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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -62.546061 0.0000000) to (25.534323 62.546061 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1282374 5.4206586 5.8968992 Created 1199 atoms using lattice units in orthogonal box = (0.0000000 -62.546061 0.0000000) to (25.534323 62.546061 8.8453488) create_atoms CPU = 0.002 seconds 1199 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1282374 5.4206586 5.8968992 Created 1207 atoms using lattice units in orthogonal box = (0.0000000 -62.546061 0.0000000) to (25.534323 62.546061 8.8453488) create_atoms CPU = 0.002 seconds 1207 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 8 37 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2406 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_260546967793_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 8 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.969 | 5.969 | 5.969 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9638.6772 0 -9638.6772 52306.063 639 0 -10222.108 0 -10222.108 6382.7901 Loop time of 194.234 on 1 procs for 639 steps with 2406 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 = -9638.67723978631 -10222.0988069697 -10222.1077552042 Force two-norm initial, final = 575.05322 0.28142130 Force max component initial, final = 72.998595 0.042090772 Final line search alpha, max atom move = 0.55136474 0.023207367 Iterations, force evaluations = 639 1224 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 193.47 | 193.47 | 193.47 | 0.0 | 99.61 Neigh | 0.48169 | 0.48169 | 0.48169 | 0.0 | 0.25 Comm | 0.12731 | 0.12731 | 0.12731 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1518 | | | 0.08 Nlocal: 2406.00 ave 2406 max 2406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8398.00 ave 8398 max 8398 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: 302522.0 ave 302522 max 302522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302522 Ave neighs/atom = 125.73649 Neighbor list builds = 23 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 8 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 639 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.985 | 5.985 | 5.985 Mbytes Step Temp E_pair E_mol TotEng Press Volume 639 0 -10222.108 0 -10222.108 6382.7901 28253.305 668 0 -10241.835 0 -10241.835 -3.8986853 28322.376 Loop time of 4.88772 on 1 procs for 29 steps with 2406 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 = -10222.1077552043 -10241.8350833087 -10241.8354618856 Force two-norm initial, final = 1095.9955 2.0822004 Force max component initial, final = 738.80037 0.84399487 Final line search alpha, max atom move = 0.00036691608 0.00030967529 Iterations, force evaluations = 29 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8271 | 4.8271 | 4.8271 | 0.0 | 98.76 Neigh | 0.041127 | 0.041127 | 0.041127 | 0.0 | 0.84 Comm | 0.0028936 | 0.0028936 | 0.0028936 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01656 | | | 0.34 Nlocal: 2406.00 ave 2406 max 2406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8190.00 ave 8190 max 8190 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: 296040.0 ave 296040 max 296040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296040 Ave neighs/atom = 123.04239 Neighbor list builds = 2 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 8 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.742 | 5.742 | 5.742 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10241.835 0 -10241.835 -3.8986853 Loop time of 2.355e-06 on 1 procs for 0 steps with 2406 atoms 212.3% 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 | | 2.355e-06 | | |100.00 Nlocal: 2406.00 ave 2406 max 2406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8187.00 ave 8187 max 8187 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: 286758.0 ave 286758 max 286758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286758 Ave neighs/atom = 119.18454 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 8 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.742 | 5.742 | 5.742 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 -10241.835 -10241.835 24.817704 127.89822 8.9228497 -3.8986853 -3.8986853 41.615422 -48.815196 -4.4962823 2.3825437 14093.752 Loop time of 2.821e-06 on 1 procs for 0 steps with 2406 atoms 283.6% 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 | | 2.821e-06 | | |100.00 Nlocal: 2406.00 ave 2406 max 2406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8187.00 ave 8187 max 8187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143379.0 ave 143379 max 143379 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 286758.0 ave 286758 max 286758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286758 Ave neighs/atom = 119.18454 Neighbor list builds = 0 Dangerous builds = 0 2406 -10241.8354618856 eV 2.38254367900243 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:03:20