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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -37.586836 0.0000000) to (26.575417 37.586836 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1285893 5.9342077 4.9780318 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.586836 0.0000000) to (26.575417 37.586836 4.9780318) create_atoms CPU = 0.005 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1285893 5.9342077 4.9780318 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.586836 0.0000000) to (26.575417 37.586836 4.9780318) create_atoms CPU = 0.004 seconds 458 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 18 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 900 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.398 | 5.398 | 5.398 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3962.5127 0 -3962.5127 6755.482 43 0 -3983.4636 0 -3983.4636 -8822.9272 Loop time of 1.61862 on 1 procs for 43 steps with 900 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 = -3962.51265828852 -3983.46016643967 -3983.46355791804 Force two-norm initial, final = 40.213691 0.18444743 Force max component initial, final = 16.318646 0.035159915 Final line search alpha, max atom move = 1.0000000 0.035159915 Iterations, force evaluations = 43 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5697 | 1.5697 | 1.5697 | 0.0 | 96.97 Neigh | 0.026765 | 0.026765 | 0.026765 | 0.0 | 1.65 Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009958 | | | 0.62 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7218.00 ave 7218 max 7218 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: 200744.0 ave 200744 max 200744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200744 Ave neighs/atom = 223.04889 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.398 | 5.398 | 5.398 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -3983.4636 0 -3983.4636 -8822.9272 9944.971 48 0 -3983.5966 0 -3983.5966 -2063.7034 9906.3558 Loop time of 0.154226 on 1 procs for 5 steps with 900 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 = -3983.46355791804 -3983.59655063195 -3983.59656702809 Force two-norm initial, final = 73.884962 0.49537543 Force max component initial, final = 67.084262 0.33294203 Final line search alpha, max atom move = 0.0092361625 0.0030751067 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14984 | 0.14984 | 0.14984 | 0.0 | 97.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010496 | 0.0010496 | 0.0010496 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003338 | | | 2.16 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7227.00 ave 7227 max 7227 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: 200796.0 ave 200796 max 200796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200796 Ave neighs/atom = 223.10667 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.536 | 5.536 | 5.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3983.5966 0 -3983.5966 -2063.7034 Loop time of 6.726e-06 on 1 procs for 0 steps with 900 atoms 178.4% 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 | | 6.726e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7236.00 ave 7236 max 7236 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: 200912.0 ave 200912 max 200912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200912 Ave neighs/atom = 223.23556 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.536 | 5.536 | 5.536 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 -3983.5966 -3983.5966 26.46801 75.173671 4.9788251 -2063.7034 -2063.7034 43.033294 -6180.2875 -53.856021 2.2818325 630.59917 Loop time of 6.665e-06 on 1 procs for 0 steps with 900 atoms 285.1% 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 | | 6.665e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7236.00 ave 7236 max 7236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100456.0 ave 100456 max 100456 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200912.0 ave 200912 max 200912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200912 Ave neighs/atom = 223.23556 Neighbor list builds = 0 Dangerous builds = 0 900 -3959.08838226809 eV 2.28183245410615 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02