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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -49.648009 0.0000000) to (13.511494 49.648009 8.8453489) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7906401 5.5160442 5.8968993 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.648009 0.0000000) to (13.511494 49.648009 8.8453489) create_atoms CPU = 0.001 seconds 507 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7906401 5.5160442 5.8968993 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.648009 0.0000000) to (13.511494 49.648009 8.8453489) create_atoms CPU = 0.001 seconds 507 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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1000 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_150993986463_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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4192.7596 0 -4192.7596 6794.2875 65 0 -4229.6235 0 -4229.6235 -8282.2904 Loop time of 7.72982 on 1 procs for 65 steps with 1000 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 = -4192.75956522857 -4229.61929595549 -4229.62350153626 Force two-norm initial, final = 47.646739 0.20365553 Force max component initial, final = 10.454351 0.053265561 Final line search alpha, max atom move = 1.0000000 0.053265561 Iterations, force evaluations = 65 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6972 | 7.6972 | 7.6972 | 0.0 | 99.58 Neigh | 0.012207 | 0.012207 | 0.012207 | 0.0 | 0.16 Comm | 0.0094431 | 0.0094431 | 0.0094431 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01097 | | | 0.14 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4067.00 ave 4067 max 4067 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: 77258.0 ave 77258 max 77258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77258 Ave neighs/atom = 77.258000 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.570 | 4.570 | 4.570 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -4229.6235 0 -4229.6235 -8282.2904 11867.252 69 0 -4229.6921 0 -4229.6921 -3681.0832 11834.908 Loop time of 0.449248 on 1 procs for 4 steps with 1000 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 = -4229.62350153627 -4229.69208297255 -4229.69208705032 Force two-norm initial, final = 56.330396 0.40683775 Force max component initial, final = 50.860675 0.24700697 Final line search alpha, max atom move = 0.010846660 0.0026792006 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4466 | 0.4466 | 0.4466 | 0.0 | 99.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045848 | 0.00045848 | 0.00045848 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002185 | | | 0.49 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940.00 ave 3940 max 3940 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: 77388.0 ave 77388 max 77388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77388 Ave neighs/atom = 77.388000 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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.708 | 4.708 | 4.708 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4229.6921 0 -4229.6921 -3681.0832 Loop time of 3.149e-06 on 1 procs for 0 steps with 1000 atoms 158.8% 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 | | 3.149e-06 | | |100.00 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940.00 ave 3940 max 3940 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: 77402.0 ave 77402 max 77402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77402 Ave neighs/atom = 77.402000 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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.708 | 4.708 | 4.708 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 -4229.6921 -4229.6921 13.510836 99.296018 8.8216708 -3681.0832 -3681.0832 33.045084 -11109.644 33.349595 2.3257325 413.39253 Loop time of 3.09e-06 on 1 procs for 0 steps with 1000 atoms 194.2% 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 | | 3.09e-06 | | |100.00 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940.00 ave 3940 max 3940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38701.0 ave 38701 max 38701 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77402.0 ave 77402 max 77402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77402 Ave neighs/atom = 77.402000 Neighbor list builds = 0 Dangerous builds = 0 1000 -4229.69208705032 eV 2.3257324542796 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08