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 = 4.05 4.05 4.05 Created orthogonal box = (0 -80.19 0) to (49.1036 80.19 9.92043) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.67865 5.72756 6.61362 Created 2357 atoms create_atoms CPU = 0.000995874 secs 2357 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.67865 5.72756 6.61362 Created 2357 atoms create_atoms CPU = 0.000839949 secs 2357 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 = 12 37 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 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 58 atoms, new total = 4656 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 = 12 37 3 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) = 12.33 | 12.33 | 12.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15594.991 0 -15594.991 -2729.001 25 0 -15614.927 0 -15614.927 -4894.2732 Loop time of 0.73137 on 1 procs for 25 steps with 4656 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15594.9906363 -15614.9172061 -15614.9266179 Force two-norm initial, final = 11.8125 0.197927 Force max component initial, final = 2.10522 0.00657872 Final line search alpha, max atom move = 1 0.00657872 Iterations, force evaluations = 25 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72304 | 0.72304 | 0.72304 | 0.0 | 98.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0039504 | 0.0039504 | 0.0039504 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004379 | | | 0.60 Nlocal: 4656 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14592 ave 14592 max 14592 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: 809472 ave 809472 max 809472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 809472 Ave neighs/atom = 173.856 Neighbor list builds = 0 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.33 | 12.33 | 12.33 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -15614.927 0 -15614.927 -4894.2732 78125.765 29 0 -15615.49 0 -15615.49 -892.89759 77727.975 Loop time of 0.139246 on 1 procs for 4 steps with 4656 atoms 100.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15614.9266179 -15615.4898744 -15615.4899667 Force two-norm initial, final = 311.182 0.242952 Force max component initial, final = 222.674 0.0325693 Final line search alpha, max atom move = 0.00060334 1.96503e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13601 | 0.13601 | 0.13601 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060081 | 0.00060081 | 0.00060081 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002637 | | | 1.89 Nlocal: 4656 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14638 ave 14638 max 14638 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: 810648 ave 810648 max 810648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 810648 Ave neighs/atom = 174.108 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 = 12 37 3 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) = 11.84 | 11.84 | 11.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15615.49 0 -15615.49 -892.89759 Loop time of 1.19209e-06 on 1 procs for 0 steps with 4656 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: 4656 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14638 ave 14638 max 14638 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: 811080 ave 811080 max 811080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 811080 Ave neighs/atom = 174.201 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) = 11.84 | 11.84 | 11.84 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 -15615.49 -15615.49 48.97297 160.37991 9.8962563 -892.89759 -892.89759 0.66955137 -2679.3658 0.0035122957 2.5056506 2323.476 Loop time of 9.53674e-07 on 1 procs for 0 steps with 4656 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: 4656 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14638 ave 14638 max 14638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 405540 ave 405540 max 405540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 811080 ave 811080 max 811080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 811080 Ave neighs/atom = 174.201 Neighbor list builds = 0 Dangerous builds = 0 4656 -15569.5398955145 eV 2.50565059098717 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01