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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -63.852908 0.0000000) to (36.865493 63.852908 6.2612927) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6716144 5.7303891 6.2612927 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -63.852908 0.0000000) to (36.865493 63.852908 6.2612927) create_atoms CPU = 0.008 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6716144 5.7303891 6.2612927 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.852908 0.0000000) to (36.865493 63.852908 6.2612927) create_atoms CPU = 0.007 seconds 1249 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 10 34 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 7.715752124786377 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2490 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_127245782811_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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 6.514 | 6.514 | 6.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8454.0329 0 -8454.0329 29203.853 125 0 -8792.1094 0 -8792.1094 5154.9008 Loop time of 9.56511 on 1 procs for 125 steps with 2490 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 = -8454.03286375045 -8792.10092275824 -8792.10937179401 Force two-norm initial, final = 481.16503 0.31361910 Force max component initial, final = 132.87680 0.073759554 Final line search alpha, max atom move = 0.87587164 0.064603902 Iterations, force evaluations = 125 208 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.115 | 9.115 | 9.115 | 0.0 | 95.29 Neigh | 0.33142 | 0.33142 | 0.33142 | 0.0 | 3.46 Comm | 0.060062 | 0.060062 | 0.060062 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05867 | | | 0.61 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10658.0 ave 10658 max 10658 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: 428938.0 ave 428938 max 428938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428938 Ave neighs/atom = 172.26426 Neighbor list builds = 6 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.514 | 6.514 | 6.514 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -8792.1094 0 -8792.1094 5154.9008 29477.777 130 0 -8792.4227 0 -8792.4227 -16.847151 29587.361 Loop time of 0.33863 on 1 procs for 5 steps with 2490 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 = -8792.10937179392 -8792.42069702601 -8792.42269119092 Force two-norm initial, final = 185.51511 2.4921714 Force max component initial, final = 157.79323 2.2115675 Final line search alpha, max atom move = 5.3902415e-05 0.00011920883 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32971 | 0.32971 | 0.32971 | 0.0 | 97.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019017 | 0.0019017 | 0.0019017 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007018 | | | 2.07 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10658.0 ave 10658 max 10658 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: 430732.0 ave 430732 max 430732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 430732 Ave neighs/atom = 172.98474 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 6.652 | 6.652 | 6.652 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8792.4227 0 -8792.4227 -16.847151 Loop time of 6.615e-06 on 1 procs for 0 steps with 2490 atoms 196.5% 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 | | 6.615e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10655.0 ave 10655 max 10655 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: 429016.0 ave 429016 max 429016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 429016 Ave neighs/atom = 172.29558 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 6.652 | 6.652 | 6.652 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 -8792.4227 -8792.4227 36.896362 128.19115 6.2555375 -16.847151 -16.847151 -119.85822 11.172553 58.144213 2.3185561 1035.4097 Loop time of 7.107e-06 on 1 procs for 0 steps with 2490 atoms 267.3% 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 | | 7.107e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10655.0 ave 10655 max 10655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 214508.0 ave 214508 max 214508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 429016.0 ave 429016 max 429016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 429016 Ave neighs/atom = 172.29558 Neighbor list builds = 0 Dangerous builds = 0 2490 -8792.42269119092 eV 2.31855613510998 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10