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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -51.128678 0.0000000) to (18.075605 51.128678 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9297105 5.4224049 4.4499063 Created 265 atoms using lattice units in orthogonal box = (0.0000000 -51.128678 0.0000000) to (18.075605 51.128678 4.4499063) create_atoms CPU = 0.003 seconds 265 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9297105 5.4224049 4.4499063 Created 265 atoms using lattice units in orthogonal box = (0.0000000 -51.128678 0.0000000) to (18.075605 51.128678 4.4499063) create_atoms CPU = 0.002 seconds 265 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 527 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3555.3365 0 -3555.3365 13884.344 20 0 -3571.9606 0 -3571.9606 4583.9994 Loop time of 1.08347 on 1 procs for 20 steps with 527 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 = -3555.33647302007 -3571.95731517515 -3571.9606321833 Force two-norm initial, final = 20.773257 0.19736534 Force max component initial, final = 6.9161773 0.059541396 Final line search alpha, max atom move = 1.0000000 0.059541396 Iterations, force evaluations = 20 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0781 | 1.0781 | 1.0781 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024585 | 0.0024585 | 0.0024585 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002904 | | | 0.27 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2825.00 ave 2825 max 2825 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: 30328.0 ave 30328 max 30328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30328 Ave neighs/atom = 57.548387 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -3571.9606 0 -3571.9606 4583.9994 8225.0449 23 0 -3571.9862 0 -3571.9862 1384.8253 8235.0128 Loop time of 0.181844 on 1 procs for 3 steps with 527 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 = -3571.9606321833 -3571.98617365905 -3571.98620353034 Force two-norm initial, final = 32.307252 0.20322583 Force max component initial, final = 31.920239 0.053419433 Final line search alpha, max atom move = 0.00090300358 4.8237939e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18002 | 0.18002 | 0.18002 | 0.0 | 99.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039573 | 0.00039573 | 0.00039573 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001425 | | | 0.78 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2825.00 ave 2825 max 2825 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: 30330.0 ave 30330 max 30330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30330 Ave neighs/atom = 57.552182 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3571.9862 0 -3571.9862 1384.8253 Loop time of 6.254e-06 on 1 procs for 0 steps with 527 atoms 159.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2825.00 ave 2825 max 2825 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: 30330.0 ave 30330 max 30330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30330 Ave neighs/atom = 57.552182 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.608 | 4.608 | 4.608 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 -3571.9862 -3571.9862 18.067215 102.25736 4.457368 1384.8253 1384.8253 4.762781 4147.7795 1.9335077 2.3271109 331.95146 Loop time of 6.856e-06 on 1 procs for 0 steps with 527 atoms 248.0% 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 | | 6.856e-06 | | |100.00 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2825.00 ave 2825 max 2825 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15165.0 ave 15165 max 15165 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30330.0 ave 30330 max 30330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30330 Ave neighs/atom = 57.552182 Neighbor list builds = 0 Dangerous builds = 0 527 -3571.98620353034 eV 2.32711088289656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01