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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -42.753328 0.0000000) to (52.361919 42.753328 8.8507797) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9842193 5.4968564 5.9005198 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -42.753328 0.0000000) to (52.361919 42.753328 8.8507797) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9842193 5.4968564 5.9005198 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -42.753328 0.0000000) to (52.361919 42.753328 8.8507797) create_atoms CPU = 0.002 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 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 6.5 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_353393547686_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.695 | 5.695 | 5.695 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11343.085 0 -11343.085 39872.175 121 0 -11803.137 0 -11803.137 4050.6443 Loop time of 18.1414 on 1 procs for 121 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 = -11343.0846041442 -11803.1268985573 -11803.136836846 Force two-norm initial, final = 392.50410 0.34635096 Force max component initial, final = 64.577116 0.097267730 Final line search alpha, max atom move = 1.0000000 0.097267730 Iterations, force evaluations = 121 211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.011 | 18.011 | 18.011 | 0.0 | 99.28 Neigh | 0.072209 | 0.072209 | 0.072209 | 0.0 | 0.40 Comm | 0.022745 | 0.022745 | 0.022745 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03513 | | | 0.19 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8524.00 ave 8524 max 8524 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: 288604.0 ave 288604 max 288604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288604 Ave neighs/atom = 86.150448 Neighbor list builds = 3 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 121 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.692 | 5.692 | 5.692 Mbytes Step Temp E_pair E_mol TotEng Press Volume 121 0 -11803.137 0 -11803.137 4050.6443 39627.53 125 0 -11803.479 0 -11803.479 -326.57881 39750.313 Loop time of 0.50494 on 1 procs for 4 steps with 3350 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 = -11803.136836846 -11803.4726975135 -11803.4791858745 Force two-norm initial, final = 208.16090 15.985157 Force max component initial, final = 164.36509 13.325662 Final line search alpha, max atom move = 4.6259590e-05 0.00061643967 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50182 | 0.50182 | 0.50182 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041665 | 0.00041665 | 0.00041665 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0027 | | | 0.53 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8269.00 ave 8269 max 8269 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: 288552.0 ave 288552 max 288552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288552 Ave neighs/atom = 86.134925 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.830 | 5.830 | 5.830 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11803.479 0 -11803.479 -326.57881 Loop time of 2.327e-06 on 1 procs for 0 steps with 3350 atoms 214.9% 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 | | 2.327e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8269.00 ave 8269 max 8269 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: 288346.0 ave 288346 max 288346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288346 Ave neighs/atom = 86.073433 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.830 | 5.830 | 5.830 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 -11803.479 -11803.479 52.44872 85.762647 8.8370534 -326.57881 -326.57881 -341.03552 -102.42961 -536.27131 2.2834672 1844.7751 Loop time of 2.59e-06 on 1 procs for 0 steps with 3350 atoms 231.7% 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 | | 2.59e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8269.00 ave 8269 max 8269 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144173.0 ave 144173 max 144173 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288346.0 ave 288346 max 288346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288346 Ave neighs/atom = 86.073433 Neighbor list builds = 0 Dangerous builds = 0 3350 -11803.4791858745 eV 2.28346717440655 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19