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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -42.122489 0.0000000) to (51.589303 42.122489 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8959203 5.4157486 5.8134559 Created 1660 atoms using lattice units in orthogonal box = (0.0000000 -42.122489 0.0000000) to (51.589303 42.122489 8.7201838) create_atoms CPU = 0.003 seconds 1660 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8959203 5.4157486 5.8134559 Created 1684 atoms using lattice units in orthogonal box = (0.0000000 -42.122489 0.0000000) to (51.589303 42.122489 8.7201838) create_atoms CPU = 0.003 seconds 1684 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3316 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.971 | 6.971 | 6.971 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14337.876 0 -14337.876 -9688.7295 177 0 -14527.275 0 -14527.275 -6131.9437 Loop time of 10.0051 on 1 procs for 177 steps with 3316 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14337.8763654605 -14527.2624199093 -14527.2754767218 Force two-norm initial, final = 66.790811 0.62520666 Force max component initial, final = 8.4154416 0.21847670 Final line search alpha, max atom move = 0.29834874 0.065182251 Iterations, force evaluations = 177 333 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.6713 | 9.6713 | 9.6713 | 0.0 | 96.66 Neigh | 0.22493 | 0.22493 | 0.22493 | 0.0 | 2.25 Comm | 0.047576 | 0.047576 | 0.047576 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06137 | | | 0.61 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11213.0 ave 11213 max 11213 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: 578354.0 ave 578354 max 578354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578354 Ave neighs/atom = 174.41315 Neighbor list builds = 6 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 177 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.975 | 6.975 | 6.975 Mbytes Step Temp E_pair E_mol TotEng Press Volume 177 0 -14527.275 0 -14527.275 -6131.9437 37899.137 179 0 -14527.511 0 -14527.511 110.96865 37776.152 Loop time of 0.118456 on 1 procs for 2 steps with 3316 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 = -14527.2754767218 -14527.5066445285 -14527.5114010763 Force two-norm initial, final = 251.64416 11.379548 Force max component initial, final = 154.72889 10.939144 Final line search alpha, max atom move = 3.9273795e-05 0.00042962169 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11574 | 0.11574 | 0.11574 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041377 | 0.00041377 | 0.00041377 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002304 | | | 1.95 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11207.0 ave 11207 max 11207 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: 578274.0 ave 578274 max 578274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578274 Ave neighs/atom = 174.38902 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.113 | 7.113 | 7.113 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14527.511 0 -14527.511 110.96865 Loop time of 2.261e-06 on 1 procs for 0 steps with 3316 atoms 176.9% 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 | | 2.261e-06 | | |100.00 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11227.0 ave 11227 max 11227 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: 578828.0 ave 578828 max 578828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578828 Ave neighs/atom = 174.55609 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.113 | 7.113 | 7.113 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 -14527.511 -14527.511 51.541925 84.142906 8.7104297 110.96865 110.96865 463.52903 -129.35749 -1.2655833 2.2561466 2011.4111 Loop time of 2.306e-06 on 1 procs for 0 steps with 3316 atoms 260.2% 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 | | 2.306e-06 | | |100.00 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11227.0 ave 11227 max 11227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 289414.0 ave 289414 max 289414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 578828.0 ave 578828 max 578828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578828 Ave neighs/atom = 174.55609 Neighbor list builds = 0 Dangerous builds = 0 3316 -14527.5114010763 eV 2.25614662100281 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10