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 = 3.61496 3.61496 3.61496 Created orthogonal box = (0 -51.6356 0) to (36.5093 51.6356 5.11233) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.72695 4.55576 5.11233 Created 823 atoms create_atoms CPU = 0.000531912 secs 823 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.72695 4.55576 5.11233 Created 823 atoms create_atoms CPU = 0.000341177 secs 823 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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 9 25 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 8.39534 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 39 atoms, new total = 1607 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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.39534 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) = 5.95 | 5.95 | 5.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5643.5803 0 -5643.5803 -2752.732 188 0 -5673.5294 0 -5673.5294 -11578.435 Loop time of 2.74301 on 1 procs for 188 steps with 1607 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5643.58032303 -5673.52457502 -5673.52944421 Force two-norm initial, final = 31.742 0.228152 Force max component initial, final = 6.39788 0.0847079 Final line search alpha, max atom move = 1 0.0847079 Iterations, force evaluations = 188 352 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6576 | 2.6576 | 2.6576 | 0.0 | 96.89 Neigh | 0.047533 | 0.047533 | 0.047533 | 0.0 | 1.73 Comm | 0.023913 | 0.023913 | 0.023913 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01398 | | | 0.51 Nlocal: 1607 ave 1607 max 1607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10004 ave 10004 max 10004 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: 320546 ave 320546 max 320546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320546 Ave neighs/atom = 199.469 Neighbor list builds = 6 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 : 188 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.954 | 5.954 | 5.954 Mbytes Step Temp E_pair E_mol TotEng Press Volume 188 0 -5673.5294 0 -5673.5294 -11578.435 19275.299 193 0 -5674.0032 0 -5674.0032 -1608.1637 19136.59 Loop time of 0.0659111 on 1 procs for 5 steps with 1607 atoms 106.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5673.52944421 -5674.00320898 -5674.00323459 Force two-norm initial, final = 184.297 0.329922 Force max component initial, final = 134.236 0.0868521 Final line search alpha, max atom move = 0.00161687 0.000140429 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.063781 | 0.063781 | 0.063781 | 0.0 | 96.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004971 | 0.0004971 | 0.0004971 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001633 | | | 2.48 Nlocal: 1607 ave 1607 max 1607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10005 ave 10005 max 10005 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: 320366 ave 320366 max 320366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320366 Ave neighs/atom = 199.357 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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.39534 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) = 6.092 | 6.092 | 6.092 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5674.0032 0 -5674.0032 -1608.1637 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1607 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: 1607 ave 1607 max 1607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10005 ave 10005 max 10005 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: 320836 ave 320836 max 320836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320836 Ave neighs/atom = 199.649 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) = 6.092 | 6.092 | 6.092 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 -5674.0032 -5674.0032 36.384428 103.27115 5.092957 -1608.1637 -1608.1637 -5.960889 -4825.6266 7.0962586 2.3607269 945.17358 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1607 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: 1607 ave 1607 max 1607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10005 ave 10005 max 10005 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160418 ave 160418 max 160418 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320836 ave 320836 max 320836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320836 Ave neighs/atom = 199.649 Neighbor list builds = 0 Dangerous builds = 0 1607 -5674.00323459032 eV 2.36072692132908 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02