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 = 4.08165 4.08165 4.08165 Created orthogonal box = (0 -52.2748 0) to (36.961 52.2748 5.77233) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.31041 7.01192 5.77233 Created 660 atoms create_atoms CPU = 0.000340223 secs 660 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.31041 7.01192 5.77233 Created 660 atoms create_atoms CPU = 0.000277996 secs 660 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 7 18 1 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 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1304 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 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) = 6.731 | 6.731 | 6.731 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4646.3145 0 -4646.3145 1697.9091 40 0 -4660.9217 0 -4660.9217 -2052.6779 Loop time of 0.888418 on 1 procs for 40 steps with 1304 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4646.31451806 -4660.91881012 -4660.92165581 Force two-norm initial, final = 15.0646 0.110811 Force max component initial, final = 4.23484 0.0130008 Final line search alpha, max atom move = 1 0.0130008 Iterations, force evaluations = 40 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86108 | 0.86108 | 0.86108 | 0.0 | 96.92 Neigh | 0.020683 | 0.020683 | 0.020683 | 0.0 | 2.33 Comm | 0.0045197 | 0.0045197 | 0.0045197 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002134 | | | 0.24 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11926 ave 11926 max 11926 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: 556192 ave 556192 max 556192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556192 Ave neighs/atom = 426.528 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.731 | 6.731 | 6.731 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -4660.9217 0 -4660.9217 -2052.6779 22305.739 42 0 -4660.9565 0 -4660.9565 -2.4126221 22256.996 Loop time of 0.0616469 on 1 procs for 2 steps with 1304 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4660.92165581 -4660.95604898 -4660.95645569 Force two-norm initial, final = 45.1597 1.13764 Force max component initial, final = 32.6612 0.999565 Final line search alpha, max atom move = 0.000238761 0.000238657 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060646 | 0.060646 | 0.060646 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026035 | 0.00026035 | 0.00026035 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007405 | | | 1.20 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11926 ave 11926 max 11926 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: 556240 ave 556240 max 556240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556240 Ave neighs/atom = 426.564 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 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) = 6.868 | 6.868 | 6.868 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4660.9565 0 -4660.9565 -2.4126221 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11926 ave 11926 max 11926 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: 556400 ave 556400 max 556400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556400 Ave neighs/atom = 426.687 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) = 6.868 | 6.868 | 6.868 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 -4660.9565 -4660.9565 36.91835 104.54954 5.7663654 -2.4126221 -2.4126221 -38.153024 -40.964477 71.879635 2.5986853 790.79426 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11926 ave 11926 max 11926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 278200 ave 278200 max 278200 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 556400 ave 556400 max 556400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556400 Ave neighs/atom = 426.687 Neighbor list builds = 0 Dangerous builds = 0 1304 -4660.95645568754 eV 2.59868534386834 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01