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 = 3.6131481 3.6131481 3.6131481 Created orthogonal box = (0.0000000 -39.580055 0.0000000) to (8.0792448 39.580055 8.8503693) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8475469 5.2773406 5.9002462 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.580055 0.0000000) to (8.0792448 39.580055 8.8503693) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8475469 5.2773406 5.9002462 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.580055 0.0000000) to (8.0792448 39.580055 8.8503693) create_atoms CPU = 0.000 seconds 242 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 2 16 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 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 476 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_173787283511_004#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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1578.3188 0 -1578.3188 22061.037 84 0 -1650.253 0 -1650.253 -4408.1449 Loop time of 1.19614 on 1 procs for 84 steps with 476 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 = -1578.31877391344 -1650.25151175354 -1650.25297245882 Force two-norm initial, final = 148.30473 0.13161212 Force max component initial, final = 52.073564 0.012732505 Final line search alpha, max atom move = 1.0000000 0.012732505 Iterations, force evaluations = 84 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1621 | 1.1621 | 1.1621 | 0.0 | 97.15 Neigh | 0.021097 | 0.021097 | 0.021097 | 0.0 | 1.76 Comm | 0.0084632 | 0.0084632 | 0.0084632 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004475 | | | 0.37 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6723.00 ave 6723 max 6723 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: 183548.0 ave 183548 max 183548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183548 Ave neighs/atom = 385.60504 Neighbor list builds = 2 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -1650.253 0 -1650.253 -4408.1449 5660.2882 88 0 -1650.2886 0 -1650.2886 10.251439 5641.7789 Loop time of 0.0541008 on 1 procs for 4 steps with 476 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 = -1650.25297245883 -1650.28852784748 -1650.28858886489 Force two-norm initial, final = 28.560200 0.20015357 Force max component initial, final = 22.692368 0.084213790 Final line search alpha, max atom move = 0.00083559707 7.0368797e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052472 | 0.052472 | 0.052472 | 0.0 | 96.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036585 | 0.00036585 | 0.00036585 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001263 | | | 2.33 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 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: 182080.0 ave 182080 max 182080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182080 Ave neighs/atom = 382.52101 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 5.187 | 5.187 | 5.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1650.2886 0 -1650.2886 10.251439 Loop time of 1.908e-06 on 1 procs for 0 steps with 476 atoms 104.8% 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 | | 1.908e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 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: 182408.0 ave 182408 max 182408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182408 Ave neighs/atom = 383.21008 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 5.187 | 5.187 | 5.187 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 -1650.2886 -1650.2886 8.0817882 78.945147 8.8426647 10.251439 10.251439 16.484224 23.850449 -9.5803572 2.3157017 261.31995 Loop time of 1.71e-06 on 1 procs for 0 steps with 476 atoms 175.4% 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 | | 1.71e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91204.0 ave 91204 max 91204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 182408.0 ave 182408 max 182408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182408 Ave neighs/atom = 383.21008 Neighbor list builds = 0 Dangerous builds = 0 476 -1650.28858886489 eV 2.31570169332275 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01