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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -52.111839 0.0000000) to (42.549138 52.111839 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2457842 4.9970257 5.7504086 Created 1752 atoms using lattice units in orthogonal box = (0.0000000 -52.111839 0.0000000) to (42.549138 52.111839 8.6256130) create_atoms CPU = 0.002 seconds 1752 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2457842 4.9970257 5.7504086 Created 1760 atoms using lattice units in orthogonal box = (0.0000000 -52.111839 0.0000000) to (42.549138 52.111839 8.6256130) create_atoms CPU = 0.002 seconds 1760 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 30 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 3504 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_663355627503_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.583 | 6.583 | 6.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13867.289 0 -13867.289 84727.989 79 0 -15525.282 0 -15525.282 10172.105 Loop time of 27.9018 on 1 procs for 79 steps with 3504 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 = -13867.2891147773 -15525.2661605055 -15525.2815314176 Force two-norm initial, final = 1459.4133 0.48402135 Force max component initial, final = 189.25803 0.052737260 Final line search alpha, max atom move = 1.0000000 0.052737260 Iterations, force evaluations = 79 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.8 | 27.8 | 27.8 | 0.0 | 99.64 Neigh | 0.05994 | 0.05994 | 0.05994 | 0.0 | 0.21 Comm | 0.017649 | 0.017649 | 0.017649 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02388 | | | 0.09 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10498.0 ave 10498 max 10498 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: 468336.0 ave 468336 max 468336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468336 Ave neighs/atom = 133.65753 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.582 | 6.582 | 6.582 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -15525.282 0 -15525.282 10172.105 38251.382 87 0 -15526.921 0 -15526.921 -167.84459 38463.385 Loop time of 1.95336 on 1 procs for 8 steps with 3504 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 = -15525.2815314176 -15526.91414468 -15526.921334956 Force two-norm initial, final = 510.05359 7.2787261 Force max component initial, final = 477.57505 5.4707777 Final line search alpha, max atom move = 5.0148345e-05 0.00027435045 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9474 | 1.9474 | 1.9474 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079805 | 0.00079805 | 0.00079805 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005131 | | | 0.26 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10507.0 ave 10507 max 10507 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: 469808.0 ave 469808 max 469808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469808 Ave neighs/atom = 134.07763 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.720 | 6.720 | 6.720 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15526.921 0 -15526.921 -167.84459 Loop time of 2.285e-06 on 1 procs for 0 steps with 3504 atoms 131.3% 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 | | 2.285e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10513.0 ave 10513 max 10513 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: 467184.0 ave 467184 max 467184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 467184 Ave neighs/atom = 133.32877 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.720 | 6.720 | 6.720 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 -15526.921 -15526.921 42.503225 105.00644 8.6180631 -167.84459 -167.84459 -227.6371 -160.87252 -115.02415 2.2292069 1606.9669 Loop time of 3.617e-06 on 1 procs for 0 steps with 3504 atoms 248.8% 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 | | 3.617e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10513.0 ave 10513 max 10513 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 233592.0 ave 233592 max 233592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 467184.0 ave 467184 max 467184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 467184 Ave neighs/atom = 133.32877 Neighbor list builds = 0 Dangerous builds = 0 3504 -15526.921334956 eV 2.22920693210131 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:31