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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -47.906636 0.0000000) to (16.937554 47.906636 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1591104 5.4439359 5.1068646 Created 350 atoms using lattice units in orthogonal box = (0.0000000 -47.906636 0.0000000) to (16.937554 47.906636 5.1068646) create_atoms CPU = 0.001 seconds 350 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1591104 5.4439359 5.1068646 Created 358 atoms using lattice units in orthogonal box = (0.0000000 -47.906636 0.0000000) to (16.937554 47.906636 5.1068646) create_atoms CPU = 0.001 seconds 358 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 32 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 708 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_179158257180_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2825.5583 0 -2825.5583 71538.133 254 0 -3001.3075 0 -3001.3075 12922.537 Loop time of 12.805 on 1 procs for 254 steps with 708 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 = -2825.55830559506 -3001.3045120589 -3001.30747254253 Force two-norm initial, final = 187.29522 0.17193783 Force max component initial, final = 37.216008 0.062497506 Final line search alpha, max atom move = 1.0000000 0.062497506 Iterations, force evaluations = 254 487 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.726 | 12.726 | 12.726 | 0.0 | 99.38 Neigh | 0.038319 | 0.038319 | 0.038319 | 0.0 | 0.30 Comm | 0.020994 | 0.020994 | 0.020994 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0197 | | | 0.15 Nlocal: 708.000 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3769.00 ave 3769 max 3769 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: 53264.0 ave 53264 max 53264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53264 Ave neighs/atom = 75.231638 Neighbor list builds = 9 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 254 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press Volume 254 0 -3001.3075 0 -3001.3075 12922.537 8287.6366 265 0 -3001.8582 0 -3001.8582 -89.299166 8349.1946 Loop time of 0.350913 on 1 procs for 11 steps with 708 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 = -3001.30747254253 -3001.85801042436 -3001.85823081258 Force two-norm initial, final = 132.50674 0.93714678 Force max component initial, final = 113.51804 0.67053254 Final line search alpha, max atom move = 0.00087317624 0.00058549309 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34379 | 0.34379 | 0.34379 | 0.0 | 97.97 Neigh | 0.004141 | 0.004141 | 0.004141 | 0.0 | 1.18 Comm | 0.00056279 | 0.00056279 | 0.00056279 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002417 | | | 0.69 Nlocal: 708.000 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3789.00 ave 3789 max 3789 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: 53100.0 ave 53100 max 53100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53100 Ave neighs/atom = 75.000000 Neighbor list builds = 1 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.672 | 4.672 | 4.672 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3001.8582 0 -3001.8582 -89.299166 Loop time of 2.393e-06 on 1 procs for 0 steps with 708 atoms 125.4% 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 | | 2.393e-06 | | |100.00 Nlocal: 708.000 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3784.00 ave 3784 max 3784 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: 53104.0 ave 53104 max 53104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53104 Ave neighs/atom = 75.005650 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.672 | 4.672 | 4.672 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 -3001.8582 -3001.8582 16.881896 96.790206 5.1096593 -89.299166 -89.299166 -128.24965 -63.473781 -76.174069 2.3609705 1261.3214 Loop time of 2.16e-06 on 1 procs for 0 steps with 708 atoms 231.5% 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 | | 2.16e-06 | | |100.00 Nlocal: 708.000 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3784.00 ave 3784 max 3784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26552.0 ave 26552 max 26552 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53104.0 ave 53104 max 53104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53104 Ave neighs/atom = 75.005650 Neighbor list builds = 0 Dangerous builds = 0 708 -3001.85823081258 eV 2.36097045130262 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13