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 = 2.8659480 2.8659480 2.8659480 Created orthogonal box = (0.0000000 -43.652820 0.0000000) to (21.826410 43.652820 2.8659480) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7631741 3.7631741 2.8659480 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -43.652820 0.0000000) to (21.826410 43.652820 2.8659480) create_atoms CPU = 0.002 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7631741 3.7631741 2.8659480 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.652820 0.0000000) to (21.826410 43.652820 2.8659480) create_atoms CPU = 0.001 seconds 233 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 24 1 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 464 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_650279905230_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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1841.7985 0 -1841.7985 92968.585 70 0 -1979.8737 0 -1979.8737 10830.496 Loop time of 1.21681 on 1 procs for 70 steps with 464 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 = -1841.79852147771 -1979.87211180939 -1979.87370380817 Force two-norm initial, final = 292.89429 0.12751882 Force max component initial, final = 92.388646 0.038044383 Final line search alpha, max atom move = 1.0000000 0.038044383 Iterations, force evaluations = 70 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1776 | 1.1776 | 1.1776 | 0.0 | 96.77 Neigh | 0.0098943 | 0.0098943 | 0.0098943 | 0.0 | 0.81 Comm | 0.017891 | 0.017891 | 0.017891 | 0.0 | 1.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01146 | | | 0.94 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5472.00 ave 5472 max 5472 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: 76516.0 ave 76516 max 76516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76516 Ave neighs/atom = 164.90517 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -1979.8737 0 -1979.8737 10830.496 5461.2608 80 0 -1980.17 0 -1980.17 102.15048 5496.928 Loop time of 0.107775 on 1 procs for 10 steps with 464 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 = -1979.87370380818 -1980.16887358324 -1980.16995218796 Force two-norm initial, final = 75.644728 0.69131196 Force max component initial, final = 69.913377 0.44740580 Final line search alpha, max atom move = 0.00045723388 0.00020456909 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10181 | 0.10181 | 0.10181 | 0.0 | 94.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014701 | 0.0014701 | 0.0014701 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004496 | | | 4.17 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 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: 76644.0 ave 76644 max 76644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76644 Ave neighs/atom = 165.18103 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.630 | 4.630 | 4.630 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1980.17 0 -1980.17 102.15048 Loop time of 6.515e-06 on 1 procs for 0 steps with 464 atoms 0.0% 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 | | 6.515e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 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: 76452.0 ave 76452 max 76452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76452 Ave neighs/atom = 164.76724 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.630 | 4.630 | 4.630 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 -1980.17 -1980.17 21.834056 88.114942 2.8571699 102.15048 102.15048 71.830936 131.61312 103.0074 2.3476814 236.4054 Loop time of 7.026e-06 on 1 procs for 0 steps with 464 atoms 227.7% 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 | | 7.026e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38226.0 ave 38226 max 38226 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76452.0 ave 76452 max 76452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76452 Ave neighs/atom = 164.76724 Neighbor list builds = 0 Dangerous builds = 0 464 -1980.16984156174 eV 2.34768143394885 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01