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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -69.695980 0.0000000) to (42.677741 69.695980 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9355211 4.9780328 5.7481372 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.695980 0.0000000) to (42.677741 69.695980 8.6222058) create_atoms CPU = 0.009 seconds 2357 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9355211 4.9780328 5.7481372 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.695980 0.0000000) to (42.677741 69.695980 8.6222058) create_atoms CPU = 0.008 seconds 2357 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 = 11 36 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 47 atoms, new total = 4667 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_820335782779_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 = 11 36 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) = 12.29 | 12.29 | 12.29 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20656.885 0 -20656.885 -3235.8344 25 0 -20694.055 0 -20694.055 -6453.1726 Loop time of 3.81819 on 1 procs for 25 steps with 4667 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20656.884685137 -20694.0355301134 -20694.054767256 Force two-norm initial, final = 27.402302 0.61061466 Force max component initial, final = 4.4639873 0.13527785 Final line search alpha, max atom move = 1.0000000 0.13527785 Iterations, force evaluations = 25 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.783 | 3.783 | 3.783 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015462 | 0.015462 | 0.015462 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01977 | | | 0.52 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14692.0 ave 14692 max 14692 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: 816522.0 ave 816522 max 816522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816522 Ave neighs/atom = 174.95650 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 36 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.29 | 12.29 | 12.29 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -20694.055 0 -20694.055 -6453.1726 51292.933 28 0 -20694.303 0 -20694.303 -1481.9036 51154.621 Loop time of 0.496814 on 1 procs for 3 steps with 4667 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20694.054767256 -20694.3034801596 -20694.3034940809 Force two-norm initial, final = 260.43532 0.85725402 Force max component initial, final = 195.23763 0.54630793 Final line search alpha, max atom move = 0.0013735390 0.00075037525 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48703 | 0.48703 | 0.48703 | 0.0 | 98.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001927 | 0.001927 | 0.001927 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007855 | | | 1.58 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14750.0 ave 14750 max 14750 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: 820262.0 ave 820262 max 820262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 820262 Ave neighs/atom = 175.75787 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 = 11 36 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) = 11.81 | 11.81 | 11.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20694.303 0 -20694.303 -1481.9036 Loop time of 6.445e-06 on 1 procs for 0 steps with 4667 atoms 201.7% 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 | | 6.445e-06 | | |100.00 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14750.0 ave 14750 max 14750 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: 820536.0 ave 820536 max 820536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 820536 Ave neighs/atom = 175.81658 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 = 11 36 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) = 11.81 | 11.81 | 11.81 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 -20694.303 -20694.303 42.622976 139.39196 8.6100046 -1481.9036 -1481.9036 17.088555 -4460.6723 -2.1270557 2.2395114 1750.2189 Loop time of 6.625e-06 on 1 procs for 0 steps with 4667 atoms 332.1% 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 | | 6.625e-06 | | |100.00 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14750.0 ave 14750 max 14750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 410268.0 ave 410268 max 410268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 820536.0 ave 820536 max 820536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 820536 Ave neighs/atom = 175.81658 Neighbor list builds = 0 Dangerous builds = 0 4667 -20694.3034940809 eV 2.23951144855675 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06