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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -47.359113 0.0000000) to (33.487950 47.359113 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2303163 6.0575610 5.1068645 Created 684 atoms using lattice units in orthogonal box = (0.0000000 -47.359113 0.0000000) to (33.487950 47.359113 5.1068645) create_atoms CPU = 0.002 seconds 684 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2303163 6.0575610 5.1068645 Created 692 atoms using lattice units in orthogonal box = (0.0000000 -47.359113 0.0000000) to (33.487950 47.359113 5.1068645) create_atoms CPU = 0.002 seconds 692 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 30 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1364 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_343168101490_001#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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.057 | 5.057 | 5.057 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5686.4217 0 -5686.4217 12474.523 550 0 -5810.294 0 -5810.294 -10478.181 Loop time of 90.7935 on 1 procs for 550 steps with 1364 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 = -5686.42170915054 -5810.28845940702 -5810.29399553525 Force two-norm initial, final = 98.769423 0.26452550 Force max component initial, final = 17.117436 0.062011876 Final line search alpha, max atom move = 0.63002757 0.039069191 Iterations, force evaluations = 550 1020 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 90.418 | 90.418 | 90.418 | 0.0 | 99.59 Neigh | 0.20619 | 0.20619 | 0.20619 | 0.0 | 0.23 Comm | 0.088144 | 0.088144 | 0.088144 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0814 | | | 0.09 Nlocal: 1364.00 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6142.00 ave 6142 max 6142 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: 126728.0 ave 126728 max 126728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126728 Ave neighs/atom = 92.909091 Neighbor list builds = 21 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 550 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.057 | 5.057 | 5.057 Mbytes Step Temp E_pair E_mol TotEng Press Volume 550 0 -5810.294 0 -5810.294 -10478.181 16198.562 577 0 -5821.4077 0 -5821.4077 0.57588378 16076.011 Loop time of 3.21474 on 1 procs for 27 steps with 1364 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 = -5810.29399553527 -5821.40723784741 -5821.40770035221 Force two-norm initial, final = 681.12150 1.5761373 Force max component initial, final = 596.35593 0.52012074 Final line search alpha, max atom move = 0.00037133174 0.00019313734 Iterations, force evaluations = 27 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1932 | 3.1932 | 3.1932 | 0.0 | 99.33 Neigh | 0.0098097 | 0.0098097 | 0.0098097 | 0.0 | 0.31 Comm | 0.0018755 | 0.0018755 | 0.0018755 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009819 | | | 0.31 Nlocal: 1364.00 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6255.00 ave 6255 max 6255 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: 131132.0 ave 131132 max 131132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131132 Ave neighs/atom = 96.137830 Neighbor list builds = 1 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.197 | 5.197 | 5.197 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5821.4077 0 -5821.4077 0.57588378 Loop time of 2.164e-06 on 1 procs for 0 steps with 1364 atoms 184.8% 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 | | 2.164e-06 | | |100.00 Nlocal: 1364.00 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6277.00 ave 6277 max 6277 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: 131344.0 ave 131344 max 131344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131344 Ave neighs/atom = 96.293255 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.197 | 5.197 | 5.197 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 -5821.4077 -5821.4077 33.457599 96.554662 4.9763427 0.57588378 0.57588378 51.789585 -24.41793 -25.644004 2.3099012 2620.7717 Loop time of 2.384e-06 on 1 procs for 0 steps with 1364 atoms 209.7% 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 | | 2.384e-06 | | |100.00 Nlocal: 1364.00 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6277.00 ave 6277 max 6277 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65672.0 ave 65672 max 65672 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 131344.0 ave 131344 max 131344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131344 Ave neighs/atom = 96.293255 Neighbor list builds = 0 Dangerous builds = 0 1364 -5821.4077003522 eV 2.30990121949157 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:34