LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.60566 3.60566 3.60566 Created orthogonal box = (0 -41.4295 0) to (29.2925 41.4295 5.09918) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.21357 5.64899 5.09918 Created 532 atoms create_atoms CPU = 0.000292778 secs 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.21357 5.64899 5.09918 Created 532 atoms create_atoms CPU = 0.000196934 secs 532 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 = 7.67337 ghost atom cutoff = 7.67337 binsize = 3.83668, bins = 8 22 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 7.67337 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1040 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.67337 ghost atom cutoff = 7.67337 binsize = 3.83668, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.67337 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) = 5.028 | 5.028 | 5.028 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4088.3907 0 -4088.3907 185416.67 496 0 -4407.2126 0 -4407.2126 -21797.7 Loop time of 2.93801 on 1 procs for 496 steps with 1040 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4088.39065135 -4407.20822825 -4407.21255691 Force two-norm initial, final = 1117.65 0.240523 Force max component initial, final = 208.615 0.066319 Final line search alpha, max atom move = 0.801213 0.0531357 Iterations, force evaluations = 496 862 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7966 | 2.7966 | 2.7966 | 0.0 | 95.19 Neigh | 0.083549 | 0.083549 | 0.083549 | 0.0 | 2.84 Comm | 0.036014 | 0.036014 | 0.036014 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02188 | | | 0.74 Nlocal: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6503 ave 6503 max 6503 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: 166796 ave 166796 max 166796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166796 Ave neighs/atom = 160.381 Neighbor list builds = 21 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 496 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press Volume 496 0 -4407.2126 0 -4407.2126 -21797.7 12376.485 518 0 -4413.9372 0 -4413.9372 26191.631 12028.43 Loop time of 0.101787 on 1 procs for 22 steps with 1040 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4407.21255691 -4413.93710516 -4413.93715952 Force two-norm initial, final = 609.543 0.966756 Force max component initial, final = 500.877 0.426122 Final line search alpha, max atom move = 0.000814657 0.000347143 Iterations, force evaluations = 22 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09719 | 0.09719 | 0.09719 | 0.0 | 95.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00099301 | 0.00099301 | 0.00099301 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003604 | | | 3.54 Nlocal: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6506 ave 6506 max 6506 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: 166796 ave 166796 max 166796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166796 Ave neighs/atom = 160.381 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 = 7.67337 ghost atom cutoff = 7.67337 binsize = 3.83668, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.67337 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) = 5.164 | 5.164 | 5.164 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4413.9372 0 -4413.9372 26191.631 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1040 atoms 0.0% 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: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6653 ave 6653 max 6653 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: 168580 ave 168580 max 168580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168580 Ave neighs/atom = 162.096 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) = 5.164 | 5.164 | 5.164 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 -4413.9372 -4413.9372 29.07301 82.859052 4.9932001 26191.631 26191.631 -56.333679 78665.384 -34.156639 2.3534475 1211.8741 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1040 atoms 0.0% 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: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6653 ave 6653 max 6653 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84290 ave 84290 max 84290 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 168580 ave 168580 max 168580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168580 Ave neighs/atom = 162.096 Neighbor list builds = 0 Dangerous builds = 0 1040 -4413.93715951723 eV 2.35344748915229 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03