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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -42.536136 0.0000000) to (52.091603 42.536136 8.6222635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950853 5.2437472 5.7481757 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -42.536136 0.0000000) to (52.091603 42.536136 8.6222635) create_atoms CPU = 0.006 seconds 1755 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950853 5.2437472 5.7481757 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -42.536136 0.0000000) to (52.091603 42.536136 8.6222635) create_atoms CPU = 0.006 seconds 1755 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 54 atoms, new total = 3456 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 7.895 | 7.895 | 7.895 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15246.557 0 -15246.557 1295.6738 61 0 -15319.974 0 -15319.974 -15133.79 Loop time of 8.38165 on 1 procs for 61 steps with 3456 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 = -15246.5571275479 -15319.9596022023 -15319.974336799 Force two-norm initial, final = 58.635433 0.39818870 Force max component initial, final = 10.165219 0.051144279 Final line search alpha, max atom move = 1.0000000 0.051144279 Iterations, force evaluations = 61 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.118 | 8.118 | 8.118 | 0.0 | 96.85 Neigh | 0.19512 | 0.19512 | 0.19512 | 0.0 | 2.33 Comm | 0.03074 | 0.03074 | 0.03074 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03779 | | | 0.45 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12492.0 ave 12492 max 12492 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: 767606.0 ave 767606 max 767606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 767606 Ave neighs/atom = 222.10822 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 7.895 | 7.895 | 7.895 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -15319.974 0 -15319.974 -15133.79 38210.001 66 0 -15321.091 0 -15321.091 -3362.2358 37952.052 Loop time of 0.599542 on 1 procs for 5 steps with 3456 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 = -15319.9743367989 -15321.0882211263 -15321.0907135902 Force two-norm initial, final = 458.86294 0.56411801 Force max component initial, final = 347.79074 0.080772187 Final line search alpha, max atom move = 7.9040709e-05 6.3842910e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58872 | 0.58872 | 0.58872 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020448 | 0.0020448 | 0.0020448 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008782 | | | 1.46 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12516.0 ave 12516 max 12516 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: 767494.0 ave 767494 max 767494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 767494 Ave neighs/atom = 222.07581 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 8.033 | 8.033 | 8.033 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15321.091 0 -15321.091 -3362.2358 Loop time of 6.706e-06 on 1 procs for 0 steps with 3456 atoms 193.9% 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 | | 6.706e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12516.0 ave 12516 max 12516 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: 768340.0 ave 768340 max 768340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 768340 Ave neighs/atom = 222.32060 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 8.033 | 8.033 | 8.033 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 -15321.091 -15321.091 51.878269 85.072272 8.5992732 -3362.2358 -3362.2358 0.5730025 -10085.743 -1.53734 2.2153626 1569.0029 Loop time of 6.775e-06 on 1 procs for 0 steps with 3456 atoms 324.7% 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 | | 6.775e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12516.0 ave 12516 max 12516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 384170.0 ave 384170 max 384170 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 768340.0 ave 768340 max 768340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 768340 Ave neighs/atom = 222.32060 Neighbor list builds = 0 Dangerous builds = 0 3456 -15226.8753089694 eV 2.2153625973201 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10