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 = 4.0500004 4.0500004 4.0500004 Created orthogonal box = (0.0000000 -43.623889 0.0000000) to (21.809920 43.623889 4.0500004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2644634 5.2644634 4.0500004 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.623889 0.0000000) to (21.809920 43.623889 4.0500004) create_atoms CPU = 0.001 seconds 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2644634 5.2644634 4.0500004 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.623889 0.0000000) to (21.809920 43.623889 4.0500004) create_atoms CPU = 0.000 seconds 233 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 = 6 23 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 456 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_820335782779_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 = 6 23 2 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) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1516.9374 0 -1516.9374 3540.5357 62 0 -1526.6052 0 -1526.6052 -6631.9808 Loop time of 0.385868 on 1 procs for 62 steps with 456 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 = -1516.93742892815 -1526.60366532644 -1526.6051675884 Force two-norm initial, final = 14.725368 0.11330673 Force max component initial, final = 4.5269086 0.028470312 Final line search alpha, max atom move = 1.0000000 0.028470312 Iterations, force evaluations = 62 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37534 | 0.37534 | 0.37534 | 0.0 | 97.27 Neigh | 0.0034014 | 0.0034014 | 0.0034014 | 0.0 | 0.88 Comm | 0.0040718 | 0.0040718 | 0.0040718 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003058 | | | 0.79 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4134.00 ave 4134 max 4134 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: 59474.0 ave 59474 max 59474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59474 Ave neighs/atom = 130.42544 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 = 6 23 2 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.471 | 4.471 | 4.471 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -1526.6052 0 -1526.6052 -6631.9808 7706.6123 67 0 -1526.7111 0 -1526.7111 -1034.0809 7653.6089 Loop time of 0.0273465 on 1 procs for 5 steps with 456 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 = -1526.6051675884 -1526.710516863 -1526.71114159922 Force two-norm initial, final = 42.821917 0.24547745 Force max component initial, final = 31.718687 0.063991936 Final line search alpha, max atom move = 0.00068729088 4.3981074e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.025909 | 0.025909 | 0.025909 | 0.0 | 94.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025163 | 0.00025163 | 0.00025163 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001186 | | | 4.34 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4179.00 ave 4179 max 4179 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: 59610.0 ave 59610 max 59610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59610 Ave neighs/atom = 130.72368 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 = 6 23 2 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) = 4.609 | 4.609 | 4.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1526.7111 0 -1526.7111 -1034.0809 Loop time of 1.89e-06 on 1 procs for 0 steps with 456 atoms 105.8% 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 | | 1.89e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4179.00 ave 4179 max 4179 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: 59676.0 ave 59676 max 59676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59676 Ave neighs/atom = 130.86842 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 = 6 23 2 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) = 4.609 | 4.609 | 4.609 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 -1526.7111 -1526.7111 21.754131 87.247779 4.0324607 -1034.0809 -1034.0809 -5.1046722 -3101.7619 4.623719 2.6108106 412.91374 Loop time of 1.848e-06 on 1 procs for 0 steps with 456 atoms 216.5% 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 | | 1.848e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4179.00 ave 4179 max 4179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29838.0 ave 29838 max 29838 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59676.0 ave 59676 max 59676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59676 Ave neighs/atom = 130.86842 Neighbor list builds = 0 Dangerous builds = 0 456 -1526.71114159922 eV 2.61081064950783 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00