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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -33.772720 0.0000000) to (29.248034 33.772720 5.7360113) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2496470 5.1958031 5.7360113 Created 620 atoms using lattice units in orthogonal box = (0.0000000 -33.772720 0.0000000) to (29.248034 33.772720 5.7360113) create_atoms CPU = 0.003 seconds 620 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2496470 5.1958031 5.7360113 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -33.772720 0.0000000) to (29.248034 33.772720 5.7360113) create_atoms CPU = 0.004 seconds 627 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 8 19 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1244 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.471 | 5.471 | 5.471 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4066.5465 0 -4066.5465 207755.11 169 0 -4814.1362 0 -4814.1362 143402.11 Loop time of 12.137 on 1 procs for 169 steps with 1244 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4066.54653599698 -4814.13183038162 -4814.13623182577 Force two-norm initial, final = 1015.3567 0.40085894 Force max component initial, final = 242.04227 0.034940924 Final line search alpha, max atom move = 0.61910815 0.021632211 Iterations, force evaluations = 169 325 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.963 | 11.963 | 11.963 | 0.0 | 98.56 Neigh | 0.066298 | 0.066298 | 0.066298 | 0.0 | 0.55 Comm | 0.058425 | 0.058425 | 0.058425 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0496 | | | 0.41 Nlocal: 1244.00 ave 1244 max 1244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6935.00 ave 6935 max 6935 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: 241658.0 ave 241658 max 241658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241658 Ave neighs/atom = 194.25884 Neighbor list builds = 2 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 169 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.468 | 5.468 | 5.468 Mbytes Step Temp E_pair E_mol TotEng Press Volume 169 0 -4814.1362 0 -4814.1362 143402.11 11331.899 718 0 -4941.2686 0 -4941.2686 836.98274 14027.097 Loop time of 21.7515 on 1 procs for 549 steps with 1244 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 = -4814.13623182578 -4941.26481539785 -4941.26856023234 Force two-norm initial, final = 1838.6393 17.012393 Force max component initial, final = 1340.1855 10.475912 Final line search alpha, max atom move = 0.00010779537 0.0011292548 Iterations, force evaluations = 549 645 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.855 | 20.855 | 20.855 | 0.0 | 95.88 Neigh | 0.40438 | 0.40438 | 0.40438 | 0.0 | 1.86 Comm | 0.10431 | 0.10431 | 0.10431 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3876 | | | 1.78 Nlocal: 1244.00 ave 1244 max 1244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7235.00 ave 7235 max 7235 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: 196880.0 ave 196880 max 196880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196880 Ave neighs/atom = 158.26367 Neighbor list builds = 14 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 10 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.615 | 5.615 | 5.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4941.2686 0 -4941.2686 836.98274 Loop time of 6.425e-06 on 1 procs for 0 steps with 1244 atoms 171.2% 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 | | 6.425e-06 | | |100.00 Nlocal: 1244.00 ave 1244 max 1244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7229.00 ave 7229 max 7229 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: 197382.0 ave 197382 max 197382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197382 Ave neighs/atom = 158.66720 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 10 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.615 | 5.615 | 5.615 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 -4941.2686 -4941.2686 33.91837 78.539217 5.2655805 836.98274 836.98274 893.72398 518.79862 1098.4256 2.2443816 1487.0677 Loop time of 6.605e-06 on 1 procs for 0 steps with 1244 atoms 302.8% 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 | | 6.605e-06 | | |100.00 Nlocal: 1244.00 ave 1244 max 1244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7229.00 ave 7229 max 7229 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98691.0 ave 98691 max 98691 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 197382.0 ave 197382 max 197382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197382 Ave neighs/atom = 158.66720 Neighbor list builds = 0 Dangerous builds = 0 1244 -4941.26856023234 eV 2.24438164568483 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:36