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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -59.669237 0.0000000) to (48.719728 59.669237 9.8765224) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0065418 5.7217077 6.5843483 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -59.669237 0.0000000) to (48.719728 59.669237 9.8765224) create_atoms CPU = 0.010 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0065418 5.7217077 6.5843483 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -59.669237 0.0000000) to (48.719728 59.669237 9.8765224) create_atoms CPU = 0.009 seconds 1756 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3504 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.537 | 6.537 | 6.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11486.304 0 -11486.304 10852.015 114 0 -11743.702 0 -11743.702 3767.5689 Loop time of 8.40061 on 1 procs for 114 steps with 3504 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 = -11486.3042594002 -11743.6911355328 -11743.7018581699 Force two-norm initial, final = 83.703092 0.27751001 Force max component initial, final = 7.1276378 0.068684680 Final line search alpha, max atom move = 1.0000000 0.068684680 Iterations, force evaluations = 114 196 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.9556 | 7.9556 | 7.9556 | 0.0 | 94.70 Neigh | 0.32462 | 0.32462 | 0.32462 | 0.0 | 3.86 Comm | 0.049412 | 0.049412 | 0.049412 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07101 | | | 0.85 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9879.00 ave 9879 max 9879 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: 461298.0 ave 461298 max 461298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461298 Ave neighs/atom = 131.64897 Neighbor list builds = 5 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.537 | 6.537 | 6.537 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -11743.702 0 -11743.702 3767.5689 57423.464 122 0 -11744.607 0 -11744.607 33.696007 57684.912 Loop time of 0.400541 on 1 procs for 8 steps with 3504 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 = -11743.7018581699 -11744.6048306463 -11744.6070649396 Force two-norm initial, final = 288.74943 2.2634554 Force max component initial, final = 272.44096 1.5895866 Final line search alpha, max atom move = 0.00012898311 0.00020502982 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38754 | 0.38754 | 0.38754 | 0.0 | 96.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021977 | 0.0021977 | 0.0021977 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01081 | | | 2.70 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9878.00 ave 9878 max 9878 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: 461412.0 ave 461412 max 461412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461412 Ave neighs/atom = 131.68151 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.675 | 6.675 | 6.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11744.607 0 -11744.607 33.696007 Loop time of 6.384e-06 on 1 procs for 0 steps with 3504 atoms 203.6% 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 | | 6.384e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9880.00 ave 9880 max 9880 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: 460960.0 ave 460960 max 460960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460960 Ave neighs/atom = 131.55251 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.675 | 6.675 | 6.675 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 -11744.607 -11744.607 48.667153 120.21438 9.8598399 33.696007 33.696007 23.07111 33.941321 44.075589 2.566473 2316.4647 Loop time of 6.916e-06 on 1 procs for 0 steps with 3504 atoms 289.2% 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 | | 6.916e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9880.00 ave 9880 max 9880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230480.0 ave 230480 max 230480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 460960.0 ave 460960 max 460960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460960 Ave neighs/atom = 131.55251 Neighbor list builds = 0 Dangerous builds = 0 3504 -11744.6070649396 eV 2.56647300690223 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09