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 = 3.63909 3.63909 3.63909 Created orthogonal box = (0 -46.3216 0) to (32.7518 46.3216 5.14644) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.06514 6.2901 5.14644 Created 650 atoms create_atoms CPU = 0.000339985 secs 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.06514 6.2901 5.14644 Created 650 atoms create_atoms CPU = 0.000246048 secs 650 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 20 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1288 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.297 | 6.297 | 6.297 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4195.0551 0 -4195.0551 5055.9544 68 0 -4218.791 0 -4218.791 -4440.2813 Loop time of 1.17006 on 1 procs for 68 steps with 1288 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 = -4195.05511336 -4218.78753001 -4218.79104536 Force two-norm initial, final = 38.1663 0.156264 Force max component initial, final = 12.9065 0.0122246 Final line search alpha, max atom move = 1 0.0122246 Iterations, force evaluations = 68 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1477 | 1.1477 | 1.1477 | 0.0 | 98.09 Neigh | 0.010896 | 0.010896 | 0.010896 | 0.0 | 0.93 Comm | 0.0074739 | 0.0074739 | 0.0074739 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00403 | | | 0.34 Nlocal: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10407 ave 10407 max 10407 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: 409152 ave 409152 max 409152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409152 Ave neighs/atom = 317.665 Neighbor list builds = 1 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.297 | 6.297 | 6.297 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -4218.791 0 -4218.791 -4440.2813 15615.495 70 0 -4218.8195 0 -4218.8195 -1812.5531 15587.136 Loop time of 0.0298471 on 1 procs for 2 steps with 1288 atoms 100.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4218.79104536 -4218.81751965 -4218.81948941 Force two-norm initial, final = 41.4799 3.17523 Force max component initial, final = 35.9398 2.88509 Final line search alpha, max atom move = 0.000142668 0.00041161 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02914 | 0.02914 | 0.02914 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020289 | 0.00020289 | 0.00020289 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005045 | | | 1.69 Nlocal: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10407 ave 10407 max 10407 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: 409044 ave 409044 max 409044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409044 Ave neighs/atom = 317.581 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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/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) = 6.435 | 6.435 | 6.435 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4218.8195 0 -4218.8195 -1812.5531 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1288 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 | | 2.146e-06 | | |100.00 Nlocal: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10407 ave 10407 max 10407 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: 409080 ave 409080 max 409080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409080 Ave neighs/atom = 317.609 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) = 6.435 | 6.435 | 6.435 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 -4218.8195 -4218.8195 32.739981 92.643261 5.138946 -1812.5531 -1812.5531 296.44687 -5869.2133 135.10714 2.3421862 492.88034 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1288 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 | | 2.146e-06 | | |100.00 Nlocal: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10407 ave 10407 max 10407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 204540 ave 204540 max 204540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 409080 ave 409080 max 409080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409080 Ave neighs/atom = 317.609 Neighbor list builds = 0 Dangerous builds = 0 1288 -4218.81948940892 eV 2.34218622850388 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01