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 = 4.03207 4.03207 4.03207 Created orthogonal box = (0 -59.6733 0) to (48.7197 59.6733 9.87652) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.00654 5.72171 6.58435 Created 1756 atoms create_atoms CPU = 0.000443935 secs 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.00654 5.72171 6.58435 Created 1756 atoms create_atoms CPU = 0.000370026 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 13 32 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 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 44 atoms, new total = 3468 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 13 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 6.555 | 6.555 | 6.555 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11577.177 0 -11577.177 1247.8367 56 0 -11623.265 0 -11623.265 -4456.1207 Loop time of 0.813063 on 1 procs for 56 steps with 3468 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 = -11577.1768484 -11623.2545049 -11623.2650074 Force two-norm initial, final = 37.8522 0.286972 Force max component initial, final = 6.13684 0.0767392 Final line search alpha, max atom move = 1 0.0767392 Iterations, force evaluations = 56 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78532 | 0.78532 | 0.78532 | 0.0 | 96.59 Neigh | 0.013955 | 0.013955 | 0.013955 | 0.0 | 1.72 Comm | 0.0064108 | 0.0064108 | 0.0064108 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007374 | | | 0.91 Nlocal: 3468 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9823 ave 9823 max 9823 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: 454486 ave 454486 max 454486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 454486 Ave neighs/atom = 131.051 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.555 | 6.555 | 6.555 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -11623.265 0 -11623.265 -4456.1207 57427.344 60 0 -11623.636 0 -11623.636 -647.91482 57154.746 Loop time of 0.0612581 on 1 procs for 4 steps with 3468 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 = -11623.2650074 -11623.6360534 -11623.636126 Force two-norm initial, final = 219.49 0.316989 Force max component initial, final = 161.812 0.0827511 Final line search alpha, max atom move = 0.000749159 6.19937e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.058906 | 0.058906 | 0.058906 | 0.0 | 96.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042295 | 0.00042295 | 0.00042295 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001929 | | | 3.15 Nlocal: 3468 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9796 ave 9796 max 9796 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: 455504 ave 455504 max 455504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 455504 Ave neighs/atom = 131.345 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 13 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 6.692 | 6.692 | 6.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11623.636 0 -11623.636 -647.91482 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3468 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: 3468 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9800 ave 9800 max 9800 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: 455796 ave 455796 max 455796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 455796 Ave neighs/atom = 131.429 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) = 6.692 | 6.692 | 6.692 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 -11623.636 -11623.636 48.613217 119.34654 9.8511768 -647.91482 -647.91482 -2.3146277 -1941.0889 -0.34089293 2.5840536 2263.8503 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3468 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: 3468 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9800 ave 9800 max 9800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 227898 ave 227898 max 227898 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 455796 ave 455796 max 455796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 455796 Ave neighs/atom = 131.429 Neighbor list builds = 0 Dangerous builds = 0 3468 -11623.6361260427 eV 2.58405361745405 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01