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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -57.612617 0.0000000) to (35.280378 57.612617 8.9612251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6903836 5.5754145 5.9741501 Created 1483 atoms using lattice units in orthogonal box = (0.0000000 -57.612617 0.0000000) to (35.280378 57.612617 8.9612251) create_atoms CPU = 0.002 seconds 1483 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6903836 5.5754145 5.9741501 Created 1489 atoms using lattice units in orthogonal box = (0.0000000 -57.612617 0.0000000) to (35.280378 57.612617 8.9612251) create_atoms CPU = 0.002 seconds 1489 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2972 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.504 | 6.504 | 6.504 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11250.323 0 -11250.323 29099.228 797 0 -11707.908 0 -11707.908 -65123.814 Loop time of 29.9121 on 1 procs for 797 steps with 2972 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 = -11250.3227631828 -11707.8981074556 -11707.9081145942 Force two-norm initial, final = 488.95012 0.34943150 Force max component initial, final = 199.35298 0.12327687 Final line search alpha, max atom move = 1.0000000 0.12327687 Iterations, force evaluations = 797 1550 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.076 | 29.076 | 29.076 | 0.0 | 97.21 Neigh | 0.51436 | 0.51436 | 0.51436 | 0.0 | 1.72 Comm | 0.13389 | 0.13389 | 0.13389 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1875 | | | 0.63 Nlocal: 2972.00 ave 2972 max 2972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9431.00 ave 9431 max 9431 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: 412110.0 ave 412110 max 412110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412110 Ave neighs/atom = 138.66420 Neighbor list builds = 19 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 797 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.502 | 6.502 | 6.502 Mbytes Step Temp E_pair E_mol TotEng Press Volume 797 0 -11707.908 0 -11707.908 -65123.814 36429.081 846 0 -11785.268 0 -11785.268 -35.755431 35021.525 Loop time of 1.03607 on 1 procs for 49 steps with 2972 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 = -11707.9081145942 -11785.264314872 -11785.2678162765 Force two-norm initial, final = 3088.1265 11.184967 Force max component initial, final = 2335.4573 7.5230380 Final line search alpha, max atom move = 0.00020772418 0.0015627169 Iterations, force evaluations = 49 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92864 | 0.92864 | 0.92864 | 0.0 | 89.63 Neigh | 0.078974 | 0.078974 | 0.078974 | 0.0 | 7.62 Comm | 0.0042336 | 0.0042336 | 0.0042336 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02422 | | | 2.34 Nlocal: 2972.00 ave 2972 max 2972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9439.00 ave 9439 max 9439 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: 420830.0 ave 420830 max 420830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 420830 Ave neighs/atom = 141.59825 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.639 | 6.639 | 6.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11785.268 0 -11785.268 -35.755431 Loop time of 1.914e-06 on 1 procs for 0 steps with 2972 atoms 209.0% 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 | | 1.914e-06 | | |100.00 Nlocal: 2972.00 ave 2972 max 2972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9370.00 ave 9370 max 9370 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: 421422.0 ave 421422 max 421422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 421422 Ave neighs/atom = 141.79744 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.639 | 6.639 | 6.639 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 -11785.268 -11785.268 33.945167 111.55659 9.2482993 -35.755431 -35.755431 184.24048 63.685124 -355.1919 2.1679675 5013.3734 Loop time of 2.317e-06 on 1 procs for 0 steps with 2972 atoms 302.1% 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 | | 2.317e-06 | | |100.00 Nlocal: 2972.00 ave 2972 max 2972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9370.00 ave 9370 max 9370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210711.0 ave 210711 max 210711 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 421422.0 ave 421422 max 421422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 421422 Ave neighs/atom = 141.79744 Neighbor list builds = 0 Dangerous builds = 0 2972 -11785.2678162765 eV 2.16796747730031 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:31