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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -62.169447 0.0000000) to (31.082917 62.169447 3.6133157) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0404730 5.0404730 3.6133157 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.169447 0.0000000) to (31.082917 62.169447 3.6133157) create_atoms CPU = 0.003 seconds 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0404730 5.0404730 3.6133157 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.169447 0.0000000) to (31.082917 62.169447 3.6133157) create_atoms CPU = 0.002 seconds 594 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1178 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4122.6872 0 -4122.6872 9742.5903 71 0 -4159.6336 0 -4159.6336 -2332.9497 Loop time of 9.95195 on 1 procs for 71 steps with 1178 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4122.68718564734 -4159.62996163649 -4159.63364459787 Force two-norm initial, final = 45.220678 0.17143804 Force max component initial, final = 15.839583 0.039821705 Final line search alpha, max atom move = 1.0000000 0.039821705 Iterations, force evaluations = 71 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.9106 | 9.9106 | 9.9106 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.022299 | 0.022299 | 0.022299 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01907 | | | 0.19 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7997.00 ave 7997 max 7997 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: 101388.0 ave 101388 max 101388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101388 Ave neighs/atom = 86.067912 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.042 | 5.042 | 5.042 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4159.6336 0 -4159.6336 -2332.9497 13964.798 73 0 -4159.6541 0 -4159.6541 73.804169 13940.876 Loop time of 0.44647 on 1 procs for 2 steps with 1178 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 = -4159.63364459786 -4159.65392113928 -4159.65406972248 Force two-norm initial, final = 33.883799 0.17115217 Force max component initial, final = 25.040595 0.034299293 Final line search alpha, max atom move = 0.00095520824 3.2762968e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44312 | 0.44312 | 0.44312 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081059 | 0.00081059 | 0.00081059 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002541 | | | 0.57 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8032.00 ave 8032 max 8032 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: 101376.0 ave 101376 max 101376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101376 Ave neighs/atom = 86.057725 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.180 | 5.180 | 5.180 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4159.6541 0 -4159.6541 73.804169 Loop time of 8.811e-06 on 1 procs for 0 steps with 1178 atoms 158.9% 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 | | 8.811e-06 | | |100.00 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8032.00 ave 8032 max 8032 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: 101384.0 ave 101384 max 101384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101384 Ave neighs/atom = 86.064516 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.180 | 5.180 | 5.180 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 -4159.6541 -4159.6541 31.059786 124.33889 3.6098122 73.804169 73.804169 -3.9389653 224.55448 0.79699479 2.2987511 322.80685 Loop time of 6.796e-06 on 1 procs for 0 steps with 1178 atoms 279.6% 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 | | 6.796e-06 | | |100.00 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8032.00 ave 8032 max 8032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50692.0 ave 50692 max 50692 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101384.0 ave 101384 max 101384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101384 Ave neighs/atom = 86.064516 Neighbor list builds = 0 Dangerous builds = 0 1178 -4159.65406972248 eV 2.2987510628052 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11