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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -42.682773 0.0000000) to (52.275507 42.682773 8.8361734) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9743437 5.4877851 5.8907823 Created 1661 atoms using lattice units in orthogonal box = (0.0000000 -42.682773 0.0000000) to (52.275507 42.682773 8.8361734) create_atoms CPU = 0.003 seconds 1661 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9743437 5.4877851 5.8907823 Created 1685 atoms using lattice units in orthogonal box = (0.0000000 -42.682773 0.0000000) to (52.275507 42.682773 8.8361734) create_atoms CPU = 0.002 seconds 1685 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 9 15 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 29 atoms, new total = 3317 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_151002396060_004#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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 9 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 16.92 | 16.92 | 16.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11463.083 0 -11463.083 5516.5942 122 0 -11656.037 0 -11656.037 -12309.834 Loop time of 19.9182 on 1 procs for 122 steps with 3317 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 = -11463.0826664217 -11656.0282667753 -11656.0372735464 Force two-norm initial, final = 95.231967 0.37613764 Force max component initial, final = 9.3150837 0.062468614 Final line search alpha, max atom move = 0.48417575 0.030245788 Iterations, force evaluations = 122 220 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.135 | 19.135 | 19.135 | 0.0 | 96.07 Neigh | 0.66485 | 0.66485 | 0.66485 | 0.0 | 3.34 Comm | 0.069758 | 0.069758 | 0.069758 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04856 | | | 0.24 Nlocal: 3317.00 ave 3317 max 3317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20100.0 ave 20100 max 20100 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: 2.07733e+06 ave 2.07733e+06 max 2.07733e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2077332 Ave neighs/atom = 626.26831 Neighbor list builds = 6 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 9 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 17.30 | 17.30 | 17.30 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -11656.037 0 -11656.037 -12309.834 39431.664 128 0 -11657.755 0 -11657.755 -28.978867 39074.497 Loop time of 0.791976 on 1 procs for 6 steps with 3317 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 = -11656.0372735464 -11657.7511458873 -11657.7548374869 Force two-norm initial, final = 553.63578 4.2437610 Force max component initial, final = 389.67946 3.2723977 Final line search alpha, max atom move = 4.1222213e-05 0.00013489547 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7823 | 0.7823 | 0.7823 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016713 | 0.0016713 | 0.0016713 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008008 | | | 1.01 Nlocal: 3317.00 ave 3317 max 3317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20112.0 ave 20112 max 20112 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: 2.07667e+06 ave 2.07667e+06 max 2.07667e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2076666 Ave neighs/atom = 626.06753 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 9 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 16.82 | 16.82 | 16.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11657.755 0 -11657.755 -28.978867 Loop time of 2.138e-06 on 1 procs for 0 steps with 3317 atoms 187.1% 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 | | 2.138e-06 | | |100.00 Nlocal: 3317.00 ave 3317 max 3317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20209.0 ave 20209 max 20209 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: 2.08746e+06 ave 2.08746e+06 max 2.08746e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2087462 Ave neighs/atom = 629.32228 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 9 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 16.82 | 16.82 | 16.82 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 -11657.755 -11657.755 52.036111 84.978713 8.836462 -28.978867 -28.978867 96.484845 -133.5705 -49.850941 2.2133784 2429.5488 Loop time of 2.595e-06 on 1 procs for 0 steps with 3317 atoms 346.8% 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 | | 2.595e-06 | | |100.00 Nlocal: 3317.00 ave 3317 max 3317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20209.0 ave 20209 max 20209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.04373e+06 ave 1.04373e+06 max 1.04373e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.08746e+06 ave 2.08746e+06 max 2.08746e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2087462 Ave neighs/atom = 629.32228 Neighbor list builds = 0 Dangerous builds = 0 3317 -11657.7548374868 eV 2.21337835756168 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22