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 = 3.615 3.615 3.615 Created orthogonal box = (0 -44.7187 0) to (21.0789 44.7187 5.11238) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.19968 6.13737 5.11238 Created 410 atoms create_atoms CPU = 0.000381947 secs 410 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.19968 6.13737 5.11238 Created 410 atoms create_atoms CPU = 0.000261068 secs 410 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 816 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.003 | 5.003 | 5.003 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2822.0117 0 -2822.0117 26386.797 42 0 -2879.7244 0 -2879.7244 5461.5986 Loop time of 0.239169 on 1 procs for 42 steps with 816 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2822.01165524 -2879.72188585 -2879.72442216 Force two-norm initial, final = 70.1193 0.143923 Force max component initial, final = 15.7335 0.0203638 Final line search alpha, max atom move = 1 0.0203638 Iterations, force evaluations = 42 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23139 | 0.23139 | 0.23139 | 0.0 | 96.75 Neigh | 0.0035219 | 0.0035219 | 0.0035219 | 0.0 | 1.47 Comm | 0.0027947 | 0.0027947 | 0.0027947 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001458 | | | 0.61 Nlocal: 816 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7005 ave 7005 max 7005 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: 167208 ave 167208 max 167208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167208 Ave neighs/atom = 204.912 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.003 | 5.003 | 5.003 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -2879.7244 0 -2879.7244 5461.5986 9638.0858 45 0 -2879.7589 0 -2879.7589 1815.7535 9663.3942 Loop time of 0.0196629 on 1 procs for 3 steps with 816 atoms 101.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2879.72442216 -2879.75887525 -2879.75893678 Force two-norm initial, final = 36.6335 0.149879 Force max component initial, final = 28.3582 0.0232675 Final line search alpha, max atom move = 0.00129622 3.01598e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.018922 | 0.018922 | 0.018922 | 0.0 | 96.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020409 | 0.00020409 | 0.00020409 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005367 | | | 2.73 Nlocal: 816 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7005 ave 7005 max 7005 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: 167252 ave 167252 max 167252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167252 Ave neighs/atom = 204.966 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.14 | 5.14 | 5.14 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2879.7589 0 -2879.7589 1815.7535 Loop time of 1.19209e-06 on 1 procs for 0 steps with 816 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: 816 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7005 ave 7005 max 7005 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: 166816 ave 166816 max 166816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166816 Ave neighs/atom = 204.431 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) = 5.14 | 5.14 | 5.14 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 -2879.7589 -2879.7589 21.111936 89.437433 5.1177883 1815.7535 1815.7535 -3.8637652 5447.2915 3.8329057 2.400996 522.51972 Loop time of 9.53674e-07 on 1 procs for 0 steps with 816 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: 816 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7005 ave 7005 max 7005 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 83408 ave 83408 max 83408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 166816 ave 166816 max 166816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166816 Ave neighs/atom = 204.431 Neighbor list builds = 0 Dangerous builds = 0 816 -2879.75893677879 eV 2.40099600737621 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00