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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -29.461410 0.0000000) to (14.729261 29.461410 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.3990602 3.3990602 2.8886457 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -29.461410 0.0000000) to (14.729261 29.461410 2.8886457) create_atoms CPU = 0.002 seconds 106 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.3990602 3.3990602 2.8886457 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -29.461410 0.0000000) to (14.729261 29.461410 2.8886457) create_atoms CPU = 0.001 seconds 106 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 8 atoms, new total = 204 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.381 | 4.381 | 4.381 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -839.51143 0 -839.51143 -6697.2694 48 0 -846.356 0 -846.356 -25134.264 Loop time of 4.03803 on 1 procs for 48 steps with 204 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -839.511429443681 -846.355184657429 -846.35599559618 Force two-norm initial, final = 10.622313 0.13055905 Force max component initial, final = 2.8958280 0.025506534 Final line search alpha, max atom move = 1.0000000 0.025506534 Iterations, force evaluations = 48 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.029 | 4.029 | 4.029 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0047519 | 0.0047519 | 0.0047519 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004247 | | | 0.11 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1662.00 ave 1662 max 1662 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: 11528.0 ave 11528 max 11528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11528 Ave neighs/atom = 56.509804 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.381 | 4.381 | 4.381 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -846.356 0 -846.356 -25134.264 2507.0255 59 0 -846.66801 0 -846.66801 -1226.2098 2471.0103 Loop time of 0.683197 on 1 procs for 11 steps with 204 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 = -846.355995596181 -846.667791438959 -846.66800652801 Force two-norm initial, final = 59.354384 0.31853615 Force max component initial, final = 46.720733 0.087406213 Final line search alpha, max atom move = 0.00088287588 7.7168837e-05 Iterations, force evaluations = 11 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67997 | 0.67997 | 0.67997 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067281 | 0.00067281 | 0.00067281 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002557 | | | 0.37 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1662.00 ave 1662 max 1662 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: 11696.0 ave 11696 max 11696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11696 Ave neighs/atom = 57.333333 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.519 | 4.519 | 4.519 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -846.66801 0 -846.66801 -1226.2098 Loop time of 8.941e-06 on 1 procs for 0 steps with 204 atoms 134.2% 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 | | 8.941e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1662.00 ave 1662 max 1662 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: 11720.0 ave 11720 max 11720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11720 Ave neighs/atom = 57.450980 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.519 | 4.519 | 4.519 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 -846.66801 -846.66801 14.596267 58.92282 2.8730899 -1226.2098 -1226.2098 -56.161536 -3652.5326 30.064646 2.3723253 143.54078 Loop time of 9.492e-06 on 1 procs for 0 steps with 204 atoms 168.6% 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 | | 9.492e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1662.00 ave 1662 max 1662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5860.00 ave 5860 max 5860 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11720.0 ave 11720 max 11720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11720 Ave neighs/atom = 57.450980 Neighbor list builds = 0 Dangerous builds = 0 204 -846.66800652801 eV 2.37232529183962 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05