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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -35.900866 0.0000000) to (31.088013 35.900866 6.0968610) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5798998 5.5226686 6.0968610 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -35.900866 0.0000000) to (31.088013 35.900866 6.0968610) create_atoms CPU = 0.004 seconds 627 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5798998 5.5226686 6.0968610 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -35.900866 0.0000000) to (31.088013 35.900866 6.0968610) create_atoms CPU = 0.003 seconds 630 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 18 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 1234 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.492 | 5.492 | 5.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5411.6113 0 -5411.6113 12560.764 93 0 -5456.3397 0 -5456.3397 -6413.8613 Loop time of 5.29683 on 1 procs for 93 steps with 1234 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 = -5411.61133489713 -5456.3356463552 -5456.33970541242 Force two-norm initial, final = 64.374623 0.19158612 Force max component initial, final = 10.197087 0.028104157 Final line search alpha, max atom move = 0.51778947 0.014552037 Iterations, force evaluations = 93 174 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1565 | 5.1565 | 5.1565 | 0.0 | 97.35 Neigh | 0.078051 | 0.078051 | 0.078051 | 0.0 | 1.47 Comm | 0.034817 | 0.034817 | 0.034817 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0275 | | | 0.52 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8122.00 ave 8122 max 8122 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: 273892.0 ave 273892 max 273892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273892 Ave neighs/atom = 221.95462 Neighbor list builds = 2 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.492 | 5.492 | 5.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -5456.3397 0 -5456.3397 -6413.8613 13609.25 96 0 -5456.4093 0 -5456.4093 -2116.862 13575.991 Loop time of 0.177431 on 1 procs for 3 steps with 1234 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 = -5456.33970541246 -5456.40839469887 -5456.40928138144 Force two-norm initial, final = 68.070404 0.20337376 Force max component initial, final = 62.541250 0.025334985 Final line search alpha, max atom move = 0.00017527993 4.4407144e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17311 | 0.17311 | 0.17311 | 0.0 | 97.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010596 | 0.0010596 | 0.0010596 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003261 | | | 1.84 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8119.00 ave 8119 max 8119 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: 273900.0 ave 273900 max 273900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273900 Ave neighs/atom = 221.96110 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.630 | 5.630 | 5.630 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5456.4093 0 -5456.4093 -2116.862 Loop time of 6.345e-06 on 1 procs for 0 steps with 1234 atoms 189.1% 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 | | 6.345e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8122.00 ave 8122 max 8122 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: 273964.0 ave 273964 max 273964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273964 Ave neighs/atom = 222.01297 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.630 | 5.630 | 5.630 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 -5456.4093 -5456.4093 31.075733 71.801731 6.0843647 -2116.862 -2116.862 -2.5530466 -6348.7216 0.6885801 2.1984982 844.60582 Loop time of 6.966e-06 on 1 procs for 0 steps with 1234 atoms 272.8% 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 | | 6.966e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8122.00 ave 8122 max 8122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136982.0 ave 136982 max 136982 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 273964.0 ave 273964 max 273964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273964 Ave neighs/atom = 222.01297 Neighbor list builds = 0 Dangerous builds = 0 1234 -5422.76871156024 eV 2.19849824896472 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06