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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -55.612540 0.0000000) to (27.804490 55.612540 3.5600001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0139244 5.0139244 3.5600001 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.612540 0.0000000) to (27.804490 55.612540 3.5600001) create_atoms CPU = 0.001 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0139244 5.0139244 3.5600001 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.612540 0.0000000) to (27.804490 55.612540 3.5600001) create_atoms CPU = 0.001 seconds 490 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 29 1 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 966 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4193.731 0 -4193.731 -3306.0641 85 0 -4241.0199 0 -4241.0199 -3747.2736 Loop time of 1.40802 on 1 procs for 85 steps with 966 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4193.73096557304 -4241.01708531496 -4241.01987103502 Force two-norm initial, final = 36.555451 0.29372697 Force max component initial, final = 6.9160880 0.078032982 Final line search alpha, max atom move = 1.0000000 0.078032982 Iterations, force evaluations = 85 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.372 | 1.372 | 1.372 | 0.0 | 97.44 Neigh | 0.017417 | 0.017417 | 0.017417 | 0.0 | 1.24 Comm | 0.010914 | 0.010914 | 0.010914 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007682 | | | 0.55 Nlocal: 966.000 ave 966 max 966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8433.00 ave 8433 max 8433 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: 169020.0 ave 169020 max 169020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169020 Ave neighs/atom = 174.96894 Neighbor list builds = 2 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -4241.0199 0 -4241.0199 -3747.2736 11009.502 94 0 -4241.3361 0 -4241.3361 -172.54455 10995.699 Loop time of 0.0987473 on 1 procs for 9 steps with 966 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 = -4241.01987103502 -4241.33551705906 -4241.33614143419 Force two-norm initial, final = 58.551882 0.75635406 Force max component initial, final = 53.953937 0.39877575 Final line search alpha, max atom move = 0.00048449995 0.00019320683 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.095269 | 0.095269 | 0.095269 | 0.0 | 96.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066757 | 0.00066757 | 0.00066757 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002811 | | | 2.85 Nlocal: 966.000 ave 966 max 966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8439.00 ave 8439 max 8439 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: 169048.0 ave 169048 max 169048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169048 Ave neighs/atom = 174.99793 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.173 | 5.173 | 5.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4241.3361 0 -4241.3361 -172.54455 Loop time of 1.664e-06 on 1 procs for 0 steps with 966 atoms 180.3% 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 | | 1.664e-06 | | |100.00 Nlocal: 966.000 ave 966 max 966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8439.00 ave 8439 max 8439 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: 168832.0 ave 168832 max 168832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168832 Ave neighs/atom = 174.77433 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.173 | 5.173 | 5.173 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 -4241.3361 -4241.3361 27.994193 111.22508 3.5314427 -172.54455 -172.54455 -58.501808 -413.17218 -45.959668 2.3098229 160.8913 Loop time of 1.556e-06 on 1 procs for 0 steps with 966 atoms 128.5% 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 | | 1.556e-06 | | |100.00 Nlocal: 966.000 ave 966 max 966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8439.00 ave 8439 max 8439 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84416.0 ave 84416 max 84416 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 168832.0 ave 168832 max 168832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168832 Ave neighs/atom = 174.77433 Neighbor list builds = 0 Dangerous builds = 0 966 -4241.33614143419 eV 2.30982285040552 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01