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 = 2.8510000 2.8510000 2.8510000 Created orthogonal box = (0.0000000 -37.284514 0.0000000) to (17.574744 37.284514 4.0319229) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6999462 4.5784498 4.0319229 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.284514 0.0000000) to (17.574744 37.284514 4.0319229) create_atoms CPU = 0.002 seconds 229 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6999462 4.5784498 4.0319229 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.284514 0.0000000) to (17.574744 37.284514 4.0319229) create_atoms CPU = 0.002 seconds 229 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 ghost atom cutoff = 6 binsize = 3, bins = 6 25 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 454 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_549900287421_001#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 ghost atom cutoff = 6 binsize = 3, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.455 | 4.455 | 4.455 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1888.3634 0 -1888.3634 37471.678 42 0 -1936.6098 0 -1936.6098 1315.6348 Loop time of 2.1423 on 1 procs for 42 steps with 454 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 = -1888.36341351415 -1936.60817028951 -1936.6098278466 Force two-norm initial, final = 137.32744 0.12534870 Force max component initial, final = 66.216488 0.019363210 Final line search alpha, max atom move = 1.0000000 0.019363210 Iterations, force evaluations = 42 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1252 | 2.1252 | 2.1252 | 0.0 | 99.20 Neigh | 0.0058613 | 0.0058613 | 0.0058613 | 0.0 | 0.27 Comm | 0.0056304 | 0.0056304 | 0.0056304 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00561 | | | 0.26 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3086.00 ave 3086 max 3086 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: 29358.0 ave 29358 max 29358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29358 Ave neighs/atom = 64.665198 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 ghost atom cutoff = 6 binsize = 3, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1936.6098 0 -1936.6098 1315.6348 5283.9624 44 0 -1936.617 0 -1936.617 1275.7231 5284.0915 Loop time of 0.119589 on 1 procs for 2 steps with 454 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 = -1936.6098278466 -1936.61633604336 -1936.6170183044 Force two-norm initial, final = 9.2428969 1.6165978 Force max component initial, final = 7.8357592 1.6109456 Final line search alpha, max atom move = 0.00028751015 0.00046316320 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11836 | 0.11836 | 0.11836 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002699 | 0.0002699 | 0.0002699 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009623 | | | 0.80 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3098.00 ave 3098 max 3098 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: 29346.0 ave 29346 max 29346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29346 Ave neighs/atom = 64.638767 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 ghost atom cutoff = 6 binsize = 3, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1936.617 0 -1936.617 1275.7231 Loop time of 6.796e-06 on 1 procs for 0 steps with 454 atoms 191.3% 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 | | 6.796e-06 | | |100.00 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3094.00 ave 3094 max 3094 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: 29340.0 ave 29340 max 29340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29340 Ave neighs/atom = 64.625551 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 ghost atom cutoff = 6 binsize = 3, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.594 | 4.594 | 4.594 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 -1936.617 -1936.617 17.592639 74.569028 4.0279201 1275.7231 1275.7231 4.9529136 4310.1822 -487.96596 2.2716362 319.87031 Loop time of 7.097e-06 on 1 procs for 0 steps with 454 atoms 267.7% 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 | | 7.097e-06 | | |100.00 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3094.00 ave 3094 max 3094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14670.0 ave 14670 max 14670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29340.0 ave 29340 max 29340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29340 Ave neighs/atom = 64.625551 Neighbor list builds = 0 Dangerous builds = 0 454 -1936.6170183044 eV 2.27163620801667 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02