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 -44.802290 0.0000000) to (31.680003 44.802290 4.9780323) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8666673 6.0842617 4.9780323 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -44.802290 0.0000000) to (31.680003 44.802290 4.9780323) create_atoms CPU = 0.005 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8666673 6.0842617 4.9780323 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.802290 0.0000000) to (31.680003 44.802290 4.9780323) create_atoms CPU = 0.004 seconds 650 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 = 9 24 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 6 atoms, new total = 1292 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 = 9 24 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) = 5.470 | 5.470 | 5.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5660.5209 0 -5660.5209 7982.2977 47 0 -5737.793 0 -5737.793 1748.205 Loop time of 2.05619 on 1 procs for 47 steps with 1292 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 = -5660.52092445934 -5737.78763912892 -5737.79303985337 Force two-norm initial, final = 49.229095 0.25509899 Force max component initial, final = 10.980245 0.035913894 Final line search alpha, max atom move = 1.0000000 0.035913894 Iterations, force evaluations = 47 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9643 | 1.9643 | 1.9643 | 0.0 | 95.53 Neigh | 0.062452 | 0.062452 | 0.062452 | 0.0 | 3.04 Comm | 0.016006 | 0.016006 | 0.016006 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01346 | | | 0.65 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8213.00 ave 8213 max 8213 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: 225452.0 ave 225452 max 225452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225452 Ave neighs/atom = 174.49845 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 = 9 24 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.470 | 5.470 | 5.470 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -5737.793 0 -5737.793 1748.205 14131.008 50 0 -5737.8316 0 -5737.8316 -6.6762653 14145.287 Loop time of 0.153027 on 1 procs for 3 steps with 1292 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 = -5737.79303985338 -5737.8315382744 -5737.83157486177 Force two-norm initial, final = 44.912320 0.36880375 Force max component initial, final = 44.890190 0.22305760 Final line search alpha, max atom move = 0.00082413882 0.00018383043 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14858 | 0.14858 | 0.14858 | 0.0 | 97.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010996 | 0.0010996 | 0.0010996 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003348 | | | 2.19 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8229.00 ave 8229 max 8229 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: 225336.0 ave 225336 max 225336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225336 Ave neighs/atom = 174.40867 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 = 9 24 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) = 5.608 | 5.608 | 5.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5737.8316 0 -5737.8316 -6.6762653 Loop time of 6.685e-06 on 1 procs for 0 steps with 1292 atoms 179.5% 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 | | 6.685e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8237.00 ave 8237 max 8237 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: 225228.0 ave 225228 max 225228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225228 Ave neighs/atom = 174.32508 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 = 9 24 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) = 5.608 | 5.608 | 5.608 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 -5737.8316 -5737.8316 31.668115 89.759817 4.9763117 -6.6762653 -6.6762653 11.899801 -6.672543 -25.256054 2.2998239 489.31874 Loop time of 9.482e-06 on 1 procs for 0 steps with 1292 atoms 210.9% 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 | | 9.482e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8237.00 ave 8237 max 8237 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112614.0 ave 112614 max 112614 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225228.0 ave 225228 max 225228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225228 Ave neighs/atom = 174.32508 Neighbor list builds = 0 Dangerous builds = 0 1292 -5737.83157486177 eV 2.29982391971908 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02