2.29244952985286 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01