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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -35.914812 0.0000000) to (31.100090 35.914812 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5820674 5.5248139 6.0992294 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -35.914812 0.0000000) to (31.100090 35.914812 6.0992294) create_atoms CPU = 0.004 seconds 629 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5820674 5.5248139 6.0992294 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -35.914812 0.0000000) to (31.100090 35.914812 6.0992294) 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 24 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 1233 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_000553624872_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.641 | 4.641 | 4.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5392.1925 0 -5392.1925 15227.658 65 0 -5448.5443 0 -5448.5443 -5744.9376 Loop time of 11.4432 on 1 procs for 65 steps with 1233 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 = -5392.19247427361 -5448.53979187165 -5448.54432986846 Force two-norm initial, final = 79.685707 0.25289809 Force max component initial, final = 13.924824 0.054794779 Final line search alpha, max atom move = 1.0000000 0.054794779 Iterations, force evaluations = 65 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.383 | 11.383 | 11.383 | 0.0 | 99.48 Neigh | 0.030737 | 0.030737 | 0.030737 | 0.0 | 0.27 Comm | 0.012532 | 0.012532 | 0.012532 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01669 | | | 0.15 Nlocal: 1233.00 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4740.00 ave 4740 max 4740 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: 95524.0 ave 95524 max 95524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95524 Ave neighs/atom = 77.472830 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.641 | 4.641 | 4.641 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -5448.5443 0 -5448.5443 -5744.9376 13625.116 68 0 -5448.6035 0 -5448.6035 -1600.5459 13594.299 Loop time of 0.6054 on 1 procs for 3 steps with 1233 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 = -5448.54432986847 -5448.60295954396 -5448.60351337019 Force two-norm initial, final = 64.688377 0.27003331 Force max component initial, final = 58.299513 0.050303172 Final line search alpha, max atom move = 0.00021707137 1.0919379e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60236 | 0.60236 | 0.60236 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064232 | 0.00064232 | 0.00064232 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002399 | | | 0.40 Nlocal: 1233.00 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4728.00 ave 4728 max 4728 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: 95554.0 ave 95554 max 95554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95554 Ave neighs/atom = 77.497161 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 ghost atom cutoff = 6 binsize = 3, bins = 11 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.779 | 4.779 | 4.779 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5448.6035 0 -5448.6035 -1600.5459 Loop time of 6.695e-06 on 1 procs for 0 steps with 1233 atoms 194.2% 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 | | 6.695e-06 | | |100.00 Nlocal: 1233.00 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4728.00 ave 4728 max 4728 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: 95562.0 ave 95562 max 95562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95562 Ave neighs/atom = 77.503650 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 ghost atom cutoff = 6 binsize = 3, bins = 11 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.779 | 4.779 | 4.779 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 -5448.6035 -5448.6035 31.085836 71.829624 6.0882247 -1600.5459 -1600.5459 -5.275286 -4794.7022 -1.6603287 2.2361982 854.63059 Loop time of 6.967e-06 on 1 procs for 0 steps with 1233 atoms 258.4% 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 | | 6.967e-06 | | |100.00 Nlocal: 1233.00 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4728.00 ave 4728 max 4728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47781.0 ave 47781 max 47781 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95562.0 ave 95562 max 95562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95562 Ave neighs/atom = 77.503650 Neighbor list builds = 0 Dangerous builds = 0 1233 -5448.60351337019 eV 2.23619823713339 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12