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 = 3.86934 3.86934 3.86934 Created orthogonal box = (0 -69.6519 0) to (49.2486 69.6519 5.47207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.68808 6.4489 5.47207 Created 1300 atoms create_atoms CPU = 0.000707865 secs 1300 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.68808 6.4489 5.47207 Created 1300 atoms create_atoms CPU = 0.00058794 secs 1300 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 13 34 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 8.19533 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 2580 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 13 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 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) = 6.153 | 6.153 | 6.153 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8155.6733 0 -8155.6733 10982.76 89 0 -8253.4714 0 -8253.4714 -2803.6276 Loop time of 1.53613 on 1 procs for 89 steps with 2580 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8155.67329109 -8253.46323398 -8253.47141823 Force two-norm initial, final = 110.062 0.290722 Force max component initial, final = 27.494 0.0372293 Final line search alpha, max atom move = 1 0.0372293 Iterations, force evaluations = 89 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5013 | 1.5013 | 1.5013 | 0.0 | 97.73 Neigh | 0.011885 | 0.011885 | 0.011885 | 0.0 | 0.77 Comm | 0.013815 | 0.013815 | 0.013815 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009149 | | | 0.60 Nlocal: 2580 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12772 ave 12772 max 12772 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: 374640 ave 374640 max 374640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374640 Ave neighs/atom = 145.209 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 : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.153 | 6.153 | 6.153 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -8253.4714 0 -8253.4714 -2803.6276 37541.256 91 0 -8253.514 0 -8253.514 -628.87886 37484.407 Loop time of 0.054034 on 1 procs for 2 steps with 2580 atoms 111.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8253.47141823 -8253.51402331 -8253.51403689 Force two-norm initial, final = 79.7753 0.475899 Force max component initial, final = 56.6483 0.283207 Final line search alpha, max atom move = 0.00166257 0.00047085 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052427 | 0.052427 | 0.052427 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039935 | 0.00039935 | 0.00039935 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001208 | | | 2.23 Nlocal: 2580 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12812 ave 12812 max 12812 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: 374280 ave 374280 max 374280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374280 Ave neighs/atom = 145.07 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 13 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 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) = 6.291 | 6.291 | 6.291 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8253.514 0 -8253.514 -628.87886 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2580 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 | | 1.192e-06 | | |100.00 Nlocal: 2580 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12812 ave 12812 max 12812 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: 378352 ave 378352 max 378352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 378352 Ave neighs/atom = 146.648 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) = 6.291 | 6.291 | 6.291 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 -8253.514 -8253.514 49.212259 139.30387 5.4678194 -628.87886 -628.87886 10.506042 -1909.2382 12.095554 2.5941908 1499.5201 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2580 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: 2580 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12812 ave 12812 max 12812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 189176 ave 189176 max 189176 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 378352 ave 378352 max 378352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 378352 Ave neighs/atom = 146.648 Neighbor list builds = 0 Dangerous builds = 0 2580 -8253.51403689295 eV 2.59419083344402 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01