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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -50.435089 0.0000000) to (29.118712 50.435089 4.9455673) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4798018 4.5262259 4.9455673 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -50.435089 0.0000000) to (29.118712 50.435089 4.9455673) create_atoms CPU = 0.005 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4798018 4.5262259 4.9455673 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -50.435089 0.0000000) to (29.118712 50.435089 4.9455673) create_atoms CPU = 0.004 seconds 627 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 27 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1248 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_267721408934_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.453 | 5.453 | 5.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4008.2786 0 -4008.2786 181625.78 96 0 -5124.2865 0 -5124.2865 2297.0807 Loop time of 3.70337 on 1 procs for 96 steps with 1248 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 = -4008.27863959307 -5124.28283642546 -5124.28645015504 Force two-norm initial, final = 2933.2644 0.21020171 Force max component initial, final = 801.37860 0.034542205 Final line search alpha, max atom move = 1.0000000 0.034542205 Iterations, force evaluations = 96 174 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6168 | 3.6168 | 3.6168 | 0.0 | 97.66 Neigh | 0.027713 | 0.027713 | 0.027713 | 0.0 | 0.75 Comm | 0.03179 | 0.03179 | 0.03179 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0271 | | | 0.73 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7514.00 ave 7514 max 7514 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: 207294.0 ave 207294 max 207294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207294 Ave neighs/atom = 166.10096 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.453 | 5.453 | 5.453 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -5124.2865 0 -5124.2865 2297.0807 14526.168 99 0 -5124.3304 0 -5124.3304 -2.1555997 14545.283 Loop time of 0.127485 on 1 procs for 3 steps with 1248 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5124.28645015503 -5124.33011664593 -5124.33036469292 Force two-norm initial, final = 48.092011 0.31730930 Force max component initial, final = 44.372283 0.15172660 Final line search alpha, max atom move = 0.00026461435 4.0149036e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12327 | 0.12327 | 0.12327 | 0.0 | 96.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097591 | 0.00097591 | 0.00097591 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003235 | | | 2.54 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7489.00 ave 7489 max 7489 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: 207928.0 ave 207928 max 207928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207928 Ave neighs/atom = 166.60897 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.591 | 5.591 | 5.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5124.3304 0 -5124.3304 -2.1555997 Loop time of 7.196e-06 on 1 procs for 0 steps with 1248 atoms 180.7% 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 | | 7.196e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7489.00 ave 7489 max 7489 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: 207912.0 ave 207912 max 207912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207912 Ave neighs/atom = 166.59615 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.591 | 5.591 | 5.591 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 -5124.3304 -5124.3304 29.09433 101.05606 4.9471088 -2.1555997 -2.1555997 -12.57961 -10.605226 16.718037 2.259527 539.66729 Loop time of 7.488e-06 on 1 procs for 0 steps with 1248 atoms 253.7% 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 | | 7.488e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7489.00 ave 7489 max 7489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103956.0 ave 103956 max 103956 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 207912.0 ave 207912 max 207912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207912 Ave neighs/atom = 166.59615 Neighbor list builds = 0 Dangerous builds = 0 1248 -5124.33036469292 eV 2.25952700895165 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04