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 = 3.4301372 3.4301372 3.4301372 Created orthogonal box = (0.0000000 -48.509466 0.0000000) to (24.254733 48.509466 3.4301372) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8807573 3.8807573 3.4301372 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -48.509466 0.0000000) to (24.254733 48.509466 3.4301372) create_atoms CPU = 0.001 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8807573 3.8807573 3.4301372 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -48.509466 0.0000000) to (24.254733 48.509466 3.4301372) create_atoms CPU = 0.000 seconds 402 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 ghost atom cutoff = 8 binsize = 4, bins = 7 25 1 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 796 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_044341472608_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 ghost atom cutoff = 8 binsize = 4, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2997.4533 0 -2997.4533 79123.857 104 0 -3169.1124 0 -3169.1124 31619.853 Loop time of 1.70242 on 1 procs for 104 steps with 796 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2997.45328191419 -3169.10979476873 -3169.11237978665 Force two-norm initial, final = 618.95908 0.17963811 Force max component initial, final = 217.41414 0.026807829 Final line search alpha, max atom move = 1.0000000 0.026807829 Iterations, force evaluations = 104 203 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6719 | 1.6719 | 1.6719 | 0.0 | 98.21 Neigh | 0.0091232 | 0.0091232 | 0.0091232 | 0.0 | 0.54 Comm | 0.013227 | 0.013227 | 0.013227 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008168 | | | 0.48 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8408.00 ave 8408 max 8408 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: 159528.0 ave 159528 max 159528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159528 Ave neighs/atom = 200.41206 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 ghost atom cutoff = 8 binsize = 4, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -3169.1124 0 -3169.1124 31619.853 8071.69 112 0 -3169.9772 0 -3169.9772 -51.253167 8132.6796 Loop time of 0.093702 on 1 procs for 8 steps with 796 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 = -3169.11237978664 -3169.97719640908 -3169.97721386891 Force two-norm initial, final = 291.51709 0.82050980 Force max component initial, final = 236.11916 0.27154684 Final line search alpha, max atom move = 0.0015321926 0.00041606207 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090284 | 0.090284 | 0.090284 | 0.0 | 96.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068272 | 0.00068272 | 0.00068272 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002736 | | | 2.92 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8408.00 ave 8408 max 8408 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: 159508.0 ave 159508 max 159508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159508 Ave neighs/atom = 200.38693 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 ghost atom cutoff = 8 binsize = 4, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.142 | 5.142 | 5.142 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3169.9772 0 -3169.9772 -51.253167 Loop time of 1.746e-06 on 1 procs for 0 steps with 796 atoms 171.8% 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 | | 1.746e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8408.00 ave 8408 max 8408 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: 158836.0 ave 158836 max 158836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158836 Ave neighs/atom = 199.54271 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 ghost atom cutoff = 8 binsize = 4, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.142 | 5.142 | 5.142 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 -3169.9772 -3169.9772 24.261467 97.695002 3.4311859 -51.253167 -51.253167 -46.912127 -53.868802 -52.978572 2.2445712 396.63612 Loop time of 1.709e-06 on 1 procs for 0 steps with 796 atoms 234.1% 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 | | 1.709e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8408.00 ave 8408 max 8408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79418.0 ave 79418 max 79418 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158836.0 ave 158836 max 158836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158836 Ave neighs/atom = 199.54271 Neighbor list builds = 0 Dangerous builds = 0 796 -3169.97721386891 eV 2.24457121773516 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02