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 = 3.5240105 3.5240105 3.5240105 Created orthogonal box = (0.0000000 -62.246436 0.0000000) to (35.937997 62.246436 6.1037652) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5289226 5.5862186 6.1037652 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -62.246436 0.0000000) to (35.937997 62.246436 6.1037652) create_atoms CPU = 0.003 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5289226 5.5862186 6.1037652 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -62.246436 0.0000000) to (35.937997 62.246436 6.1037652) create_atoms CPU = 0.003 seconds 1251 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 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, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2490 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_535504325462_003#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.525 | 6.525 | 6.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11137.757 0 -11137.757 9405.1643 79 0 -11240.212 0 -11240.212 5483.2222 Loop time of 3.12342 on 1 procs for 79 steps with 2490 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11137.7572137759 -11240.2022163509 -11240.2117758941 Force two-norm initial, final = 72.399826 0.33916834 Force max component initial, final = 10.447375 0.10182624 Final line search alpha, max atom move = 1.0000000 0.10182624 Iterations, force evaluations = 79 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0161 | 3.0161 | 3.0161 | 0.0 | 96.56 Neigh | 0.074162 | 0.074162 | 0.074162 | 0.0 | 2.37 Comm | 0.015966 | 0.015966 | 0.015966 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01719 | | | 0.55 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10836.0 ave 10836 max 10836 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: 434860.0 ave 434860 max 434860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434860 Ave neighs/atom = 174.64257 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.525 | 6.525 | 6.525 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -11240.212 0 -11240.212 5483.2222 27308.395 83 0 -11240.499 0 -11240.499 117.4038 27389.351 Loop time of 0.128412 on 1 procs for 4 steps with 2490 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 = -11240.2117758942 -11240.4976097652 -11240.4987083654 Force two-norm initial, final = 194.76800 5.2272419 Force max component initial, final = 173.60610 4.9289857 Final line search alpha, max atom move = 9.7984907e-05 0.00048296620 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12542 | 0.12542 | 0.12542 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048516 | 0.00048516 | 0.00048516 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002502 | | | 1.95 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10793.0 ave 10793 max 10793 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: 434950.0 ave 434950 max 434950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434950 Ave neighs/atom = 174.67871 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.662 | 6.662 | 6.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11240.499 0 -11240.499 117.4038 Loop time of 2.174e-06 on 1 procs for 0 steps with 2490 atoms 184.0% 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 | | 2.174e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10747.0 ave 10747 max 10747 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: 434822.0 ave 434822 max 434822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434822 Ave neighs/atom = 174.62731 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.662 | 6.662 | 6.662 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 -11240.499 -11240.499 35.960404 124.86835 6.0996485 117.4038 117.4038 -31.03604 289.19718 94.050271 2.2279042 953.25328 Loop time of 2.266e-06 on 1 procs for 0 steps with 2490 atoms 264.8% 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 | | 2.266e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10747.0 ave 10747 max 10747 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 217411.0 ave 217411 max 217411 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 434822.0 ave 434822 max 434822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434822 Ave neighs/atom = 174.62731 Neighbor list builds = 0 Dangerous builds = 0 2490 -11240.4987083654 eV 2.22790419835773 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03