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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -52.115360 0.0000000) to (42.549138 52.115360 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2457842 4.9970257 5.7504086 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -52.115360 0.0000000) to (42.549138 52.115360 8.6256130) create_atoms CPU = 0.003 seconds 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2457842 4.9970257 5.7504086 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -52.115360 0.0000000) to (42.549138 52.115360 8.6256130) create_atoms CPU = 0.003 seconds 1758 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 52 atoms, new total = 3464 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 6.095 | 6.095 | 6.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15285.941 0 -15285.941 1665.0113 61 0 -15352.768 0 -15352.768 -10400.666 Loop time of 24.5487 on 1 procs for 61 steps with 3464 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 = -15285.9407889065 -15352.7566682819 -15352.7679464883 Force two-norm initial, final = 71.577672 0.39415428 Force max component initial, final = 12.469131 0.084541592 Final line search alpha, max atom move = 1.0000000 0.084541592 Iterations, force evaluations = 61 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.444 | 24.444 | 24.444 | 0.0 | 99.57 Neigh | 0.046988 | 0.046988 | 0.046988 | 0.0 | 0.19 Comm | 0.022692 | 0.022692 | 0.022692 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03509 | | | 0.14 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8687.00 ave 8687 max 8687 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: 296638.0 ave 296638 max 296638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296638 Ave neighs/atom = 85.634527 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.103 | 6.103 | 6.103 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -15352.768 0 -15352.768 -10400.666 38253.967 65 0 -15353.281 0 -15353.281 -2269.526 38083.985 Loop time of 1.5642 on 1 procs for 4 steps with 3464 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 = -15352.7679464884 -15353.2795702873 -15353.2813392663 Force two-norm initial, final = 320.43796 0.45428168 Force max component initial, final = 243.25870 0.066936493 Final line search alpha, max atom move = 8.9657901e-05 6.0013854e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5568 | 1.5568 | 1.5568 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00099255 | 0.00099255 | 0.00099255 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006379 | | | 0.41 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8781.00 ave 8781 max 8781 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: 296512.0 ave 296512 max 296512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296512 Ave neighs/atom = 85.598152 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 6.241 | 6.241 | 6.241 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15353.281 0 -15353.281 -2269.526 Loop time of 3.978e-06 on 1 procs for 0 steps with 3464 atoms 176.0% 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 | | 3.978e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8798.00 ave 8798 max 8798 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: 296560.0 ave 296560 max 296560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296560 Ave neighs/atom = 85.612009 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 6.241 | 6.241 | 6.241 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 -15353.281 -15353.281 42.431741 104.23072 8.6110437 -2269.526 -2269.526 -1.9172226 -6804.4845 -2.1763749 2.1971968 1644.7871 Loop time of 3.475e-06 on 1 procs for 0 steps with 3464 atoms 230.2% 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 | | 3.475e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8798.00 ave 8798 max 8798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 148280.0 ave 148280 max 148280 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 296560.0 ave 296560 max 296560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296560 Ave neighs/atom = 85.612009 Neighbor list builds = 0 Dangerous builds = 0 3464 -15353.2813392663 eV 2.19719680421665 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27