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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -32.018800 0.0000000) to (6.4037600 32.018800 2.8638485) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8422560 3.8422560 2.8638485 Created 50 atoms using lattice units in orthogonal box = (0.0000000 -32.018800 0.0000000) to (6.4037600 32.018800 2.8638485) create_atoms CPU = 0.001 seconds 50 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8422560 3.8422560 2.8638485 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -32.018800 0.0000000) to (6.4037600 32.018800 2.8638485) create_atoms CPU = 0.000 seconds 51 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 11 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 99 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 11 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -401.68618 0 -401.68618 17983.887 40 0 -410.08318 0 -410.08318 -5046.1056 Loop time of 0.721172 on 1 procs for 40 steps with 99 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 = -401.686177756359 -410.082804903125 -410.083183451127 Force two-norm initial, final = 22.994405 0.080478777 Force max component initial, final = 10.558774 0.021082800 Final line search alpha, max atom move = 1.0000000 0.021082800 Iterations, force evaluations = 40 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70661 | 0.70661 | 0.70661 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010417 | 0.010417 | 0.010417 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004142 | | | 0.57 Nlocal: 99.0000 ave 99 max 99 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5733.00 ave 5733 max 5733 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: 59716.0 ave 59716 max 59716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59716 Ave neighs/atom = 603.19192 Neighbor list builds = 0 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 11 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -410.08318 0 -410.08318 -5046.1056 1174.4111 526 0 -413.18789 0 -413.18789 -1169.4881 1167.5384 Loop time of 5.62095 on 1 procs for 486 steps with 99 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 = -410.083183451126 -413.187477926642 -413.187889033349 Force two-norm initial, final = 23.726281 1.6012931 Force max component initial, final = 20.593928 0.90253521 Final line search alpha, max atom move = 0.0046656645 0.0042109265 Iterations, force evaluations = 486 577 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3214 | 5.3214 | 5.3214 | 0.0 | 94.67 Neigh | 0.032979 | 0.032979 | 0.032979 | 0.0 | 0.59 Comm | 0.074951 | 0.074951 | 0.074951 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1917 | | | 3.41 Nlocal: 99.0000 ave 99 max 99 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6111.00 ave 6111 max 6111 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: 60754.0 ave 60754 max 60754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60754 Ave neighs/atom = 613.67677 Neighbor list builds = 5 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -413.18789 0 -413.18789 -1169.4881 Loop time of 6.375e-06 on 1 procs for 0 steps with 99 atoms 172.5% 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 | | 6.375e-06 | | |100.00 Nlocal: 99.0000 ave 99 max 99 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6111.00 ave 6111 max 6111 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: 60710.0 ave 60710 max 60710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60710 Ave neighs/atom = 613.23232 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 4.615 | 4.615 | 4.615 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 -413.18789 -413.18789 6.5049023 69.307252 2.5897134 -1169.4881 -1169.4881 -1192.9934 -1195.5046 -1119.9664 2.3716583 359.26959 Loop time of 8.099e-06 on 1 procs for 0 steps with 99 atoms 271.6% 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 | | 8.099e-06 | | |100.00 Nlocal: 99.0000 ave 99 max 99 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6111.00 ave 6111 max 6111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30355.0 ave 30355 max 30355 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60710.0 ave 60710 max 60710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60710 Ave neighs/atom = 613.23232 Neighbor list builds = 0 Dangerous builds = 0 99 -413.187889033349 eV 2.37165827101179 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06