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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -45.081688 0.0000000) to (31.875078 45.081688 4.9780508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4420865 6.0470713 4.9780508 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.081688 0.0000000) to (31.875078 45.081688 4.9780508) create_atoms CPU = 0.005 seconds 660 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4420865 6.0470713 4.9780508 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.081688 0.0000000) to (31.875078 45.081688 4.9780508) create_atoms CPU = 0.004 seconds 660 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 = 8 22 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1304 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 22 2 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) = 5.511 | 5.511 | 5.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5755.4817 0 -5755.4817 4791.6832 62 0 -5782.0912 0 -5782.0912 -3230.086 Loop time of 3.48647 on 1 procs for 62 steps with 1304 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5755.48165105414 -5782.08640248936 -5782.09118057897 Force two-norm initial, final = 24.487746 0.22005624 Force max component initial, final = 5.8919258 0.015352200 Final line search alpha, max atom move = 1.0000000 0.015352200 Iterations, force evaluations = 62 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4052 | 3.4052 | 3.4052 | 0.0 | 97.67 Neigh | 0.038873 | 0.038873 | 0.038873 | 0.0 | 1.11 Comm | 0.023759 | 0.023759 | 0.023759 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01863 | | | 0.53 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9361.00 ave 9361 max 9361 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: 292320.0 ave 292320 max 292320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292320 Ave neighs/atom = 224.17178 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 22 2 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.511 | 5.511 | 5.511 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -5782.0912 0 -5782.0912 -3230.086 14306.742 65 0 -5782.1252 0 -5782.1252 -833.49609 14287.283 Loop time of 0.184822 on 1 procs for 3 steps with 1304 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5782.09118057896 -5782.12505526253 -5782.12515346906 Force two-norm initial, final = 42.453045 0.23601839 Force max component initial, final = 41.362981 0.025232205 Final line search alpha, max atom move = 0.00039790609 1.0040048e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18008 | 0.18008 | 0.18008 | 0.0 | 97.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011829 | 0.0011829 | 0.0011829 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003555 | | | 1.92 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9379.00 ave 9379 max 9379 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: 292384.0 ave 292384 max 292384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292384 Ave neighs/atom = 224.22086 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 = 8 22 2 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) = 5.649 | 5.649 | 5.649 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5782.1252 0 -5782.1252 -833.49609 Loop time of 6.916e-06 on 1 procs for 0 steps with 1304 atoms 159.1% 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 | | 6.916e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9379.00 ave 9379 max 9379 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: 292456.0 ave 292456 max 292456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292456 Ave neighs/atom = 224.27607 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 = 8 22 2 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) = 5.649 | 5.649 | 5.649 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 -5782.1252 -5782.1252 31.820144 90.163375 4.9798626 -833.49609 -833.49609 -1.9962417 -2495.6615 -2.8305702 2.2526845 634.63041 Loop time of 6.946e-06 on 1 procs for 0 steps with 1304 atoms 259.1% 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 | | 6.946e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9379.00 ave 9379 max 9379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146228.0 ave 146228 max 146228 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 292456.0 ave 292456 max 292456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292456 Ave neighs/atom = 224.27607 Neighbor list builds = 0 Dangerous builds = 0 1304 -5746.57628558448 eV 2.2526844623525 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04