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 = 2.8553125 2.8553125 2.8553125 Created orthogonal box = (0.0000000 -44.965507 0.0000000) to (27.535637 44.965507 6.9940587) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4412317 4.3515006 4.6627058 Created 743 atoms using lattice units in orthogonal box = (0.0000000 -44.965507 0.0000000) to (27.535637 44.965507 6.9940587) create_atoms CPU = 0.003 seconds 743 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4412317 4.3515006 4.6627058 Created 749 atoms using lattice units in orthogonal box = (0.0000000 -44.965507 0.0000000) to (27.535637 44.965507 6.9940587) create_atoms CPU = 0.003 seconds 749 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1488 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_143977152728_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.519 | 5.519 | 5.519 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3185.6618 0 -3185.6618 349914.08 92 0 -5944.8494 0 -5944.8494 3317.6601 Loop time of 3.90899 on 1 procs for 92 steps with 1488 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3185.66179914809 -5944.84406987639 -5944.84942689551 Force two-norm initial, final = 4909.1404 0.29877227 Force max component initial, final = 861.56860 0.092549435 Final line search alpha, max atom move = 1.0000000 0.092549435 Iterations, force evaluations = 92 173 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8204 | 3.8204 | 3.8204 | 0.0 | 97.73 Neigh | 0.030304 | 0.030304 | 0.030304 | 0.0 | 0.78 Comm | 0.029444 | 0.029444 | 0.029444 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02887 | | | 0.74 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6648.00 ave 6648 max 6648 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: 204246.0 ave 204246 max 204246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204246 Ave neighs/atom = 137.26210 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.516 | 5.516 | 5.516 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -5944.8494 0 -5944.8494 3317.6601 17319.442 98 0 -5945.1631 0 -5945.1631 -51.732726 17353.573 Loop time of 0.179836 on 1 procs for 6 steps with 1488 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5944.84942689549 -5945.16294846162 -5945.16306886878 Force two-norm initial, final = 118.86502 1.1312175 Force max component initial, final = 115.71348 0.69756543 Final line search alpha, max atom move = 0.00062560392 0.00043639966 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17415 | 0.17415 | 0.17415 | 0.0 | 96.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011107 | 0.0011107 | 0.0011107 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004579 | | | 2.55 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6561.00 ave 6561 max 6561 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: 203300.0 ave 203300 max 203300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203300 Ave neighs/atom = 136.62634 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.655 | 5.655 | 5.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5945.1631 0 -5945.1631 -51.732726 Loop time of 6.285e-06 on 1 procs for 0 steps with 1488 atoms 190.9% 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 | | 6.285e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6645.00 ave 6645 max 6645 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: 203064.0 ave 203064 max 203064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203064 Ave neighs/atom = 136.46774 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.655 | 5.655 | 5.655 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 -5945.1631 -5945.1631 27.513455 90.388017 6.9780314 -51.732726 -51.732726 -54.281844 -36.660874 -64.255461 2.2330638 914.78761 Loop time of 6.916e-06 on 1 procs for 0 steps with 1488 atoms 231.3% 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 | | 6.916e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6645.00 ave 6645 max 6645 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101532.0 ave 101532 max 101532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203064.0 ave 203064 max 203064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203064 Ave neighs/atom = 136.46774 Neighbor list builds = 0 Dangerous builds = 0 1488 -5945.16306886878 eV 2.23306378128323 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05