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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -67.345344 0.0000000) to (38.879820 67.345344 6.0968422) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7363669 5.1518335 6.0968422 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.345344 0.0000000) to (38.879820 67.345344 6.0968422) create_atoms CPU = 0.003 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7363669 5.1518335 6.0968422 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.345344 0.0000000) to (38.879820 67.345344 6.0968422) create_atoms CPU = 0.002 seconds 1466 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2904 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.30 | 11.30 | 11.30 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12851.309 0 -12851.309 -233.49815 42 0 -12880.22 0 -12880.22 -8413.2823 Loop time of 2.32026 on 1 procs for 42 steps with 2904 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12851.3090835173 -12880.2084257974 -12880.2202017149 Force two-norm initial, final = 23.188165 0.33751930 Force max component initial, final = 3.4512418 0.038857372 Final line search alpha, max atom move = 0.93801793 0.036448912 Iterations, force evaluations = 42 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2623 | 2.2623 | 2.2623 | 0.0 | 97.50 Neigh | 0.035203 | 0.035203 | 0.035203 | 0.0 | 1.52 Comm | 0.012394 | 0.012394 | 0.012394 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0104 | | | 0.45 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14276.0 ave 14276 max 14276 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: 649800.0 ave 649800 max 649800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 649800 Ave neighs/atom = 223.76033 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.30 | 11.30 | 11.30 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -12880.22 0 -12880.22 -8413.2823 31927.637 45 0 -12880.376 0 -12880.376 -3752.9524 31843.455 Loop time of 0.177548 on 1 procs for 3 steps with 2904 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 = -12880.2202017149 -12880.37508338 -12880.3763830196 Force two-norm initial, final = 158.33604 0.34999620 Force max component initial, final = 130.63370 0.049979473 Final line search alpha, max atom move = 0.00010304345 5.1500574e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17402 | 0.17402 | 0.17402 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064794 | 0.00064794 | 0.00064794 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002876 | | | 1.62 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14276.0 ave 14276 max 14276 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: 649860.0 ave 649860 max 649860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 649860 Ave neighs/atom = 223.78099 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.81 | 10.81 | 10.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12880.376 0 -12880.376 -3752.9524 Loop time of 1.51e-06 on 1 procs for 0 steps with 2904 atoms 198.7% 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 | | 1.51e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14305.0 ave 14305 max 14305 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: 650008.0 ave 650008 max 650008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 650008 Ave neighs/atom = 223.83196 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.81 | 10.81 | 10.81 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 -12880.376 -12880.376 38.808415 134.69069 6.0919552 -3752.9524 -3752.9524 -1.4294541 -11254.915 -2.5126593 2.2310123 861.19014 Loop time of 3.669e-06 on 1 procs for 0 steps with 2904 atoms 218.0% 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 | | 3.669e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14305.0 ave 14305 max 14305 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325004.0 ave 325004 max 325004 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 650008.0 ave 650008 max 650008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 650008 Ave neighs/atom = 223.83196 Neighbor list builds = 0 Dangerous builds = 0 2904 -12801.2092723319 eV 2.23101229383838 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03