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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -59.889322 0.0000000) to (42.345559 59.889322 5.1733334) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3202327 5.8098032 5.1733334 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -59.889322 0.0000000) to (42.345559 59.889322 5.1733334) create_atoms CPU = 0.003 seconds 1079 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3202327 5.8098032 5.1733334 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -59.889322 0.0000000) to (42.345559 59.889322 5.1733334) create_atoms CPU = 0.002 seconds 1079 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 33 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 2127 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.640 | 5.640 | 5.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8241.8586 0 -8241.8586 -2374.554 1417 0 -8406.8473 0 -8406.8473 -76260.217 Loop time of 39.0588 on 1 procs for 1417 steps with 2127 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 = -8241.85864161837 -8406.8400465175 -8406.84725241131 Force two-norm initial, final = 15.742078 0.38214863 Force max component initial, final = 2.4537531 0.12675950 Final line search alpha, max atom move = 0.82935144 0.10512817 Iterations, force evaluations = 1417 2786 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38.195 | 38.195 | 38.195 | 0.0 | 97.79 Neigh | 0.37739 | 0.37739 | 0.37739 | 0.0 | 0.97 Comm | 0.25954 | 0.25954 | 0.25954 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2269 | | | 0.58 Nlocal: 2127.00 ave 2127 max 2127 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10114.0 ave 10114 max 10114 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: 286416.0 ave 286416 max 286416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286416 Ave neighs/atom = 134.65726 Neighbor list builds = 22 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1417 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.643 | 5.643 | 5.643 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1417 0 -8406.8473 0 -8406.8473 -76260.217 26239.632 1458 0 -8469.4629 0 -8469.4629 17250.22 24590.022 Loop time of 0.653837 on 1 procs for 41 steps with 2127 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 = -8406.8472524113 -8469.4619201428 -8469.46286302159 Force two-norm initial, final = 2509.9248 8.8280244 Force max component initial, final = 1865.0498 6.1123988 Final line search alpha, max atom move = 0.00028889402 0.0017658354 Iterations, force evaluations = 41 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6149 | 0.6149 | 0.6149 | 0.0 | 94.05 Neigh | 0.017571 | 0.017571 | 0.017571 | 0.0 | 2.69 Comm | 0.0035419 | 0.0035419 | 0.0035419 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01782 | | | 2.73 Nlocal: 2127.00 ave 2127 max 2127 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10480.0 ave 10480 max 10480 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: 304310.0 ave 304310 max 304310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304310 Ave neighs/atom = 143.07005 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.166 | 6.166 | 6.166 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8469.4629 0 -8469.4629 17250.22 Loop time of 1.528e-06 on 1 procs for 0 steps with 2127 atoms 130.9% 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 | | 1.528e-06 | | |100.00 Nlocal: 2127.00 ave 2127 max 2127 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10599.0 ave 10599 max 10599 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: 306774.0 ave 306774 max 306774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306774 Ave neighs/atom = 144.22849 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.166 | 6.166 | 6.166 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 -8469.4629 -8469.4629 41.315155 119.77864 4.9690129 17250.22 17250.22 -388.56587 52370.409 -231.18422 2.2149777 5483.3708 Loop time of 1.757e-06 on 1 procs for 0 steps with 2127 atoms 227.7% 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 | | 1.757e-06 | | |100.00 Nlocal: 2127.00 ave 2127 max 2127 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10599.0 ave 10599 max 10599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 153387.0 ave 153387 max 153387 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 306774.0 ave 306774 max 306774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306774 Ave neighs/atom = 144.22849 Neighbor list builds = 0 Dangerous builds = 0 2127 -8168.65906895813 eV 2.21497771130235 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:40