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 = 3.4921275 3.4921275 3.4921275 Created orthogonal box = (0.0000000 -42.195538 0.0000000) to (51.678768 42.195538 8.5539306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9554983 5.2021896 5.7026204 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -42.195538 0.0000000) to (51.678768 42.195538 8.5539306) create_atoms CPU = 0.005 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9554983 5.2021896 5.7026204 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.195538 0.0000000) to (51.678768 42.195538 8.5539306) create_atoms CPU = 0.002 seconds 1754 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 13 22 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 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 3482 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_270337113239_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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 13 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 7.866 | 7.866 | 7.866 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10195.843 0 -10195.843 85832.407 85 0 -11537.707 0 -11537.707 -3010.2897 Loop time of 4.84409 on 1 procs for 85 steps with 3482 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 = -10195.8426511971 -11537.6960037243 -11537.7068825556 Force two-norm initial, final = 2022.1304 0.25649125 Force max component initial, final = 394.99076 0.021036098 Final line search alpha, max atom move = 1.0000000 0.021036098 Iterations, force evaluations = 85 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7063 | 4.7063 | 4.7063 | 0.0 | 97.15 Neigh | 0.086822 | 0.086822 | 0.086822 | 0.0 | 1.79 Comm | 0.022077 | 0.022077 | 0.022077 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02893 | | | 0.60 Nlocal: 3482.00 ave 3482 max 3482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12138.0 ave 12138 max 12138 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: 691448.0 ave 691448 max 691448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 691448 Ave neighs/atom = 198.57783 Neighbor list builds = 2 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 13 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.863 | 7.863 | 7.863 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -11537.707 0 -11537.707 -3010.2897 37305.632 89 0 -11537.854 0 -11537.854 -0.41762659 37194.409 Loop time of 0.245588 on 1 procs for 4 steps with 3482 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 = -11537.7068825557 -11537.8532585968 -11537.85367251 Force two-norm initial, final = 127.20581 0.28679887 Force max component initial, final = 96.352470 0.035949770 Final line search alpha, max atom move = 0.00033631190 1.2090335e-05 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2406 | 0.2406 | 0.2406 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072631 | 0.00072631 | 0.00072631 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004257 | | | 1.73 Nlocal: 3482.00 ave 3482 max 3482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11884.0 ave 11884 max 11884 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: 692736.0 ave 692736 max 692736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 692736 Ave neighs/atom = 198.94773 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 13 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 8.001 | 8.001 | 8.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11537.854 0 -11537.854 -0.41762659 Loop time of 2.248e-06 on 1 procs for 0 steps with 3482 atoms 177.9% 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 | | 2.248e-06 | | |100.00 Nlocal: 3482.00 ave 3482 max 3482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11884.0 ave 11884 max 11884 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: 693252.0 ave 693252 max 693252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 693252 Ave neighs/atom = 199.09592 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 13 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 8.001 | 8.001 | 8.001 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 -11537.854 -11537.854 51.639041 84.164427 8.5579732 -0.41762659 -0.41762659 -1.5473723 0.14811255 0.14638 2.2811526 1296.7717 Loop time of 2.242e-06 on 1 procs for 0 steps with 3482 atoms 267.6% 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 | | 2.242e-06 | | |100.00 Nlocal: 3482.00 ave 3482 max 3482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11884.0 ave 11884 max 11884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 346626.0 ave 346626 max 346626 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 693252.0 ave 693252 max 693252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 693252 Ave neighs/atom = 199.09592 Neighbor list builds = 0 Dangerous builds = 0 3482 -11390.830985503 eV 2.28115256392104 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05