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 = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -35.683341 0.0000000) to (30.899649 35.683341 6.0599198) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5460909 5.4892064 6.0599198 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -35.683341 0.0000000) to (30.899649 35.683341 6.0599198) create_atoms CPU = 0.004 seconds 628 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5460909 5.4892064 6.0599198 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -35.683341 0.0000000) to (30.899649 35.683341 6.0599198) create_atoms CPU = 0.004 seconds 627 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 29 atoms, new total = 1226 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.451 | 5.451 | 5.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4984.8883 0 -4984.8883 3031.5481 82 0 -5017.4069 0 -5017.4069 -15201.16 Loop time of 3.79174 on 1 procs for 82 steps with 1226 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 = -4984.88825021197 -5017.4024699815 -5017.40689311334 Force two-norm initial, final = 28.280952 0.27165672 Force max component initial, final = 7.8279062 0.067162951 Final line search alpha, max atom move = 1.0000000 0.067162951 Iterations, force evaluations = 82 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6894 | 3.6894 | 3.6894 | 0.0 | 97.30 Neigh | 0.055132 | 0.055132 | 0.055132 | 0.0 | 1.45 Comm | 0.024343 | 0.024343 | 0.024343 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0229 | | | 0.60 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6191.00 ave 6191 max 6191 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: 212392.0 ave 212392 max 212392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212392 Ave neighs/atom = 173.23980 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.451 | 5.451 | 5.451 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -5017.4069 0 -5017.4069 -15201.16 13363.368 87 0 -5017.7051 0 -5017.7051 -7196.5705 13270.976 Loop time of 0.168237 on 1 procs for 5 steps with 1226 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5017.40689311333 -5017.70265310229 -5017.70509036512 Force two-norm initial, final = 117.34289 1.9669705 Force max component initial, final = 96.075109 1.8862656 Final line search alpha, max atom move = 0.00010097578 0.00019046715 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.164 | 0.164 | 0.164 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090648 | 0.00090648 | 0.00090648 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003329 | | | 1.98 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6195.00 ave 6195 max 6195 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: 212478.0 ave 212478 max 212478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212478 Ave neighs/atom = 173.30995 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.589 | 5.589 | 5.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5017.7051 0 -5017.7051 -7196.5705 Loop time of 6.295e-06 on 1 procs for 0 steps with 1226 atoms 174.7% 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 | | 6.295e-06 | | |100.00 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6211.00 ave 6211 max 6211 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: 212776.0 ave 212776 max 212776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212776 Ave neighs/atom = 173.55302 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.589 | 5.589 | 5.589 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 -5017.7051 -5017.7051 30.760997 71.366681 6.0451481 -7196.5705 -7196.5705 -14.069491 -21802.812 227.16971 2.2353163 994.05919 Loop time of 6.545e-06 on 1 procs for 0 steps with 1226 atoms 275.0% 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 | | 6.545e-06 | | |100.00 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6211.00 ave 6211 max 6211 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106388.0 ave 106388 max 106388 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 212776.0 ave 212776 max 212776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212776 Ave neighs/atom = 173.55302 Neighbor list builds = 0 Dangerous builds = 0 1226 -5017.70509036512 eV 2.23531630961098 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04