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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -69.989371 0.0000000) to (40.408382 69.989371 6.3365399) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9618925 5.3543781 6.3365399 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.989371 0.0000000) to (40.408382 69.989371 6.3365399) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9618925 5.3543781 6.3365399 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.989371 0.0000000) to (40.408382 69.989371 6.3365399) 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 33 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 0 atoms, new total = 2930 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 33 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) = 10.91 | 10.91 | 10.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10839.597 0 -10839.597 53520.386 811 0 -11571.342 0 -11571.342 -63557.013 Loop time of 52.1212 on 1 procs for 811 steps with 2930 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 = -10839.5974126731 -11571.3318675983 -11571.341810877 Force two-norm initial, final = 825.36375 0.31102617 Force max component initial, final = 208.52223 0.071127409 Final line search alpha, max atom move = 1.0000000 0.071127409 Iterations, force evaluations = 811 1580 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 51.044 | 51.044 | 51.044 | 0.0 | 97.93 Neigh | 0.56435 | 0.56435 | 0.56435 | 0.0 | 1.08 Comm | 0.27739 | 0.27739 | 0.27739 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2357 | | | 0.45 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14236.0 ave 14236 max 14236 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: 592082.0 ave 592082 max 592082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 592082 Ave neighs/atom = 202.07577 Neighbor list builds = 15 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 33 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 : 811 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.29 | 11.29 | 11.29 Mbytes Step Temp E_pair E_mol TotEng Press Volume 811 0 -11571.342 0 -11571.342 -63557.013 35841.463 838 0 -11608.834 0 -11608.834 -1.6222133 34325.824 Loop time of 1.08064 on 1 procs for 27 steps with 2930 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 = -11571.3418108769 -11608.8293711473 -11608.8338583877 Force two-norm initial, final = 2537.4573 5.3341761 Force max component initial, final = 1744.3178 1.3424737 Final line search alpha, max atom move = 7.9593279e-05 0.00010685189 Iterations, force evaluations = 27 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95519 | 0.95519 | 0.95519 | 0.0 | 88.39 Neigh | 0.10437 | 0.10437 | 0.10437 | 0.0 | 9.66 Comm | 0.0042215 | 0.0042215 | 0.0042215 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01686 | | | 1.56 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14355.0 ave 14355 max 14355 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: 644460.0 ave 644460 max 644460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 644460 Ave neighs/atom = 219.95222 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 33 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 -11608.834 0 -11608.834 -1.6222133 Loop time of 2.202e-06 on 1 procs for 0 steps with 2930 atoms 136.2% 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 | | 2.202e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14327.0 ave 14327 max 14327 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: 645312.0 ave 645312 max 645312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 645312 Ave neighs/atom = 220.24300 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 33 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 -11608.834 -11608.834 39.619646 136.47866 6.3481274 -1.6222133 -1.6222133 14.173082 43.735556 -62.775277 2.1788917 9445.6343 Loop time of 3.073e-06 on 1 procs for 0 steps with 2930 atoms 260.3% 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 | | 3.073e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14327.0 ave 14327 max 14327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 322656.0 ave 322656 max 322656 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 645312.0 ave 645312 max 645312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 645312 Ave neighs/atom = 220.24300 Neighbor list builds = 0 Dangerous builds = 0 2930 -11608.8338583877 eV 2.17889167388065 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:53