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 = 3.58787 3.58787 3.58787 Created orthogonal box = (0 -40.5957 0) to (17.5769 40.5957 6.21438) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.85897 5.07402 6.21438 Created 396 atoms create_atoms CPU = 0.000226021 secs 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.85897 5.07402 6.21438 Created 396 atoms create_atoms CPU = 9.48906e-05 secs 396 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 5 20 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 8.23106 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 766 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 5 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.23106 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) = 5.005 | 5.005 | 5.005 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2584.6641 0 -2584.6641 49662.115 117 0 -2687.0936 0 -2687.0936 3202.217 Loop time of 1.83481 on 1 procs for 117 steps with 766 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2584.66413105 -2687.09115059 -2687.09355281 Force two-norm initial, final = 101.638 0.152526 Force max component initial, final = 16.9331 0.0312516 Final line search alpha, max atom move = 1 0.0312516 Iterations, force evaluations = 117 213 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8066 | 1.8066 | 1.8066 | 0.0 | 98.46 Neigh | 0.015734 | 0.015734 | 0.015734 | 0.0 | 0.86 Comm | 0.0082254 | 0.0082254 | 0.0082254 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004219 | | | 0.23 Nlocal: 766 ave 766 max 766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5741 ave 5741 max 5741 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: 152184 ave 152184 max 152184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152184 Ave neighs/atom = 198.674 Neighbor list builds = 4 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 : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.005 | 5.005 | 5.005 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -2687.0936 0 -2687.0936 3202.217 8868.5025 121 0 -2687.1428 0 -2687.1428 691.67408 8884.0192 Loop time of 0.0758679 on 1 procs for 4 steps with 766 atoms 105.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2687.09355281 -2687.1427439 -2687.14280643 Force two-norm initial, final = 34.617 0.170985 Force max component initial, final = 34.6143 0.0393251 Final line search alpha, max atom move = 0.000800832 3.14928e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07484 | 0.07484 | 0.07484 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025296 | 0.00025296 | 0.00025296 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007753 | | | 1.02 Nlocal: 766 ave 766 max 766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5735 ave 5735 max 5735 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: 152350 ave 152350 max 152350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152350 Ave neighs/atom = 198.89 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.23106 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) = 5.142 | 5.142 | 5.142 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2687.1428 0 -2687.1428 691.67408 Loop time of 9.53674e-07 on 1 procs for 0 steps with 766 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: 766 ave 766 max 766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5739 ave 5739 max 5739 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: 152298 ave 152298 max 152298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152298 Ave neighs/atom = 198.822 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) = 5.142 | 5.142 | 5.142 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 -2687.1428 -2687.1428 17.55762 81.191443 6.2320883 691.67408 691.67408 2.4122132 2071.1521 1.457892 2.3166988 448.90684 Loop time of 1.90735e-06 on 1 procs for 0 steps with 766 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: 766 ave 766 max 766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5739 ave 5739 max 5739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76149 ave 76149 max 76149 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 152298 ave 152298 max 152298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152298 Ave neighs/atom = 198.822 Neighbor list builds = 0 Dangerous builds = 0 766 -2687.14280642682 eV 2.31669884631466 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01