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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -43.744247 0.0000000) to (53.571109 43.744247 8.8671530) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1369556 5.3926800 5.9114353 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -43.744247 0.0000000) to (53.571109 43.744247 8.8671530) create_atoms CPU = 0.005 seconds 1754 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1369556 5.3926800 5.9114353 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -43.744247 0.0000000) to (53.571109 43.744247 8.8671530) create_atoms CPU = 0.004 seconds 1754 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 23 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 3468 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.404 | 7.404 | 7.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12145.237 0 -12145.237 1033.4237 70 0 -12241.051 0 -12241.051 -8922.2664 Loop time of 7.67465 on 1 procs for 70 steps with 3468 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 = -12145.237310267 -12241.0405027142 -12241.0509097901 Force two-norm initial, final = 42.871803 0.46337657 Force max component initial, final = 4.5043388 0.10779392 Final line search alpha, max atom move = 1.0000000 0.10779392 Iterations, force evaluations = 70 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.4636 | 7.4636 | 7.4636 | 0.0 | 97.25 Neigh | 0.14736 | 0.14736 | 0.14736 | 0.0 | 1.92 Comm | 0.02684 | 0.02684 | 0.02684 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03686 | | | 0.48 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11090.0 ave 11090 max 11090 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: 598564.0 ave 598564 max 598564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 598564 Ave neighs/atom = 172.59631 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.405 | 7.405 | 7.405 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -12241.051 0 -12241.051 -8922.2664 41559.066 75 0 -12241.905 0 -12241.905 -183.37685 41285.701 Loop time of 0.444917 on 1 procs for 5 steps with 3468 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 = -12241.0509097901 -12241.9008331836 -12241.9045700331 Force two-norm initial, final = 358.22574 0.63849954 Force max component initial, final = 276.93629 0.14875090 Final line search alpha, max atom move = 7.7668419e-05 1.1553247e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43589 | 0.43589 | 0.43589 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013472 | 0.0013472 | 0.0013472 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007679 | | | 1.73 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11125.0 ave 11125 max 11125 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: 598688.0 ave 598688 max 598688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 598688 Ave neighs/atom = 172.63206 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.543 | 7.543 | 7.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12241.905 0 -12241.905 -183.37685 Loop time of 4.318e-06 on 1 procs for 0 steps with 3468 atoms 185.3% 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 | | 4.318e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11174.0 ave 11174 max 11174 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: 600272.0 ave 600272 max 600272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 600272 Ave neighs/atom = 173.08881 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.543 | 7.543 | 7.543 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 -12241.905 -12241.905 53.344247 87.488494 8.8462892 -183.37685 -183.37685 1.8955592 -552.18908 0.16297538 2.2942816 1508.9146 Loop time of 3.77e-06 on 1 procs for 0 steps with 3468 atoms 212.2% 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 | | 3.77e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11174.0 ave 11174 max 11174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 300136.0 ave 300136 max 300136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 600272.0 ave 600272 max 600272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 600272 Ave neighs/atom = 173.08881 Neighbor list builds = 0 Dangerous builds = 0 3468 -12241.9045700331 eV 2.29428159674399 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09