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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -46.775715 0.0000000) to (33.072547 46.775715 5.7571914) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.0153887 6.3779515 5.7571914 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -46.775715 0.0000000) to (33.072547 46.775715 5.7571914) create_atoms CPU = 0.004 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.0153887 6.3779515 5.7571914 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -46.775715 0.0000000) to (33.072547 46.775715 5.7571914) create_atoms CPU = 0.003 seconds 532 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 31 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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_304347095149_000#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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3504.8602 0 -3504.8602 1714.3722 12 0 -3519.3679 0 -3519.3679 -3359.4261 Loop time of 1.34269 on 1 procs for 12 steps with 1048 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 = -3504.86017015201 -3519.36626155512 -3519.36792538554 Force two-norm initial, final = 17.438822 1.0161412 Force max component initial, final = 3.1947510 0.22784652 Final line search alpha, max atom move = 0.37033372 0.084379251 Iterations, force evaluations = 12 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3381 | 1.3381 | 1.3381 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019056 | 0.0019056 | 0.0019056 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002666 | | | 0.20 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4236.00 ave 4236 max 4236 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: 56256.0 ave 56256 max 56256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56256 Ave neighs/atom = 53.679389 Neighbor list builds = 0 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -3519.3679 0 -3519.3679 -3359.4261 17812.659 15 0 -3519.4379 0 -3519.4379 -171.61761 17752.057 Loop time of 0.427282 on 1 procs for 3 steps with 1048 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 = -3519.36792538554 -3519.43695849414 -3519.43787176731 Force two-norm initial, final = 58.225260 1.1136928 Force max component initial, final = 42.428417 0.32126733 Final line search alpha, max atom move = 0.00044801927 0.00014393395 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42449 | 0.42449 | 0.42449 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055709 | 0.00055709 | 0.00055709 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002231 | | | 0.52 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4236.00 ave 4236 max 4236 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: 56368.0 ave 56368 max 56368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56368 Ave neighs/atom = 53.786260 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.730 | 4.730 | 4.730 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3519.4379 0 -3519.4379 -171.61761 Loop time of 6.435e-06 on 1 procs for 0 steps with 1048 atoms 186.5% 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 | | 6.435e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4236.00 ave 4236 max 4236 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: 56400.0 ave 56400 max 56400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56400 Ave neighs/atom = 53.816794 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.730 | 4.730 | 4.730 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 -3519.4379 -3519.4379 32.999843 93.551431 5.7502452 -171.61761 -171.61761 28.931602 -526.6404 -17.144034 2.6117673 614.22962 Loop time of 7.087e-06 on 1 procs for 0 steps with 1048 atoms 254.0% 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 | | 7.087e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4236.00 ave 4236 max 4236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28200.0 ave 28200 max 28200 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56400.0 ave 56400 max 56400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56400 Ave neighs/atom = 53.816794 Neighbor list builds = 0 Dangerous builds = 0 1048 -3519.43787176731 eV 2.61176734475537 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02