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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -63.749918 0.0000000) to (22.539000 63.749918 4.9780323) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0470487 5.4420662 4.9780323 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -63.749918 0.0000000) to (22.539000 63.749918 4.9780323) create_atoms CPU = 0.006 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0470487 5.4420662 4.9780323 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.749918 0.0000000) to (22.539000 63.749918 4.9780323) create_atoms CPU = 0.007 seconds 658 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 = 6 34 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 2 atoms, new total = 1312 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_418978237058_005#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 = 6 34 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) = 5.511 | 5.511 | 5.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5758.7061 0 -5758.7061 8746.6788 86 0 -5828.9773 0 -5828.9773 6674.1105 Loop time of 4.09033 on 1 procs for 86 steps with 1312 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 = -5758.70607967386 -5828.97285613459 -5828.97730261132 Force two-norm initial, final = 47.928062 0.23230652 Force max component initial, final = 10.014006 0.035335371 Final line search alpha, max atom move = 1.0000000 0.035335371 Iterations, force evaluations = 86 155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.967 | 3.967 | 3.967 | 0.0 | 96.98 Neigh | 0.065313 | 0.065313 | 0.065313 | 0.0 | 1.60 Comm | 0.032384 | 0.032384 | 0.032384 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02566 | | | 0.63 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8584.00 ave 8584 max 8584 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: 229656.0 ave 229656 max 229656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229656 Ave neighs/atom = 175.04268 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 34 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 : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.511 | 5.511 | 5.511 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -5828.9773 0 -5828.9773 6674.1105 14305.465 89 0 -5829.1136 0 -5829.1136 8.4547013 14358.999 Loop time of 0.156358 on 1 procs for 3 steps with 1312 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 = -5828.97730261131 -5829.10836962463 -5829.1136301063 Force two-norm initial, final = 107.42497 2.4257372 Force max component initial, final = 73.032623 1.8134221 Final line search alpha, max atom move = 7.0589938e-05 0.00012800936 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15174 | 0.15174 | 0.15174 | 0.0 | 97.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011026 | 0.0011026 | 0.0011026 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003518 | | | 2.25 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8568.00 ave 8568 max 8568 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: 229224.0 ave 229224 max 229224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229224 Ave neighs/atom = 174.71341 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 = 6 34 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) = 5.649 | 5.649 | 5.649 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5829.1136 0 -5829.1136 8.4547013 Loop time of 6.044e-06 on 1 procs for 0 steps with 1312 atoms 198.5% 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 | | 6.044e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8568.00 ave 8568 max 8568 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: 229080.0 ave 229080 max 229080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229080 Ave neighs/atom = 174.60366 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 = 6 34 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) = 5.649 | 5.649 | 5.649 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 -5829.1136 -5829.1136 22.577923 127.773 4.9773835 8.4547013 8.4547013 -202.69099 167.29181 60.763284 2.3149286 419.67825 Loop time of 6.866e-06 on 1 procs for 0 steps with 1312 atoms 276.7% 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 | | 6.866e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8568.00 ave 8568 max 8568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114540.0 ave 114540 max 114540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229080.0 ave 229080 max 229080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229080 Ave neighs/atom = 174.60366 Neighbor list builds = 0 Dangerous builds = 0 1312 -5829.1136301063 eV 2.31492864473065 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04