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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -41.758127 0.0000000) to (29.527454 41.758127 5.1015671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7292076 6.2325562 5.1015671 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.758127 0.0000000) to (29.527454 41.758127 5.1015671) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7292076 6.2325562 5.1015671 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.758127 0.0000000) to (29.527454 41.758127 5.1015671) create_atoms CPU = 0.001 seconds 538 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 14 1 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1070 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_151002396060_004#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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.097 | 7.097 | 7.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3571.4558 0 -3571.4558 32110.532 85 0 -3770.951 0 -3770.951 355.725 Loop time of 7.5898 on 1 procs for 85 steps with 1070 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 = -3571.45581354975 -3770.94729731606 -3770.95098854095 Force two-norm initial, final = 288.05713 0.24311939 Force max component initial, final = 89.941988 0.035583450 Final line search alpha, max atom move = 1.0000000 0.035583450 Iterations, force evaluations = 85 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5003 | 7.5003 | 7.5003 | 0.0 | 98.82 Neigh | 0.0351 | 0.0351 | 0.0351 | 0.0 | 0.46 Comm | 0.036123 | 0.036123 | 0.036123 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0183 | | | 0.24 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13401.0 ave 13401 max 13401 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: 675984.0 ave 675984 max 675984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 675984 Ave neighs/atom = 631.76075 Neighbor list builds = 1 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.105 | 7.105 | 7.105 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -3770.951 0 -3770.951 355.725 12580.579 92 0 -3771.3927 0 -3771.3927 -0.24318475 12582.951 Loop time of 0.591308 on 1 procs for 7 steps with 1070 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 = -3770.95098854094 -3771.39256331396 -3771.39265730954 Force two-norm initial, final = 120.60979 0.42568922 Force max component initial, final = 93.130791 0.083351015 Final line search alpha, max atom move = 0.00074732638 6.2290413e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58135 | 0.58135 | 0.58135 | 0.0 | 98.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00205 | 0.00205 | 0.00205 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00791 | | | 1.34 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13923.0 ave 13923 max 13923 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: 675216.0 ave 675216 max 675216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 675216 Ave neighs/atom = 631.04299 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.242 | 7.242 | 7.242 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3771.3927 0 -3771.3927 -0.24318475 Loop time of 3.243e-06 on 1 procs for 0 steps with 1070 atoms 154.2% 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 | | 3.243e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13810.0 ave 13810 max 13810 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: 674644.0 ave 674644 max 674644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 674644 Ave neighs/atom = 630.50841 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.242 | 7.242 | 7.242 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 -3771.3927 -3771.3927 29.370833 83.945829 5.1034883 -0.24318475 -0.24318475 1.3234561 8.5640005 -10.617011 2.3416225 609.84973 Loop time of 3.831e-06 on 1 procs for 0 steps with 1070 atoms 208.8% 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 | | 3.831e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13810.0 ave 13810 max 13810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 337322.0 ave 337322 max 337322 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 674644.0 ave 674644 max 674644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 674644 Ave neighs/atom = 630.50841 Neighbor list builds = 0 Dangerous builds = 0 1070 -3771.39265730954 eV 2.34162247621076 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10