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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -57.932001 0.0000000) to (35.473708 57.932001 9.0103308) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7215658 5.6059667 6.0068872 Created 1490 atoms using lattice units in orthogonal box = (0.0000000 -57.932001 0.0000000) to (35.473708 57.932001 9.0103308) create_atoms CPU = 0.006 seconds 1490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7215658 5.6059667 6.0068872 Created 1490 atoms using lattice units in orthogonal box = (0.0000000 -57.932001 0.0000000) to (35.473708 57.932001 9.0103308) create_atoms CPU = 0.006 seconds 1490 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 38 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2952 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.619 | 5.619 | 5.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12368.832 0 -12368.832 2408.2168 63 0 -12441.741 0 -12441.741 -11415.881 Loop time of 2.06997 on 1 procs for 63 steps with 2952 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12368.8319595053 -12441.728877791 -12441.7406788506 Force two-norm initial, final = 53.324210 0.36139139 Force max component initial, final = 8.2735063 0.055882672 Final line search alpha, max atom move = 1.0000000 0.055882672 Iterations, force evaluations = 63 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9771 | 1.9771 | 1.9771 | 0.0 | 95.51 Neigh | 0.039185 | 0.039185 | 0.039185 | 0.0 | 1.89 Comm | 0.020808 | 0.020808 | 0.020808 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03291 | | | 1.59 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7624.00 ave 7624 max 7624 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: 229456.0 ave 229456 max 229456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229456 Ave neighs/atom = 77.728997 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.619 | 5.619 | 5.619 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -12441.741 0 -12441.741 -11415.881 37033.593 68 0 -12442.465 0 -12442.465 -3885.6534 36770.768 Loop time of 0.146423 on 1 procs for 5 steps with 2952 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 = -12441.7406788507 -12442.4645821637 -12442.4648327653 Force two-norm initial, final = 285.62005 0.49108518 Force max component initial, final = 216.24562 0.069328229 Final line search alpha, max atom move = 0.00033062697 2.2921783e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13853 | 0.13853 | 0.13853 | 0.0 | 94.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013501 | 0.0013501 | 0.0013501 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00654 | | | 4.47 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7618.00 ave 7618 max 7618 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: 229334.0 ave 229334 max 229334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229334 Ave neighs/atom = 77.687669 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.757 | 5.757 | 5.757 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12442.465 0 -12442.465 -3885.6534 Loop time of 6.665e-06 on 1 procs for 0 steps with 2952 atoms 195.0% 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 | | 6.665e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7641.00 ave 7641 max 7641 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: 229550.0 ave 229550 max 229550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229550 Ave neighs/atom = 77.760840 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.757 | 5.757 | 5.757 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 -12442.465 -12442.465 35.363344 115.864 8.9743054 -3885.6534 -3885.6534 -2.3361352 -11656.038 1.4138452 2.3547121 1190.2703 Loop time of 6.546e-06 on 1 procs for 0 steps with 2952 atoms 290.3% 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 | | 6.546e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7641.00 ave 7641 max 7641 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114775.0 ave 114775 max 114775 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229550.0 ave 229550 max 229550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229550 Ave neighs/atom = 77.760840 Neighbor list builds = 0 Dangerous builds = 0 2952 -12442.4645375653 eV 2.35471205385962 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02