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 = 3.52 3.52 3.52 Created orthogonal box = (0 -52.0948 0) to (42.5323 52.0948 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.24371 4.99505 5.74814 Created 1756 atoms create_atoms CPU = 0.000699043 secs 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.24371 4.99505 5.74814 Created 1756 atoms create_atoms CPU = 0.000576973 secs 1756 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 11 26 3 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 3472 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 11.77 | 11.77 | 11.77 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15352.632 0 -15352.632 68.195492 46 0 -15388.306 0 -15388.306 -6625.5967 Loop time of 1.30212 on 1 procs for 46 steps with 3472 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15352.6315404 -15388.2920364 -15388.3061282 Force two-norm initial, final = 25.9665 0.388314 Force max component initial, final = 3.25586 0.0508007 Final line search alpha, max atom move = 0.938838 0.0476937 Iterations, force evaluations = 46 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.255 | 1.255 | 1.255 | 0.0 | 96.38 Neigh | 0.033946 | 0.033946 | 0.033946 | 0.0 | 2.61 Comm | 0.0067527 | 0.0067527 | 0.0067527 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006444 | | | 0.49 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12804 ave 12804 max 12804 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: 764920 ave 764920 max 764920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 764920 Ave neighs/atom = 220.311 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.77 | 11.77 | 11.77 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -15388.306 0 -15388.306 -6625.5967 38208.63 49 0 -15388.547 0 -15388.547 -1095.3047 38089.124 Loop time of 0.0895441 on 1 procs for 3 steps with 3472 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 = -15388.3061282 -15388.5463501 -15388.5467697 Force two-norm initial, final = 216.918 0.441584 Force max component initial, final = 153.703 0.103513 Final line search alpha, max atom move = 0.000227932 2.35938e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087605 | 0.087605 | 0.087605 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042129 | 0.00042129 | 0.00042129 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001518 | | | 1.69 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12810 ave 12810 max 12810 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: 766070 ave 766070 max 766070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 766070 Ave neighs/atom = 220.642 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 11.28 | 11.28 | 11.28 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15388.547 0 -15388.547 -1095.3047 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3472 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 | | 1.907e-06 | | |100.00 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12827 ave 12827 max 12827 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: 767174 ave 767174 max 767174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 767174 Ave neighs/atom = 220.96 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) = 11.28 | 11.28 | 11.28 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 -15388.547 -15388.547 42.460113 104.18953 8.6098538 -1095.3047 -1095.3047 -2.5912343 -3278.9751 -4.3479039 2.2117327 1671.5972 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3472 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12827 ave 12827 max 12827 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 383587 ave 383587 max 383587 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 767174 ave 767174 max 767174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 767174 Ave neighs/atom = 220.96 Neighbor list builds = 0 Dangerous builds = 0 3472 -15310.2655415923 eV 2.21173273332919 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01