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 = 3.17012 3.17012 3.17012 Created orthogonal box = (0 -35.869 0) to (15.5304 35.869 5.49081) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.17679 4.48323 5.49081 Created 204 atoms create_atoms CPU = 0.000169039 secs 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.17679 4.48323 5.49081 Created 204 atoms create_atoms CPU = 5.00679e-05 secs 204 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 5 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 7.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 384 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 5 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 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) = 4.463 | 4.463 | 4.463 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4158.6349 0 -4158.6349 4379.277 7 0 -4159.8827 0 -4159.8827 3498.2019 Loop time of 0.977579 on 1 procs for 7 steps with 384 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4158.63494577 -4159.88081995 -4159.88272583 Force two-norm initial, final = 4.15034 0.0857103 Force max component initial, final = 0.528059 0.0113614 Final line search alpha, max atom move = 1 0.0113614 Iterations, force evaluations = 7 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9771 | 0.9771 | 0.9771 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029755 | 0.00029755 | 0.00029755 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001812 | | | 0.02 Nlocal: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2915 ave 2915 max 2915 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: 42272 ave 42272 max 42272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42272 Ave neighs/atom = 110.083 Neighbor list builds = 0 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 : 7 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.463 | 4.463 | 4.463 Mbytes Step Temp E_pair E_mol TotEng Press Volume 7 0 -4159.8827 0 -4159.8827 3498.2019 6117.4073 9 0 -4159.8944 0 -4159.8944 3094.9156 6118.3261 Loop time of 0.204307 on 1 procs for 2 steps with 384 atoms 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4159.88272583 -4159.89271506 -4159.89436024 Force two-norm initial, final = 14.7366 3.39652 Force max component initial, final = 13.5036 3.3504 Final line search alpha, max atom move = 0.000155314 0.000520365 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20404 | 0.20404 | 0.20404 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.4135e-05 | 6.4135e-05 | 6.4135e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002 | | | 0.10 Nlocal: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2915 ave 2915 max 2915 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: 42336 ave 42336 max 42336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42336 Ave neighs/atom = 110.25 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 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) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4159.8944 0 -4159.8944 3094.9156 Loop time of 9.53674e-07 on 1 procs for 0 steps with 384 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: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2915 ave 2915 max 2915 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: 42336 ave 42336 max 42336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42336 Ave neighs/atom = 110.25 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) = 4.601 | 4.601 | 4.601 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 -4159.8944 -4159.8944 15.547188 71.738005 5.4856926 3094.9156 3094.9156 878.30307 8262.2009 144.24291 2.6924317 167.519 Loop time of 9.53674e-07 on 1 procs for 0 steps with 384 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: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2915 ave 2915 max 2915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21168 ave 21168 max 21168 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42336 ave 42336 max 42336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42336 Ave neighs/atom = 110.25 Neighbor list builds = 0 Dangerous builds = 0 384 -2537.32307479814 eV 2.692431678755 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01