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 = 4.04093 4.04093 4.04093 Created orthogonal box = (0 -46.7811 0) to (33.0764 46.7811 5.71473) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.41781 6.98166 5.71473 Created 538 atoms create_atoms CPU = 0.000446081 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.41781 6.98166 5.71473 Created 538 atoms create_atoms CPU = 0.000358105 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 = 10 ghost atom cutoff = 10 binsize = 5, 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 10 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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 -4133.2392 0 -4133.2392 5204.3416 48 0 -4155.9707 0 -4155.9707 -1429.9763 Loop time of 0.616408 on 1 procs for 48 steps with 1066 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4133.23915449 -4155.96721334 -4155.97073328 Force two-norm initial, final = 26.782 0.146923 Force max component initial, final = 8.23753 0.0338448 Final line search alpha, max atom move = 1 0.0338448 Iterations, force evaluations = 48 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59493 | 0.59493 | 0.59493 | 0.0 | 96.52 Neigh | 0.014613 | 0.014613 | 0.014613 | 0.0 | 2.37 Comm | 0.0044215 | 0.0044215 | 0.0044215 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002447 | | | 0.40 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: 262860 ave 262860 max 262860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262860 Ave neighs/atom = 246.585 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 : 48 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 48 0 -4155.9707 0 -4155.9707 -1429.9763 17685.411 50 0 -4155.9876 0 -4155.9876 19.310199 17653.843 Loop time of 0.032774 on 1 procs for 2 steps with 1066 atoms 91.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4155.97073328 -4155.98753575 -4155.9876433 Force two-norm initial, final = 26.4405 0.149392 Force max component initial, final = 19.8892 0.0344925 Final line search alpha, max atom move = 0.00108446 3.74059e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.031836 | 0.031836 | 0.031836 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021744 | 0.00021744 | 0.00021744 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007203 | | | 2.20 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: 263060 ave 263060 max 263060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263060 Ave neighs/atom = 246.773 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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 -4155.9876 0 -4155.9876 19.310199 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: 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: 263236 ave 263236 max 263236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263236 Ave neighs/atom = 246.938 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 -4155.9876 -4155.9876 33.04103 93.562293 5.7106404 19.310199 19.310199 0.8966577 58.579296 -1.5453575 2.641941 593.36785 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: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131618 ave 131618 max 131618 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 263236 ave 263236 max 263236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263236 Ave neighs/atom = 246.938 Neighbor list builds = 0 Dangerous builds = 0 1066 -4155.98764329881 eV 2.64194104797909 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00