LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.06121 4.06121 4.06121 Created orthogonal box = (0 -42.5984 0) to (52.1672 42.5984 9.9479) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.63947 6.19554 6.63193 Created 1323 atoms create_atoms CPU = 0.00168514 secs 1323 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.63947 6.19554 6.63193 Created 1323 atoms create_atoms CPU = 0.00146294 secs 1323 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 11 18 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 42 atoms, new total = 2604 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 11 18 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 6.941 | 6.941 | 6.941 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6886.1643 0 -6886.1643 2670.9377 75 0 -6985.5677 0 -6985.5677 -5452.0417 Loop time of 2.32823 on 1 procs for 75 steps with 2604 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6886.16432875 -6985.56093812 -6985.56767315 Force two-norm initial, final = 46.7149 0.245748 Force max component initial, final = 6.90206 0.0174044 Final line search alpha, max atom move = 1 0.0174044 Iterations, force evaluations = 75 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.235 | 2.235 | 2.235 | 0.0 | 95.99 Neigh | 0.071771 | 0.071771 | 0.071771 | 0.0 | 3.08 Comm | 0.010933 | 0.010933 | 0.010933 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01057 | | | 0.45 Nlocal: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10291 ave 10291 max 10291 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: 583484 ave 583484 max 583484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583484 Ave neighs/atom = 224.072 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.943 | 6.943 | 6.943 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -6985.5677 0 -6985.5677 -5452.0417 44213.287 83 0 -6986.4796 0 -6986.4796 -1528.5257 43968.495 Loop time of 0.17915 on 1 procs for 8 steps with 2604 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6985.56767315 -6986.47933836 -6986.47964672 Force two-norm initial, final = 265.764 0.416902 Force max component initial, final = 265.636 0.101309 Final line search alpha, max atom move = 0.000203253 2.05914e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17501 | 0.17501 | 0.17501 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082064 | 0.00082064 | 0.00082064 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003319 | | | 1.85 Nlocal: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10497 ave 10497 max 10497 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: 583752 ave 583752 max 583752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583752 Ave neighs/atom = 224.175 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 11 18 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 7.081 | 7.081 | 7.081 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6986.4796 0 -6986.4796 -1528.5257 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2604 atoms 209.7% 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: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10497 ave 10497 max 10497 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: 584832 ave 584832 max 584832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 584832 Ave neighs/atom = 224.59 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) = 7.081 | 7.081 | 7.081 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 -6986.4796 -6986.4796 51.809174 85.196855 9.9611934 -1528.5257 -1528.5257 -3.6662803 -4580.8762 -1.0346278 2.6774829 2907.5515 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2604 atoms 251.7% 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: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10497 ave 10497 max 10497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 292416 ave 292416 max 292416 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 584832 ave 584832 max 584832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 584832 Ave neighs/atom = 224.59 Neighbor list builds = 0 Dangerous builds = 0 2604 -6986.47964672422 eV 2.67748291081407 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02