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 -72.580777 0.0000000) to (41.904531 72.580777 6.2700241) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6289669 5.7775743 6.2700241 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -72.580777 0.0000000) to (41.904531 72.580777 6.2700241) create_atoms CPU = 0.016 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6289669 5.7775743 6.2700241 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.580777 0.0000000) to (41.904531 72.580777 6.2700241) create_atoms CPU = 0.014 seconds 1610 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 = 11 38 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3214 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_657255834688_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 = 11 38 2 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) = 7.052 | 7.052 | 7.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10941.566 0 -10941.566 30442.359 119 0 -11351.158 0 -11351.158 4345.0655 Loop time of 13.7552 on 1 procs for 119 steps with 3214 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 = -10941.5656443685 -11351.1470061601 -11351.1580973366 Force two-norm initial, final = 610.95723 0.41622573 Force max component initial, final = 145.15105 0.10967780 Final line search alpha, max atom move = 1.0000000 0.10967780 Iterations, force evaluations = 119 221 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.467 | 13.467 | 13.467 | 0.0 | 97.90 Neigh | 0.1458 | 0.1458 | 0.1458 | 0.0 | 1.06 Comm | 0.071688 | 0.071688 | 0.071688 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07101 | | | 0.52 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13055.0 ave 13055 max 13055 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: 560484.0 ave 560484 max 560484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560484 Ave neighs/atom = 174.38830 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 = 11 38 2 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 : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.052 | 7.052 | 7.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -11351.158 0 -11351.158 4345.0655 38140.098 124 0 -11351.597 0 -11351.597 -204.36166 38269.015 Loop time of 0.440221 on 1 procs for 5 steps with 3214 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11351.1580973366 -11351.5934955618 -11351.5968024121 Force two-norm initial, final = 222.58268 8.9940898 Force max component initial, final = 206.60295 7.0486617 Final line search alpha, max atom move = 6.9096566e-05 0.00048703832 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43021 | 0.43021 | 0.43021 | 0.0 | 97.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020453 | 0.0020453 | 0.0020453 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007963 | | | 1.81 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13048.0 ave 13048 max 13048 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: 561000.0 ave 561000 max 561000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561000 Ave neighs/atom = 174.54885 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 = 11 38 2 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) = 7.190 | 7.190 | 7.190 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11351.597 0 -11351.597 -204.36166 Loop time of 6.886e-06 on 1 procs for 0 steps with 3214 atoms 203.3% 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 | | 6.886e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13048.0 ave 13048 max 13048 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: 560684.0 ave 560684 max 560684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560684 Ave neighs/atom = 174.45053 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 = 11 38 2 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) = 7.190 | 7.190 | 7.190 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 -11351.597 -11351.597 41.904967 145.801 6.2635607 -204.36166 -204.36166 -295.10343 -115.90782 -202.07372 2.314603 1071.0205 Loop time of 7.006e-06 on 1 procs for 0 steps with 3214 atoms 242.6% 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 | | 7.006e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13048.0 ave 13048 max 13048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 280342.0 ave 280342 max 280342 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 560684.0 ave 560684 max 560684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560684 Ave neighs/atom = 174.45053 Neighbor list builds = 0 Dangerous builds = 0 3214 -11351.5968024121 eV 2.31460297147602 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15