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 = 4.03208 4.03208 4.03208 Created orthogonal box = (0 -42.2929 0) to (51.793 42.2929 9.87654) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.59184 6.1511 6.58436 Created 1326 atoms create_atoms CPU = 0.000623941 secs 1326 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.59184 6.1511 6.58436 Created 1326 atoms create_atoms CPU = 0.000507116 secs 1326 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 14 23 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 2604 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 5.994 | 5.994 | 5.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8675.1253 0 -8675.1253 1218.7816 46 0 -8719.64 0 -8719.64 -5501.8395 Loop time of 0.579116 on 1 procs for 46 steps with 2604 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 = -8675.12532652 -8719.63158879 -8719.63998136 Force two-norm initial, final = 37.731 0.226303 Force max component initial, final = 6.15995 0.0306582 Final line search alpha, max atom move = 1 0.0306582 Iterations, force evaluations = 46 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55999 | 0.55999 | 0.55999 | 0.0 | 96.70 Neigh | 0.0097332 | 0.0097332 | 0.0097332 | 0.0 | 1.68 Comm | 0.0043256 | 0.0043256 | 0.0043256 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005072 | | | 0.88 Nlocal: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7599 ave 7599 max 7599 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: 289824 ave 289824 max 289824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289824 Ave neighs/atom = 111.3 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.994 | 5.994 | 5.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -8719.64 0 -8719.64 -5501.8395 43268.671 50 0 -8719.9801 0 -8719.9801 -1279.9631 43040.715 Loop time of 0.0430391 on 1 procs for 4 steps with 2604 atoms 116.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8719.63998136 -8719.97638967 -8719.98009599 Force two-norm initial, final = 179.864 5.91773 Force max component initial, final = 143.185 5.46101 Final line search alpha, max atom move = 8.2511e-05 0.000450593 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041514 | 0.041514 | 0.041514 | 0.0 | 96.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028014 | 0.00028014 | 0.00028014 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001245 | | | 2.89 Nlocal: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7595 ave 7595 max 7595 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: 292572 ave 292572 max 292572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292572 Ave neighs/atom = 112.355 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 6.132 | 6.132 | 6.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8719.9801 0 -8719.9801 -1279.9631 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2604 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: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7595 ave 7595 max 7595 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: 309120 ave 309120 max 309120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309120 Ave neighs/atom = 118.71 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) = 6.132 | 6.132 | 6.132 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 -8719.9801 -8719.9801 51.702058 84.585739 9.8417992 -1279.9631 -1279.9631 202.92732 -4126.7905 83.973702 2.5973578 2345.402 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2604 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: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7595 ave 7595 max 7595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 154560 ave 154560 max 154560 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 309120 ave 309120 max 309120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309120 Ave neighs/atom = 118.71 Neighbor list builds = 0 Dangerous builds = 0 2604 -8719.98009599083 eV 2.59735780054413 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00