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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -76.077008 0.0000000) to (38.038504 76.077008 4.0320734) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5561860 5.5561860 4.0320734 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -76.077008 0.0000000) to (38.038504 76.077008 4.0320734) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5561860 5.5561860 4.0320734 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.077008 0.0000000) to (38.038504 76.077008 4.0320734) create_atoms CPU = 0.002 seconds 714 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 40 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1426 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.104 | 5.104 | 5.104 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4692.1643 0 -4692.1643 10493.606 70 0 -4782.3561 0 -4782.3561 4110.4946 Loop time of 2.53135 on 1 procs for 70 steps with 1426 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4692.16425622726 -4782.35272200997 -4782.35606769013 Force two-norm initial, final = 51.607073 0.15702973 Force max component initial, final = 7.4247627 0.036148455 Final line search alpha, max atom move = 1.0000000 0.036148455 Iterations, force evaluations = 70 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4815 | 2.4815 | 2.4815 | 0.0 | 98.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.027847 | 0.027847 | 0.027847 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02204 | | | 0.87 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9589.00 ave 9589 max 9589 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: 189932.0 ave 189932 max 189932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189932 Ave neighs/atom = 133.19215 Neighbor list builds = 0 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -4782.3561 0 -4782.3561 4110.4946 23336.476 78 0 -4782.7689 0 -4782.7689 -20.645858 23453.449 Loop time of 0.213572 on 1 procs for 8 steps with 1426 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 = -4782.35606769013 -4782.76784940895 -4782.76889346335 Force two-norm initial, final = 127.74949 0.77986112 Force max component initial, final = 118.13343 0.63753001 Final line search alpha, max atom move = 0.00026416357 0.00016841220 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18191 | 0.18191 | 0.18191 | 0.0 | 85.18 Neigh | 0.022692 | 0.022692 | 0.022692 | 0.0 | 10.62 Comm | 0.0022633 | 0.0022633 | 0.0022633 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006703 | | | 3.14 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8502.00 ave 8502 max 8502 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: 188500.0 ave 188500 max 188500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188500 Ave neighs/atom = 132.18794 Neighbor list builds = 1 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.234 | 5.234 | 5.234 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4782.7689 0 -4782.7689 -20.645858 Loop time of 6.415e-06 on 1 procs for 0 steps with 1426 atoms 171.5% 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 | | 6.415e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8502.00 ave 8502 max 8502 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: 188492.0 ave 188492 max 188492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188492 Ave neighs/atom = 132.18233 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.234 | 5.234 | 5.234 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 -4782.7689 -4782.7689 37.947193 153.27911 4.0322187 -20.645858 -20.645858 2.9789531 -21.363342 -43.553186 2.5809156 606.24194 Loop time of 7.347e-06 on 1 procs for 0 steps with 1426 atoms 217.8% 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 | | 7.347e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8502.00 ave 8502 max 8502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94246.0 ave 94246 max 94246 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188492.0 ave 188492 max 188492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188492 Ave neighs/atom = 132.18233 Neighbor list builds = 0 Dangerous builds = 0 1426 -4782.76889346335 eV 2.5809155621838 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03