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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -48.534201 0.0000000) to (29.721007 48.534201 8.9612207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4038194 5.5152501 5.9741471 Created 1050 atoms using lattice units in orthogonal box = (0.0000000 -48.534201 0.0000000) to (29.721007 48.534201 8.9612207) create_atoms CPU = 0.002 seconds 1050 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4038194 5.5152501 5.9741471 Created 1074 atoms using lattice units in orthogonal box = (0.0000000 -48.534201 0.0000000) to (29.721007 48.534201 8.9612207) create_atoms CPU = 0.001 seconds 1074 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 23 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 2112 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.474 | 6.474 | 6.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8168.7235 0 -8168.7235 6381.8016 489 0 -8307.4378 0 -8307.4378 -71575.882 Loop time of 21.0386 on 1 procs for 489 steps with 2112 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8168.72346473317 -8307.42964068413 -8307.43779525929 Force two-norm initial, final = 53.531221 0.32473583 Force max component initial, final = 7.1282293 0.025751062 Final line search alpha, max atom move = 1.0000000 0.025751062 Iterations, force evaluations = 489 955 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.595 | 20.595 | 20.595 | 0.0 | 97.89 Neigh | 0.27778 | 0.27778 | 0.27778 | 0.0 | 1.32 Comm | 0.078329 | 0.078329 | 0.078329 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08708 | | | 0.41 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9162.00 ave 9162 max 9162 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: 428240.0 ave 428240 max 428240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428240 Ave neighs/atom = 202.76515 Neighbor list builds = 10 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 489 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.473 | 6.473 | 6.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 489 0 -8307.4378 0 -8307.4378 -71575.882 25852.859 530 0 -8360.3603 0 -8360.3603 24.460138 24572.959 Loop time of 1.06418 on 1 procs for 41 steps with 2112 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 = -8307.43779525921 -8360.35523799083 -8360.36026296406 Force two-norm initial, final = 2235.8775 16.326801 Force max component initial, final = 1598.1955 11.156809 Final line search alpha, max atom move = 0.0010217225 0.011399163 Iterations, force evaluations = 41 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99019 | 0.99019 | 0.99019 | 0.0 | 93.05 Neigh | 0.052711 | 0.052711 | 0.052711 | 0.0 | 4.95 Comm | 0.0034091 | 0.0034091 | 0.0034091 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01786 | | | 1.68 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9530.00 ave 9530 max 9530 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: 451048.0 ave 451048 max 451048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451048 Ave neighs/atom = 213.56439 Neighbor list builds = 2 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.615 | 6.615 | 6.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8360.3603 0 -8360.3603 24.460138 Loop time of 1.821e-06 on 1 procs for 0 steps with 2112 atoms 164.7% 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 | | 1.821e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9544.00 ave 9544 max 9544 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: 450628.0 ave 450628 max 450628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450628 Ave neighs/atom = 213.36553 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.615 | 6.615 | 6.615 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 -8360.3603 -8360.3603 28.698106 98.764848 8.669655 24.460138 24.460138 -690.81073 60.426331 703.76481 2.2456885 4438.9241 Loop time of 2.268e-06 on 1 procs for 0 steps with 2112 atoms 264.6% 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 | | 2.268e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9544.00 ave 9544 max 9544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 225314.0 ave 225314 max 225314 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 450628.0 ave 450628 max 450628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450628 Ave neighs/atom = 213.36553 Neighbor list builds = 0 Dangerous builds = 0 2112 -8360.36026296406 eV 2.24568850249901 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22