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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -37.341156 0.0000000) to (45.729030 37.341156 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8200583 5.4309231 5.8134559 Created 1321 atoms using lattice units in orthogonal box = (0.0000000 -37.341156 0.0000000) to (45.729030 37.341156 8.7201838) create_atoms CPU = 0.002 seconds 1321 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8200583 5.4309231 5.8134559 Created 1321 atoms using lattice units in orthogonal box = (0.0000000 -37.341156 0.0000000) to (45.729030 37.341156 8.7201838) create_atoms CPU = 0.002 seconds 1321 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 50 atoms, new total = 2592 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.485 | 6.485 | 6.485 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11257.306 0 -11257.306 -11851.648 32 0 -11345.29 0 -11345.29 -13728.384 Loop time of 1.10776 on 1 procs for 32 steps with 2592 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11257.306144237 -11345.2791911786 -11345.2903242898 Force two-norm initial, final = 48.895987 0.50192715 Force max component initial, final = 6.2925711 0.065750342 Final line search alpha, max atom move = 1.0000000 0.065750342 Iterations, force evaluations = 32 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0712 | 1.0712 | 1.0712 | 0.0 | 96.70 Neigh | 0.026017 | 0.026017 | 0.026017 | 0.0 | 2.35 Comm | 0.0041362 | 0.0041362 | 0.0041362 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006409 | | | 0.58 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8926.00 ave 8926 max 8926 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: 450674.0 ave 450674 max 450674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450674 Ave neighs/atom = 173.87114 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.485 | 6.485 | 6.485 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -11345.29 0 -11345.29 -13728.384 29780.733 38 0 -11346.198 0 -11346.198 -2327.8355 29600.978 Loop time of 0.163742 on 1 procs for 6 steps with 2592 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 = -11345.2903242898 -11346.1918322203 -11346.1982324733 Force two-norm initial, final = 351.96891 13.156970 Force max component initial, final = 299.39993 12.782766 Final line search alpha, max atom move = 4.1062601e-05 0.00052489364 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16024 | 0.16024 | 0.16024 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005224 | 0.0005224 | 0.0005224 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00298 | | | 1.82 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8929.00 ave 8929 max 8929 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: 451046.0 ave 451046 max 451046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451046 Ave neighs/atom = 174.01466 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.623 | 6.623 | 6.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11346.198 0 -11346.198 -2327.8355 Loop time of 2.329e-06 on 1 procs for 0 steps with 2592 atoms 128.8% 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 | | 2.329e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8931.00 ave 8931 max 8931 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: 451594.0 ave 451594 max 451594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451594 Ave neighs/atom = 174.22608 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.623 | 6.623 | 6.623 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 -11346.198 -11346.198 45.686528 74.682313 8.6756126 -2327.8355 -2327.8355 -162.79411 -6132.3714 -688.34104 2.356976 1439.7322 Loop time of 2.129e-06 on 1 procs for 0 steps with 2592 atoms 187.9% 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 | | 2.129e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8931.00 ave 8931 max 8931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 225797.0 ave 225797 max 225797 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 451594.0 ave 451594 max 451594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451594 Ave neighs/atom = 174.22608 Neighbor list builds = 0 Dangerous builds = 0 2592 -11346.1982324733 eV 2.35697598399932 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01