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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -41.254670 0.0000000) to (35.727592 41.254670 7.0067573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4126448 6.3468723 7.0067573 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -41.254670 0.0000000) to (35.727592 41.254670 7.0067573) create_atoms CPU = 0.001 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4126448 6.3468723 7.0067573 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -41.254670 0.0000000) to (35.727592 41.254670 7.0067573) create_atoms CPU = 0.001 seconds 628 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1246 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3969.7107 0 -3969.7107 21515.369 77 0 -4166.9348 0 -4166.9348 3856.3191 Loop time of 4.16533 on 1 procs for 77 steps with 1246 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 = -3969.71070218925 -4166.93209851553 -4166.93478107159 Force two-norm initial, final = 261.67773 0.19230942 Force max component initial, final = 57.516016 0.058573688 Final line search alpha, max atom move = 1.0000000 0.058573688 Iterations, force evaluations = 77 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1258 | 4.1258 | 4.1258 | 0.0 | 99.05 Neigh | 0.024937 | 0.024937 | 0.024937 | 0.0 | 0.60 Comm | 0.0054267 | 0.0054267 | 0.0054267 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009207 | | | 0.22 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3895.00 ave 3895 max 3895 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: 68084.0 ave 68084 max 68084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68084 Ave neighs/atom = 54.642055 Neighbor list builds = 4 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -4166.9348 0 -4166.9348 3856.3191 20654.94 85 0 -4167.2416 0 -4167.2416 46.969736 20760.286 Loop time of 0.357291 on 1 procs for 8 steps with 1246 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4166.93478107158 -4167.24095376535 -4167.24163171961 Force two-norm initial, final = 100.76196 1.1078587 Force max component initial, final = 91.960605 0.68127203 Final line search alpha, max atom move = 0.00042165582 0.00028726232 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35494 | 0.35494 | 0.35494 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032304 | 0.00032304 | 0.00032304 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002028 | | | 0.57 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3899.00 ave 3899 max 3899 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: 68068.0 ave 68068 max 68068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68068 Ave neighs/atom = 54.629213 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.746 | 4.746 | 4.746 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4167.2416 0 -4167.2416 46.969736 Loop time of 1.934e-06 on 1 procs for 0 steps with 1246 atoms 206.8% 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 | | 1.934e-06 | | |100.00 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3899.00 ave 3899 max 3899 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: 67994.0 ave 67994 max 67994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67994 Ave neighs/atom = 54.569823 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.746 | 4.746 | 4.746 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 -4167.2416 -4167.2416 35.710449 83.112845 6.9947125 46.969736 46.969736 39.799484 52.961786 48.147938 2.4840278 1045.169 Loop time of 2.285e-06 on 1 procs for 0 steps with 1246 atoms 218.8% 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 | | 2.285e-06 | | |100.00 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3899.00 ave 3899 max 3899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33997.0 ave 33997 max 33997 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67994.0 ave 67994 max 67994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67994 Ave neighs/atom = 54.569823 Neighbor list builds = 0 Dangerous builds = 0 1246 -4167.24163171961 eV 2.4840277628602 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04