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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -41.269881 0.0000000) to (29.179987 41.269881 4.4499064) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4288349 5.2783032 4.4499064 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -41.269881 0.0000000) to (29.179987 41.269881 4.4499064) create_atoms CPU = 0.003 seconds 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4288349 5.2783032 4.4499064 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -41.269881 0.0000000) to (29.179987 41.269881 4.4499064) create_atoms CPU = 0.003 seconds 345 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 684 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_831380044253_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4451.4172 0 -4451.4172 81178.081 28 0 -4635.1964 0 -4635.1964 -7556.3461 Loop time of 2.17461 on 1 procs for 28 steps with 684 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 = -4451.41718561561 -4635.192500139 -4635.19635423653 Force two-norm initial, final = 339.09887 0.28713749 Force max component initial, final = 86.243481 0.084659280 Final line search alpha, max atom move = 0.86832583 0.073511840 Iterations, force evaluations = 28 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1582 | 2.1582 | 2.1582 | 0.0 | 99.25 Neigh | 0.0075073 | 0.0075073 | 0.0075073 | 0.0 | 0.35 Comm | 0.0041014 | 0.0041014 | 0.0041014 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004776 | | | 0.22 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3332.00 ave 3332 max 3332 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: 43796.0 ave 43796 max 43796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43796 Ave neighs/atom = 64.029240 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -4635.1964 0 -4635.1964 -7556.3461 10717.64 30 0 -4635.2187 0 -4635.2187 -3849.13 10702.386 Loop time of 0.239726 on 1 procs for 2 steps with 684 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 = -4635.19635423652 -4635.21807238226 -4635.21865949187 Force two-norm initial, final = 41.390475 0.28806536 Force max component initial, final = 34.202827 0.078819694 Final line search alpha, max atom move = 0.00030184462 2.3791300e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23793 | 0.23793 | 0.23793 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036412 | 0.00036412 | 0.00036412 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001431 | | | 0.60 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3332.00 ave 3332 max 3332 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: 43824.0 ave 43824 max 43824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43824 Ave neighs/atom = 64.070175 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.642 | 4.642 | 4.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4635.2187 0 -4635.2187 -3849.13 Loop time of 6.695e-06 on 1 procs for 0 steps with 684 atoms 164.3% 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 | | 6.695e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3332.00 ave 3332 max 3332 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: 43824.0 ave 43824 max 43824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43824 Ave neighs/atom = 64.070175 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.642 | 4.642 | 4.642 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 -4635.2187 -4635.2187 29.168839 82.539761 4.4452711 -3849.13 -3849.13 -4.0534384 -11543.491 0.15458685 2.5121191 494.59677 Loop time of 6.836e-06 on 1 procs for 0 steps with 684 atoms 263.3% 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 | | 6.836e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3332.00 ave 3332 max 3332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21912.0 ave 21912 max 21912 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43824.0 ave 43824 max 43824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43824 Ave neighs/atom = 64.070175 Neighbor list builds = 0 Dangerous builds = 0 684 -4635.21865949187 eV 2.51211909125022 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02