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 = 4.03299 4.03299 4.03299 Created orthogonal box = (0 -53.5077 0) to (32.7642 53.5077 9.87876) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.95712 6.07996 6.58584 Created 1080 atoms create_atoms CPU = 0.000986099 secs 1080 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.95712 6.07996 6.58584 Created 1080 atoms create_atoms CPU = 0.000724077 secs 1080 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 16 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 72 atoms, new total = 2088 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 14.39 | 14.39 | 14.39 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5999.9489 0 -5999.9489 2777.4875 56 0 -6090.2671 0 -6090.2671 -7592.675 Loop time of 6.20036 on 1 procs for 56 steps with 2088 atoms 78.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5999.94890721 -6090.26106509 -6090.26709059 Force two-norm initial, final = 46.1429 0.25623 Force max component initial, final = 5.62721 0.0120947 Final line search alpha, max atom move = 1 0.0120947 Iterations, force evaluations = 56 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0676 | 6.0676 | 6.0676 | 0.0 | 97.86 Neigh | 0.11008 | 0.11008 | 0.11008 | 0.0 | 1.78 Comm | 0.015262 | 0.015262 | 0.015262 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007406 | | | 0.12 Nlocal: 2088 ave 2088 max 2088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16164 ave 16164 max 16164 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: 1.3799e+06 ave 1.3799e+06 max 1.3799e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1379904 Ave neighs/atom = 660.874 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 14.39 | 14.39 | 14.39 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -6090.2671 0 -6090.2671 -7592.675 34637.585 63 0 -6090.9925 0 -6090.9925 -1655.0936 34355.681 Loop time of 0.540379 on 1 procs for 7 steps with 2088 atoms 78.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6090.26709059 -6090.99041328 -6090.99248413 Force two-norm initial, final = 221.951 0.633447 Force max component initial, final = 196.557 0.394411 Final line search alpha, max atom move = 0.000138347 5.45657e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53556 | 0.53556 | 0.53556 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011094 | 0.0011094 | 0.0011094 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003705 | | | 0.69 Nlocal: 2088 ave 2088 max 2088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16154 ave 16154 max 16154 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: 1.37938e+06 ave 1.37938e+06 max 1.37938e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1379376 Ave neighs/atom = 660.621 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 13.91 | 13.91 | 13.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6090.9925 0 -6090.9925 -1655.0936 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2088 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 2088 ave 2088 max 2088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16235 ave 16235 max 16235 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: 1.38566e+06 ave 1.38566e+06 max 1.38566e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1385664 Ave neighs/atom = 663.632 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) = 13.91 | 13.91 | 13.91 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 -6090.9925 -6090.9925 32.5582 107.01534 9.8603456 -1655.0936 -1655.0936 -18.277717 -4928.719 -18.284118 2.735392 550.2968 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2088 atoms 314.6% 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 | | 9.537e-07 | | |100.00 Nlocal: 2088 ave 2088 max 2088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16235 ave 16235 max 16235 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 692832 ave 692832 max 692832 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.38566e+06 ave 1.38566e+06 max 1.38566e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1385664 Ave neighs/atom = 663.632 Neighbor list builds = 0 Dangerous builds = 0 2088 -6090.99248412552 eV 2.73539199453608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07