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 = 3.6284291 3.6284291 3.6284291 Created orthogonal box = (0.0000000 -42.932152 0.0000000) to (52.580932 42.932152 8.8877998) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0092494 5.5198481 5.9251998 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -42.932152 0.0000000) to (52.580932 42.932152 8.8877998) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0092494 5.5198481 5.9251998 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -42.932152 0.0000000) to (52.580932 42.932152 8.8877998) create_atoms CPU = 0.003 seconds 1687 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 14 23 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3350 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_650279905230_005#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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 6.551 | 6.551 | 6.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13187.631 0 -13187.631 60267.663 896 0 -14213.683 0 -14213.683 -28404.558 Loop time of 41.2285 on 1 procs for 896 steps with 3350 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 = -13187.6312938266 -14213.6697896807 -14213.6826233741 Force two-norm initial, final = 1412.5860 0.35910323 Force max component initial, final = 287.28240 0.031011749 Final line search alpha, max atom move = 1.0000000 0.031011749 Iterations, force evaluations = 896 1642 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 39.57 | 39.57 | 39.57 | 0.0 | 95.98 Neigh | 1.233 | 1.233 | 1.233 | 0.0 | 2.99 Comm | 0.17259 | 0.17259 | 0.17259 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2527 | | | 0.61 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10341.0 ave 10341 max 10341 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: 501640.0 ave 501640 max 501640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 501640 Ave neighs/atom = 149.74328 Neighbor list builds = 34 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 896 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.933 | 6.933 | 6.933 Mbytes Step Temp E_pair E_mol TotEng Press Volume 896 0 -14213.683 0 -14213.683 -28404.558 40126.862 953 0 -14314.111 0 -14314.111 -10.309917 39499.992 Loop time of 1.52266 on 1 procs for 57 steps with 3350 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14213.682623374 -14314.1090362149 -14314.1113096034 Force two-norm initial, final = 2860.2333 3.9019379 Force max component initial, final = 1997.7762 1.0601446 Final line search alpha, max atom move = 0.00010525314 0.00011158355 Iterations, force evaluations = 57 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3725 | 1.3725 | 1.3725 | 0.0 | 90.14 Neigh | 0.10631 | 0.10631 | 0.10631 | 0.0 | 6.98 Comm | 0.005864 | 0.005864 | 0.005864 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03803 | | | 2.50 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10105.0 ave 10105 max 10105 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: 521158.0 ave 521158 max 521158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 521158 Ave neighs/atom = 155.56955 Neighbor list builds = 3 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 7.068 | 7.068 | 7.068 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14314.111 0 -14314.111 -10.309917 Loop time of 2.17e-06 on 1 procs for 0 steps with 3350 atoms 184.3% 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 | | 2.17e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10026.0 ave 10026 max 10026 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: 533266.0 ave 533266 max 533266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533266 Ave neighs/atom = 159.18388 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 7.068 | 7.068 | 7.068 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 -14314.111 -14314.111 51.115362 82.495321 9.3673392 -10.309917 -10.309917 29.707998 -15.316647 -45.321102 2.3655769 2540.6012 Loop time of 2.729e-06 on 1 procs for 0 steps with 3350 atoms 256.5% 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 | | 2.729e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10026.0 ave 10026 max 10026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 266633.0 ave 266633 max 266633 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 533266.0 ave 533266 max 533266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533266 Ave neighs/atom = 159.18388 Neighbor list builds = 0 Dangerous builds = 0 3350 -14314.1105109012 eV 2.36557685460474 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:43