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 = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -62.142409 0.0000000) to (35.877937 62.142409 6.0935645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5196825 5.5768829 6.0935645 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -62.142409 0.0000000) to (35.877937 62.142409 6.0935645) create_atoms CPU = 0.008 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5196825 5.5768829 6.0935645 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.142409 0.0000000) to (35.877937 62.142409 6.0935645) create_atoms CPU = 0.008 seconds 1250 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2488 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_149104665840_005#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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.02 | 12.02 | 12.02 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10450.685 0 -10450.685 54532.633 83 0 -10873.734 0 -10873.734 981.12232 Loop time of 16.1263 on 1 procs for 83 steps with 2488 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 = -10450.6849456252 -10873.7233207288 -10873.7336377939 Force two-norm initial, final = 548.13146 0.33248546 Force max component initial, final = 125.86317 0.057002290 Final line search alpha, max atom move = 1.0000000 0.057002290 Iterations, force evaluations = 83 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.727 | 15.727 | 15.727 | 0.0 | 97.53 Neigh | 0.30272 | 0.30272 | 0.30272 | 0.0 | 1.88 Comm | 0.055981 | 0.055981 | 0.055981 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04022 | | | 0.25 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15148.0 ave 15148 max 15148 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: 810496.0 ave 810496 max 810496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 810496 Ave neighs/atom = 325.76206 Neighbor list builds = 3 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.02 | 12.02 | 12.02 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -10873.734 0 -10873.734 981.12232 27171.709 84 0 -10873.739 0 -10873.739 -61.815211 27187.993 Loop time of 0.324096 on 1 procs for 1 steps with 2488 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10873.7336377939 -10873.7336377939 -10873.7391512099 Force two-norm initial, final = 30.345668 5.6166422 Force max component initial, final = 24.084371 3.9658634 Final line search alpha, max atom move = 4.1520702e-05 0.00016466543 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32059 | 0.32059 | 0.32059 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096271 | 0.00096271 | 0.00096271 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002539 | | | 0.78 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15152.0 ave 15152 max 15152 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: 808388.0 ave 808388 max 808388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 808388 Ave neighs/atom = 324.91479 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 11.53 | 11.53 | 11.53 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10873.739 0 -10873.739 -61.815211 Loop time of 6.856e-06 on 1 procs for 0 steps with 2488 atoms 189.6% 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 | | 6.856e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15152.0 ave 15152 max 15152 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: 807520.0 ave 807520 max 807520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 807520 Ave neighs/atom = 324.56592 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 11.53 | 11.53 | 11.53 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 -10873.739 -10873.739 35.888309 124.30688 6.0943723 -61.815211 -61.815211 187.56629 -139.27435 -233.73757 2.1853357 874.05176 Loop time of 6.856e-06 on 1 procs for 0 steps with 2488 atoms 262.5% 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 | | 6.856e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15152.0 ave 15152 max 15152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 403760.0 ave 403760 max 403760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 807520.0 ave 807520 max 807520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 807520 Ave neighs/atom = 324.56592 Neighbor list builds = 0 Dangerous builds = 0 2488 -10873.7391512099 eV 2.18533566076007 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18