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 = 3.63366 3.63366 3.63366 Created orthogonal box = (0 -58.5947 0) to (29.2955 58.5947 3.63366) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0563 4.0563 3.63366 Created 522 atoms create_atoms CPU = 0.00019002 secs 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0563 4.0563 3.63366 Created 522 atoms create_atoms CPU = 8.39233e-05 secs 522 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 42 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1036 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.596 | 4.596 | 4.596 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4207.4208 0 -4207.4208 11092.289 23 0 -4239.3644 0 -4239.3644 54.759558 Loop time of 10.1903 on 1 procs for 23 steps with 1036 atoms 48.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4207.4207906 -4239.36068392 -4239.36442651 Force two-norm initial, final = 31.428 0.173224 Force max component initial, final = 7.29273 0.0329688 Final line search alpha, max atom move = 1 0.0329688 Iterations, force evaluations = 23 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.188 | 10.188 | 10.188 | 0.0 | 99.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012069 | 0.0012069 | 0.0012069 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009577 | | | 0.01 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5296 ave 5296 max 5296 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: 56152 ave 56152 max 56152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56152 Ave neighs/atom = 54.2008 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 : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.596 | 4.596 | 4.596 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -4239.3644 0 -4239.3644 54.759558 12474.809 26 0 -4239.3844 0 -4239.3844 -803.25897 12482.496 Loop time of 1.47723 on 1 procs for 3 steps with 1036 atoms 51.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4239.36442651 -4239.38215445 -4239.38442868 Force two-norm initial, final = 16.9748 3.86351 Force max component initial, final = 16.8584 3.15746 Final line search alpha, max atom move = 0.000281758 0.000889638 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4766 | 1.4766 | 1.4766 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015497 | 0.00015497 | 0.00015497 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005209 | | | 0.04 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5292 ave 5292 max 5292 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: 57896 ave 57896 max 57896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57896 Ave neighs/atom = 55.8842 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.734 | 4.734 | 4.734 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4239.3844 0 -4239.3844 -803.25897 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1036 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: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5304 ave 5304 max 5304 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: 57920 ave 57920 max 57920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57920 Ave neighs/atom = 55.9073 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) = 4.734 | 4.734 | 4.734 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 -4239.3844 -4239.3844 29.244489 117.18935 3.6422458 -803.25897 -803.25897 284.04209 -3100.0482 406.22926 2.3755467 208.54007 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1036 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: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5304 ave 5304 max 5304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28960 ave 28960 max 28960 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57920 ave 57920 max 57920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57920 Ave neighs/atom = 55.9073 Neighbor list builds = 0 Dangerous builds = 0 1036 -2648.88094834231 eV 2.37554669332851 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13