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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -51.662871 0.0000000) to (36.529137 51.662871 4.0587930) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9607470 4.7833335 4.0587930 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.662871 0.0000000) to (36.529137 51.662871 4.0587930) create_atoms CPU = 0.004 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9607470 4.7833335 4.0587930 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.662871 0.0000000) to (36.529137 51.662871 4.0587930) create_atoms CPU = 0.003 seconds 650 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 34 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1292 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.652 | 4.652 | 4.652 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5392.307 0 -5392.307 22418.863 78 0 -5513.3771 0 -5513.3771 -14.624443 Loop time of 1.28606 on 1 procs for 78 steps with 1292 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5392.30696267599 -5513.37191040595 -5513.37710976079 Force two-norm initial, final = 115.39762 0.27002649 Force max component initial, final = 21.731786 0.045972588 Final line search alpha, max atom move = 1.0000000 0.045972588 Iterations, force evaluations = 78 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2246 | 1.2246 | 1.2246 | 0.0 | 95.22 Neigh | 0.030699 | 0.030699 | 0.030699 | 0.0 | 2.39 Comm | 0.01562 | 0.01562 | 0.01562 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01518 | | | 1.18 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6585.00 ave 6585 max 6585 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: 84428.0 ave 84428 max 84428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84428 Ave neighs/atom = 65.346749 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.663 | 4.663 | 4.663 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -5513.3771 0 -5513.3771 -14.624443 15319.509 80 0 -5513.4156 0 -5513.4156 -215.3396 15321.429 Loop time of 0.0367515 on 1 procs for 2 steps with 1292 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 = -5513.37710976079 -5513.41053974043 -5513.41560936931 Force two-norm initial, final = 40.874614 1.5105588 Force max component initial, final = 33.416962 1.2098515 Final line search alpha, max atom move = 8.3109188e-05 0.00010054978 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.034542 | 0.034542 | 0.034542 | 0.0 | 93.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042686 | 0.00042686 | 0.00042686 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001783 | | | 4.85 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7402.00 ave 7402 max 7402 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: 84280.0 ave 84280 max 84280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84280 Ave neighs/atom = 65.232198 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.801 | 4.801 | 4.801 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5513.4156 0 -5513.4156 -215.3396 Loop time of 3.021e-06 on 1 procs for 0 steps with 1292 atoms 132.4% 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 | | 3.021e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7392.00 ave 7392 max 7392 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: 84252.0 ave 84252 max 84252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84252 Ave neighs/atom = 65.210526 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.801 | 4.801 | 4.801 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 -5513.4156 -5513.4156 36.580139 103.32574 4.0536419 -215.3396 -215.3396 126.69198 -862.5355 89.824719 2.2805014 532.01253 Loop time of 3.33e-06 on 1 procs for 0 steps with 1292 atoms 180.2% 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 | | 3.33e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7392.00 ave 7392 max 7392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42126.0 ave 42126 max 42126 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84252.0 ave 84252 max 84252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84252 Ave neighs/atom = 65.210526 Neighbor list builds = 0 Dangerous builds = 0 1292 -5513.41548016931 eV 2.28050140371964 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01