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 = 3.5224675 3.5224675 3.5224675 Created orthogonal box = (0.0000000 -70.625253 0.0000000) to (40.775509 70.625253 6.1010926) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4773072 5.6219107 6.1010926 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.625253 0.0000000) to (40.775509 70.625253 6.1010926) create_atoms CPU = 0.005 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4773072 5.6219107 6.1010926 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.625253 0.0000000) to (40.775509 70.625253 6.1010926) create_atoms CPU = 0.005 seconds 1610 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 40 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_763197941039_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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 6.656 | 6.656 | 6.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12787.43 0 -12787.43 111081.18 104 0 -14266.503 0 -14266.503 13166.981 Loop time of 3.97157 on 1 procs for 104 steps with 3216 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12787.4296201506 -14266.4892752019 -14266.5029825874 Force two-norm initial, final = 2265.1052 0.56483829 Force max component initial, final = 628.58175 0.15073361 Final line search alpha, max atom move = 0.35313072 0.053228670 Iterations, force evaluations = 104 189 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7708 | 3.7708 | 3.7708 | 0.0 | 94.94 Neigh | 0.13788 | 0.13788 | 0.13788 | 0.0 | 3.47 Comm | 0.031759 | 0.031759 | 0.031759 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03115 | | | 0.78 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13230.0 ave 13230 max 13230 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: 447916.0 ave 447916 max 447916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447916 Ave neighs/atom = 139.27736 Neighbor list builds = 5 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.41 | 10.41 | 10.41 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -14266.503 0 -14266.503 13166.981 35139.617 112 0 -14268.261 0 -14268.261 -50.62923 35375.381 Loop time of 0.266274 on 1 procs for 8 steps with 3216 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 = -14266.5029825874 -14268.2600418743 -14268.2607751468 Force two-norm initial, final = 580.37310 3.7682155 Force max component initial, final = 521.29725 3.3373532 Final line search alpha, max atom move = 0.00010555442 0.00035227239 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22749 | 0.22749 | 0.22749 | 0.0 | 85.44 Neigh | 0.03018 | 0.03018 | 0.03018 | 0.0 | 11.33 Comm | 0.0017514 | 0.0017514 | 0.0017514 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006851 | | | 2.57 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13220.0 ave 13220 max 13220 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: 447532.0 ave 447532 max 447532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447532 Ave neighs/atom = 139.15796 Neighbor list builds = 1 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 9.927 | 9.927 | 9.927 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14268.261 0 -14268.261 -50.62923 Loop time of 2.304e-06 on 1 procs for 0 steps with 3216 atoms 173.6% 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 | | 2.304e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13258.0 ave 13258 max 13258 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: 447596.0 ave 447596 max 447596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447596 Ave neighs/atom = 139.17786 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 9.927 | 9.927 | 9.927 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 -14268.261 -14268.261 40.798815 142.23764 6.0959169 -50.62923 -50.62923 -151.23753 -49.654289 49.004126 2.3004412 1139.5055 Loop time of 2.302e-06 on 1 procs for 0 steps with 3216 atoms 260.6% 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 | | 2.302e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13258.0 ave 13258 max 13258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 223798.0 ave 223798 max 223798 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 447596.0 ave 447596 max 447596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447596 Ave neighs/atom = 139.17786 Neighbor list builds = 0 Dangerous builds = 0 3216 -14268.2607751468 eV 2.30044121792389 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04