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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -74.678310 0.0000000) to (37.339155 74.678310 4.0500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7106943 5.7106943 4.0500000 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -74.678310 0.0000000) to (37.339155 74.678310 4.0500000) create_atoms CPU = 0.001 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7106943 5.7106943 4.0500000 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.678310 0.0000000) to (37.339155 74.678310 4.0500000) create_atoms CPU = 0.001 seconds 682 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_971738391444_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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.052 | 5.052 | 5.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4497.7359 0 -4497.7359 6297.2479 40 0 -4559.0197 0 -4559.0197 1559.0543 Loop time of 4.58081 on 1 procs for 40 steps with 1362 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 = -4497.73585176631 -4559.01822688288 -4559.01974975909 Force two-norm initial, final = 70.006457 0.25371526 Force max component initial, final = 25.284438 0.042174131 Final line search alpha, max atom move = 0.25000000 0.010543533 Iterations, force evaluations = 40 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5608 | 4.5608 | 4.5608 | 0.0 | 99.56 Neigh | 0.0078919 | 0.0078919 | 0.0078919 | 0.0 | 0.17 Comm | 0.0061354 | 0.0061354 | 0.0061354 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005974 | | | 0.13 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6830.00 ave 6830 max 6830 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: 108172.0 ave 108172 max 108172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108172 Ave neighs/atom = 79.421439 Neighbor list builds = 1 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.055 | 5.055 | 5.055 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -4559.0197 0 -4559.0197 1559.0543 22586.242 42 0 -4559.0428 0 -4559.0428 -1.5805028 22631.888 Loop time of 0.313095 on 1 procs for 2 steps with 1362 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 = -4559.01974975909 -4559.04236331578 -4559.04279733185 Force two-norm initial, final = 38.309084 0.30521246 Force max component initial, final = 24.297236 0.15668501 Final line search alpha, max atom move = 0.00040656989 6.3703406e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31162 | 0.31162 | 0.31162 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026805 | 0.00026805 | 0.00026805 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00121 | | | 0.39 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6830.00 ave 6830 max 6830 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: 108260.0 ave 108260 max 108260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108260 Ave neighs/atom = 79.486050 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.193 | 5.193 | 5.193 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4559.0428 0 -4559.0428 -1.5805028 Loop time of 1.983e-06 on 1 procs for 0 steps with 1362 atoms 151.3% 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 | | 1.983e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6830.00 ave 6830 max 6830 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: 107996.0 ave 107996 max 107996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107996 Ave neighs/atom = 79.292217 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.193 | 5.193 | 5.193 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 -4559.0428 -4559.0428 37.368019 149.49198 4.0513784 -1.5805028 -1.5805028 -11.100757 4.5522113 1.8070377 1.8909015 141.37938 Loop time of 2.168e-06 on 1 procs for 0 steps with 1362 atoms 230.6% 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 | | 2.168e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6830.00 ave 6830 max 6830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53998.0 ave 53998 max 53998 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107996.0 ave 107996 max 107996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107996 Ave neighs/atom = 79.292217 Neighbor list builds = 0 Dangerous builds = 0 1362 -4559.04279733185 eV 1.89090153387431 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05