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 -40.7505 0) to (28.8124 40.7505 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.59047 6.08163 4.97803 Created 538 atoms create_atoms CPU = 0.000462055 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.59047 6.08163 4.97803 Created 538 atoms create_atoms CPU = 0.000354052 secs 538 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 7 19 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 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1066 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 5.445 | 5.445 | 5.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4705.3083 0 -4705.3083 6007.3134 61 0 -4732.0924 0 -4732.0924 -5504.8161 Loop time of 0.723643 on 1 procs for 61 steps with 1066 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4705.30830037 -4732.08779635 -4732.09237861 Force two-norm initial, final = 24.5026 0.223245 Force max component initial, final = 5.90871 0.0218487 Final line search alpha, max atom move = 1 0.0218487 Iterations, force evaluations = 61 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70264 | 0.70264 | 0.70264 | 0.0 | 97.10 Neigh | 0.012497 | 0.012497 | 0.012497 | 0.0 | 1.73 Comm | 0.0054641 | 0.0054641 | 0.0054641 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003043 | | | 0.42 Nlocal: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 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: 263372 ave 263372 max 263372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263372 Ave neighs/atom = 247.066 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.445 | 5.445 | 5.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -4732.0924 0 -4732.0924 -5504.8161 11689.618 65 0 -4732.2082 0 -4732.2082 -366.50905 11655.722 Loop time of 0.0470369 on 1 procs for 4 steps with 1066 atoms 85.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4732.09237861 -4732.20595216 -4732.20823941 Force two-norm initial, final = 75.8889 4.09775 Force max component initial, final = 71.855 3.95615 Final line search alpha, max atom move = 0.000110902 0.000438747 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.045811 | 0.045811 | 0.045811 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028348 | 0.00028348 | 0.00028348 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009427 | | | 2.00 Nlocal: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8213 ave 8213 max 8213 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: 263500 ave 263500 max 263500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263500 Ave neighs/atom = 247.186 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 5.583 | 5.583 | 5.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4732.2082 0 -4732.2082 -366.50905 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1066 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: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8249 ave 8249 max 8249 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: 263808 ave 263808 max 263808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263808 Ave neighs/atom = 247.475 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) = 5.583 | 5.583 | 5.583 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 -4732.2082 -4732.2082 28.72249 81.500932 4.9791419 -366.50905 -366.50905 -542.10834 -414.54757 -142.87124 2.301575 511.21713 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1066 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: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8249 ave 8249 max 8249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131904 ave 131904 max 131904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 263808 ave 263808 max 263808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263808 Ave neighs/atom = 247.475 Neighbor list builds = 0 Dangerous builds = 0 1066 -4708.17031234501 eV 2.30157503163863 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00