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 = 3.99461 3.99461 3.99461 Created orthogonal box = (0 -51.78 0) to (29.8929 51.78 6.91886) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.40562 6.16381 6.91886 Created 676 atoms create_atoms CPU = 0.000334978 secs 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.40562 6.16381 6.91886 Created 676 atoms create_atoms CPU = 0.000258923 secs 676 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 8 28 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 7.6001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1328 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 8 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6001 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) = 5.087 | 5.087 | 5.087 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4332.8775 0 -4332.8775 1427.2461 45 0 -4350.3031 0 -4350.3031 -3576.3683 Loop time of 0.73474 on 1 procs for 45 steps with 1328 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4332.87754485 -4350.29957004 -4350.30312547 Force two-norm initial, final = 15.8613 0.119836 Force max component initial, final = 3.29521 0.0153136 Final line search alpha, max atom move = 1 0.0153136 Iterations, force evaluations = 45 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72012 | 0.72012 | 0.72012 | 0.0 | 98.01 Neigh | 0.0085411 | 0.0085411 | 0.0085411 | 0.0 | 1.16 Comm | 0.0035281 | 0.0035281 | 0.0035281 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002551 | | | 0.35 Nlocal: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6250 ave 6250 max 6250 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: 173176 ave 173176 max 173176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173176 Ave neighs/atom = 130.404 Neighbor list builds = 2 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 : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.087 | 5.087 | 5.087 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -4350.3031 0 -4350.3031 -3576.3683 21418.813 48 0 -4350.338 0 -4350.338 -2353.3 21352.831 Loop time of 0.0504439 on 1 procs for 3 steps with 1328 atoms 118.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4350.30312547 -4350.33750626 -4350.33801769 Force two-norm initial, final = 29.0883 0.297704 Force max component initial, final = 25.4683 0.241165 Final line search alpha, max atom move = 0.000386928 9.33132e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049588 | 0.049588 | 0.049588 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020361 | 0.00020361 | 0.00020361 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006526 | | | 1.29 Nlocal: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6250 ave 6250 max 6250 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: 173064 ave 173064 max 173064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173064 Ave neighs/atom = 130.319 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 8 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6001 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) = 5.225 | 5.225 | 5.225 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4350.338 0 -4350.338 -2353.3 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1328 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: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6250 ave 6250 max 6250 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: 173192 ave 173192 max 173192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173192 Ave neighs/atom = 130.416 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) = 5.225 | 5.225 | 5.225 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 -4350.338 -4350.338 29.824442 103.56007 6.9133856 -2353.3 -2353.3 8.9526851 -7086.9338 18.081084 2.5518735 983.60397 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1328 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: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6250 ave 6250 max 6250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86596 ave 86596 max 86596 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 173192 ave 173192 max 173192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173192 Ave neighs/atom = 130.416 Neighbor list builds = 0 Dangerous builds = 0 1328 -4350.33801769157 eV 2.55187351570201 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00