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 = 4.0501996 4.0501996 4.0501996 Created orthogonal box = (0.0000000 -46.533251 0.0000000) to (32.903977 46.533251 5.7278472) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9796316 6.3454433 5.7278472 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -46.533251 0.0000000) to (32.903977 46.533251 5.7278472) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9796316 6.3454433 5.7278472 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -46.533251 0.0000000) to (32.903977 46.533251 5.7278472) create_atoms CPU = 0.001 seconds 532 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 8 23 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 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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_060567868558_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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.013 | 5.013 | 5.013 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3692.647 0 -3692.647 5718.2572 52 0 -3747.6509 0 -3747.6509 787.9353 Loop time of 0.693839 on 1 procs for 52 steps with 1048 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 = -3692.64698499365 -3747.64767369761 -3747.65088566192 Force two-norm initial, final = 65.720629 0.11152815 Force max component initial, final = 15.851476 0.0086388722 Final line search alpha, max atom move = 1.0000000 0.0086388722 Iterations, force evaluations = 52 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66469 | 0.66469 | 0.66469 | 0.0 | 95.80 Neigh | 0.019776 | 0.019776 | 0.019776 | 0.0 | 2.85 Comm | 0.004776 | 0.004776 | 0.004776 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004593 | | | 0.66 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5984.00 ave 5984 max 5984 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: 146576.0 ave 146576 max 146576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146576 Ave neighs/atom = 139.86260 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.013 | 5.013 | 5.013 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -3747.6509 0 -3747.6509 787.9353 17540.146 56 0 -3747.6932 0 -3747.6932 -2.9607489 17560.18 Loop time of 0.0573553 on 1 procs for 4 steps with 1048 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 = -3747.65088566192 -3747.69118226032 -3747.69320345811 Force two-norm initial, final = 25.654314 0.43757452 Force max component initial, final = 18.762590 0.35798037 Final line search alpha, max atom move = 0.00011114462 3.9787591e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.05566 | 0.05566 | 0.05566 | 0.0 | 97.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031133 | 0.00031133 | 0.00031133 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001384 | | | 2.41 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5951.00 ave 5951 max 5951 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: 147056.0 ave 147056 max 147056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147056 Ave neighs/atom = 140.32061 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.151 | 5.151 | 5.151 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3747.6932 0 -3747.6932 -2.9607489 Loop time of 1.585e-06 on 1 procs for 0 steps with 1048 atoms 189.3% 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 | | 1.585e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5951.00 ave 5951 max 5951 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: 147016.0 ave 147016 max 147016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147016 Ave neighs/atom = 140.28244 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.151 | 5.151 | 5.151 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 -3747.6932 -3747.6932 32.95165 93.278342 5.713089 -2.9607489 -2.9607489 -32.709158 19.522801 4.3041102 2.6823576 627.23144 Loop time of 1.619e-06 on 1 procs for 0 steps with 1048 atoms 185.3% 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 | | 1.619e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5951.00 ave 5951 max 5951 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73508.0 ave 73508 max 73508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 147016.0 ave 147016 max 147016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147016 Ave neighs/atom = 140.28244 Neighbor list builds = 0 Dangerous builds = 0 1048 -3747.69320345811 eV 2.68235759973555 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01