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 = 3.5200010 3.5200010 3.5200010 Created orthogonal box = (0.0000000 -35.897108 0.0000000) to (31.087807 35.897108 6.0968206) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5798628 5.5226319 6.0968206 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -35.897108 0.0000000) to (31.087807 35.897108 6.0968206) create_atoms CPU = 0.004 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5798628 5.5226319 6.0968206 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -35.897108 0.0000000) to (31.087807 35.897108 6.0968206) create_atoms CPU = 0.004 seconds 629 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1251 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.450 | 5.450 | 5.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4404.1616 0 -4404.1616 179965.19 118 0 -5534.6923 0 -5534.6923 21728.166 Loop time of 5.43783 on 1 procs for 118 steps with 1251 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 = -4404.16160082833 -5534.68699738015 -5534.69230664378 Force two-norm initial, final = 1500.4784 0.31430117 Force max component initial, final = 339.52113 0.12578901 Final line search alpha, max atom move = 0.79645895 0.10018578 Iterations, force evaluations = 118 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2557 | 5.2557 | 5.2557 | 0.0 | 96.65 Neigh | 0.11398 | 0.11398 | 0.11398 | 0.0 | 2.10 Comm | 0.034755 | 0.034755 | 0.034755 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03337 | | | 0.61 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6251.00 ave 6251 max 6251 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: 216948.0 ave 216948 max 216948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216948 Ave neighs/atom = 173.41966 Neighbor list builds = 4 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 118 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.450 | 5.450 | 5.450 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -5534.6923 0 -5534.6923 21728.166 13607.644 130 0 -5536.5662 0 -5536.5662 -104.15491 13769.696 Loop time of 0.346444 on 1 procs for 12 steps with 1251 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5534.69230664375 -5536.56533157354 -5536.56615039144 Force two-norm initial, final = 367.02231 1.7608025 Force max component initial, final = 323.65085 1.0124515 Final line search alpha, max atom move = 0.00023472952 0.00023765226 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33692 | 0.33692 | 0.33692 | 0.0 | 97.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019805 | 0.0019805 | 0.0019805 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007548 | | | 2.18 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6257.00 ave 6257 max 6257 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: 217046.0 ave 217046 max 217046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217046 Ave neighs/atom = 173.49800 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.588 | 5.588 | 5.588 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5536.5662 0 -5536.5662 -104.15491 Loop time of 6.425e-06 on 1 procs for 0 steps with 1251 atoms 171.2% 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 | | 6.425e-06 | | |100.00 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6251.00 ave 6251 max 6251 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: 216370.0 ave 216370 max 216370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216370 Ave neighs/atom = 172.95763 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.588 | 5.588 | 5.588 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 -5536.5662 -5536.5662 31.141862 72.602289 6.0901708 -104.15491 -104.15491 -118.00889 -94.630594 -99.825252 2.2517561 861.7831 Loop time of 7.146e-06 on 1 procs for 0 steps with 1251 atoms 265.9% 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 | | 7.146e-06 | | |100.00 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6251.00 ave 6251 max 6251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108185.0 ave 108185 max 108185 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 216370.0 ave 216370 max 216370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216370 Ave neighs/atom = 172.95763 Neighbor list builds = 0 Dangerous builds = 0 1251 -5490.9644274845 eV 2.25175612921814 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06