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 -42.532331 0.0000000) to (52.091254 42.532331 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950518 5.2437120 5.7481372 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -42.532331 0.0000000) to (52.091254 42.532331 8.6222058) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950518 5.2437120 5.7481372 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.532331 0.0000000) to (52.091254 42.532331 8.6222058) create_atoms CPU = 0.002 seconds 1754 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 = 14 22 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 8 atoms, new total = 3494 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_657255834688_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 = 14 22 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) = 7.388 | 7.388 | 7.388 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14072.001 0 -14072.001 78178.17 64 0 -15485.533 0 -15485.533 1588.4134 Loop time of 3.32549 on 1 procs for 64 steps with 3494 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14072.0009199277 -15485.5184778372 -15485.5334282594 Force two-norm initial, final = 1512.6422 0.52222952 Force max component initial, final = 217.47869 0.042908516 Final line search alpha, max atom move = 1.0000000 0.042908516 Iterations, force evaluations = 64 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1991 | 3.1991 | 3.1991 | 0.0 | 96.20 Neigh | 0.075969 | 0.075969 | 0.075969 | 0.0 | 2.28 Comm | 0.025802 | 0.025802 | 0.025802 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0246 | | | 0.74 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11376.0 ave 11376 max 11376 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: 619168.0 ave 619168 max 619168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 619168 Ave neighs/atom = 177.20893 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.388 | 7.388 | 7.388 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -15485.533 0 -15485.533 1588.4134 38206.071 66 0 -15485.554 0 -15485.554 -0.22666245 38237.639 Loop time of 0.143683 on 1 procs for 2 steps with 3494 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 = -15485.5334282596 -15485.5521252941 -15485.5537279353 Force two-norm initial, final = 69.375956 0.90370114 Force max component initial, final = 55.366554 0.59213278 Final line search alpha, max atom move = 0.00010208804 6.0449676e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14075 | 0.14075 | 0.14075 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045704 | 0.00045704 | 0.00045704 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00248 | | | 1.73 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11319.0 ave 11319 max 11319 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: 619832.0 ave 619832 max 619832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 619832 Ave neighs/atom = 177.39897 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 = 14 22 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) = 7.526 | 7.526 | 7.526 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15485.554 0 -15485.554 -0.22666245 Loop time of 2.379e-06 on 1 procs for 0 steps with 3494 atoms 210.2% 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 | | 2.379e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11318.0 ave 11318 max 11318 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: 619528.0 ave 619528 max 619528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 619528 Ave neighs/atom = 177.31196 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 = 14 22 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) = 7.526 | 7.526 | 7.526 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 -15485.554 -15485.554 52.092131 85.083079 8.6273168 -0.22666245 -0.22666245 -15.785781 24.816036 -9.7102428 2.3172485 1421.981 Loop time of 2.89e-06 on 1 procs for 0 steps with 3494 atoms 311.4% 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 | | 2.89e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11318.0 ave 11318 max 11318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 309764.0 ave 309764 max 309764 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 619528.0 ave 619528 max 619528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 619528 Ave neighs/atom = 177.31196 Neighbor list builds = 0 Dangerous builds = 0 3494 -15485.5537279353 eV 2.31724848095109 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04