LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.0398 4.0398 4.0398 Created orthogonal box = (0 -48.984 0) to (39.992 48.984 9.89544) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.71314 5.66435 6.59696 Created 1184 atoms create_atoms CPU = 0.000968933 secs 1184 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.71314 5.66435 6.59696 Created 1184 atoms create_atoms CPU = 0.000854015 secs 1184 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 7 17 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 2328 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 7 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 8.914 | 8.914 | 8.914 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6593.9624 0 -6593.9624 3394.7725 55 0 -6672.4091 0 -6672.4091 -3907.3127 Loop time of 2.75984 on 1 procs for 55 steps with 2328 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 = -6593.96237628 -6672.40289799 -6672.40910535 Force two-norm initial, final = 49.2286 0.253934 Force max component initial, final = 6.63047 0.0363566 Final line search alpha, max atom move = 1 0.0363566 Iterations, force evaluations = 55 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7163 | 2.7163 | 2.7163 | 0.0 | 98.42 Neigh | 0.02459 | 0.02459 | 0.02459 | 0.0 | 0.89 Comm | 0.011843 | 0.011843 | 0.011843 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007066 | | | 0.26 Nlocal: 2328 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13337 ave 13337 max 13337 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 921328 ave 921328 max 921328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 921328 Ave neighs/atom = 395.759 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.914 | 8.914 | 8.914 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -6672.4091 0 -6672.4091 -3907.3127 38769.682 58 0 -6672.5492 0 -6672.5492 -1194.9123 38628.704 Loop time of 0.108336 on 1 procs for 3 steps with 2328 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 = -6672.40910535 -6672.54798273 -6672.54919978 Force two-norm initial, final = 107.263 0.528966 Force max component initial, final = 81.535 0.368028 Final line search alpha, max atom move = 0.000161148 5.93071e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10664 | 0.10664 | 0.10664 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045705 | 0.00045705 | 0.00045705 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001235 | | | 1.14 Nlocal: 2328 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13359 ave 13359 max 13359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 913728 ave 913728 max 913728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 913728 Ave neighs/atom = 392.495 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 7 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.67 | 8.67 | 8.67 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6672.5492 0 -6672.5492 -1194.9123 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2328 atoms 251.7% 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 | | 1.192e-06 | | |100.00 Nlocal: 2328 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13366 ave 13366 max 13366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 940752 ave 940752 max 940752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 940752 Ave neighs/atom = 404.103 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.67 | 8.67 | 8.67 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 -6672.5492 -6672.5492 39.901189 97.967986 9.8818925 -1194.9123 -1194.9123 9.9337274 -3609.9143 15.243549 2.5111955 1782.3489 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2328 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 2328 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13366 ave 13366 max 13366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 470376 ave 470376 max 470376 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 940752 ave 940752 max 940752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 940752 Ave neighs/atom = 404.103 Neighbor list builds = 0 Dangerous builds = 0 2328 -6672.54919977971 eV 2.51119550943759 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03