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 = 3.70048 3.70048 3.70048 Created orthogonal box = (0 -50.8768 0) to (13.8459 50.8768 9.06428) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.93396 5.65257 6.04285 Created 508 atoms create_atoms CPU = 0.000180006 secs 508 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.93396 5.65257 6.04285 Created 508 atoms create_atoms CPU = 0.000138998 secs 508 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 4 27 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1000 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 4 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3947.0745 0 -3947.0745 12157.142 149 0 -3994.7052 0 -3994.7052 -38177.172 Loop time of 1.14704 on 1 procs for 149 steps with 1000 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3947.07445905 -3994.70128296 -3994.70516984 Force two-norm initial, final = 68.2437 0.1885 Force max component initial, final = 13.1501 0.0222016 Final line search alpha, max atom move = 1 0.0222016 Iterations, force evaluations = 149 282 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1211 | 1.1211 | 1.1211 | 0.0 | 97.74 Neigh | 0.0085979 | 0.0085979 | 0.0085979 | 0.0 | 0.75 Comm | 0.010091 | 0.010091 | 0.010091 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007221 | | | 0.63 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5706 ave 5706 max 5706 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: 148976 ave 148976 max 148976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148976 Ave neighs/atom = 148.976 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 : 149 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press Volume 149 0 -3994.7052 0 -3994.7052 -38177.172 12770.407 170 0 -3999.663 0 -3999.663 -4338.6295 12415.685 Loop time of 0.100923 on 1 procs for 21 steps with 1000 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3994.70516984 -3999.66211345 -3999.66299436 Force two-norm initial, final = 445.082 3.22604 Force max component initial, final = 371.078 1.77125 Final line search alpha, max atom move = 0.000219931 0.000389553 Iterations, force evaluations = 21 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.097207 | 0.097207 | 0.097207 | 0.0 | 96.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079823 | 0.00079823 | 0.00079823 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002918 | | | 2.89 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5712 ave 5712 max 5712 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: 148952 ave 148952 max 148952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148952 Ave neighs/atom = 148.952 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 4 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.187 | 5.187 | 5.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3999.663 0 -3999.663 -4338.6295 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1000 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: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5777 ave 5777 max 5777 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: 158408 ave 158408 max 158408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158408 Ave neighs/atom = 158.408 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) = 5.187 | 5.187 | 5.187 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 -3999.663 -3999.663 13.733828 101.75366 8.8844195 -4338.6295 -4338.6295 -226.71994 -12749.469 -39.699409 2.3284945 1435.8505 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1000 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: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5777 ave 5777 max 5777 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79204 ave 79204 max 79204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158408 ave 158408 max 158408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158408 Ave neighs/atom = 158.408 Neighbor list builds = 0 Dangerous builds = 0 1000 -3999.66299435895 eV 2.32849453825596 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01