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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -48.533827 0.0000000) to (29.718538 48.533827 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4033705 5.5147920 5.9736509 Created 1063 atoms using lattice units in orthogonal box = (0.0000000 -48.533827 0.0000000) to (29.718538 48.533827 8.9604763) create_atoms CPU = 0.001 seconds 1063 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4033705 5.5147920 5.9736509 Created 1063 atoms using lattice units in orthogonal box = (0.0000000 -48.533827 0.0000000) to (29.718538 48.533827 8.9604763) create_atoms CPU = 0.001 seconds 1063 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 62 atoms, new total = 2064 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.564 | 5.564 | 5.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7959.3581 0 -7959.3581 -5448.6229 727 0 -8115.891 0 -8115.891 -93237.81 Loop time of 18.6934 on 1 procs for 727 steps with 2064 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 = -7959.35806886829 -8115.88323705869 -8115.89095169733 Force two-norm initial, final = 5.5381144 0.25500892 Force max component initial, final = 0.70256702 0.020070863 Final line search alpha, max atom move = 1.0000000 0.020070863 Iterations, force evaluations = 727 1404 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.215 | 18.215 | 18.215 | 0.0 | 97.44 Neigh | 0.28705 | 0.28705 | 0.28705 | 0.0 | 1.54 Comm | 0.085028 | 0.085028 | 0.085028 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1064 | | | 0.57 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7263.00 ave 7263 max 7263 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: 272446.0 ave 272446 max 272446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272446 Ave neighs/atom = 131.99903 Neighbor list builds = 16 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 727 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.566 | 5.566 | 5.566 Mbytes Step Temp E_pair E_mol TotEng Press Volume 727 0 -8115.891 0 -8115.891 -93237.81 25848.365 769 0 -8208.032 0 -8208.032 20325.925 23801.369 Loop time of 0.58799 on 1 procs for 42 steps with 2064 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 = -8115.89095169732 -8208.02688904428 -8208.0319759601 Force two-norm initial, final = 2980.1278 14.840287 Force max component initial, final = 2176.7396 8.9769598 Final line search alpha, max atom move = 0.00028509114 0.0025592517 Iterations, force evaluations = 42 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55235 | 0.55235 | 0.55235 | 0.0 | 93.94 Neigh | 0.018492 | 0.018492 | 0.018492 | 0.0 | 3.14 Comm | 0.0025246 | 0.0025246 | 0.0025246 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01462 | | | 2.49 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7575.00 ave 7575 max 7575 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: 296862.0 ave 296862 max 296862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296862 Ave neighs/atom = 143.82849 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.087 | 6.087 | 6.087 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8208.032 0 -8208.032 20325.925 Loop time of 1.715e-06 on 1 procs for 0 steps with 2064 atoms 116.6% 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 | | 1.715e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7622.00 ave 7622 max 7622 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: 298610.0 ave 298610 max 298610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298610 Ave neighs/atom = 144.67539 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.087 | 6.087 | 6.087 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 -8208.032 -8208.032 28.535549 97.067655 8.5929279 20325.925 20325.925 -580.22507 60987.091 570.9085 2.3407115 5483.9283 Loop time of 1.703e-06 on 1 procs for 0 steps with 2064 atoms 234.9% 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 | | 1.703e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7622.00 ave 7622 max 7622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149305.0 ave 149305 max 149305 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 298610.0 ave 298610 max 298610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298610 Ave neighs/atom = 144.67539 Neighbor list builds = 0 Dangerous builds = 0 2064 -7916.13774420317 eV 2.34071153960295 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19