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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -47.681868 0.0000000) to (27.527015 47.681868 6.3712660) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8986461 5.6759749 6.3712660 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -47.681868 0.0000000) to (27.527015 47.681868 6.3712660) create_atoms CPU = 0.004 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8986461 5.6759749 6.3712660 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -47.681868 0.0000000) to (27.527015 47.681868 6.3712660) create_atoms CPU = 0.003 seconds 676 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 31 3 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1328 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.055 | 5.055 | 5.055 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5550.1444 0 -5550.1444 2805.9181 53 0 -5588.7833 0 -5588.7833 -15485.83 Loop time of 0.801108 on 1 procs for 53 steps with 1328 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 = -5550.14441854848 -5588.77793527037 -5588.78328289559 Force two-norm initial, final = 33.166279 0.24047137 Force max component initial, final = 7.0629413 0.022131186 Final line search alpha, max atom move = 1.0000000 0.022131186 Iterations, force evaluations = 53 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75868 | 0.75868 | 0.75868 | 0.0 | 94.70 Neigh | 0.016956 | 0.016956 | 0.016956 | 0.0 | 2.12 Comm | 0.011138 | 0.011138 | 0.011138 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01433 | | | 1.79 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5202.00 ave 5202 max 5202 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: 102392.0 ave 102392 max 102392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102392 Ave neighs/atom = 77.102410 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.054 | 5.054 | 5.054 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -5588.7833 0 -5588.7833 -15485.83 16725.077 61 0 -5589.3441 0 -5589.3441 -6870.3831 16590.557 Loop time of 0.0892471 on 1 procs for 8 steps with 1328 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 = -5588.78328289559 -5589.34371078947 -5589.34414023143 Force two-norm initial, final = 161.41390 1.1686854 Force max component initial, final = 149.12141 1.0590312 Final line search alpha, max atom move = 0.00022916045 0.00024268806 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083084 | 0.083084 | 0.083084 | 0.0 | 93.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010633 | 0.0010633 | 0.0010633 | 0.0 | 1.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005099 | | | 5.71 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5166.00 ave 5166 max 5166 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: 102528.0 ave 102528 max 102528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102528 Ave neighs/atom = 77.204819 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.192 | 5.192 | 5.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5589.3441 0 -5589.3441 -6870.3831 Loop time of 6.365e-06 on 1 procs for 0 steps with 1328 atoms 172.8% 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 | | 6.365e-06 | | |100.00 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5200.00 ave 5200 max 5200 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: 102640.0 ave 102640 max 102640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102640 Ave neighs/atom = 77.289157 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.192 | 5.192 | 5.192 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 -5589.3441 -5589.3441 27.334175 95.363735 6.3646094 -6870.3831 -6870.3831 -101.55586 -20500.873 -8.7200606 2.3104281 956.08585 Loop time of 7.166e-06 on 1 procs for 0 steps with 1328 atoms 265.1% 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 | | 7.166e-06 | | |100.00 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5200.00 ave 5200 max 5200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51320.0 ave 51320 max 51320 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102640.0 ave 102640 max 102640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102640 Ave neighs/atom = 77.289157 Neighbor list builds = 0 Dangerous builds = 0 1328 -5589.34400743143 eV 2.31042814905576 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01