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 = 3.63552 3.63552 3.63552 Created orthogonal box = (0 -54.8988 0) to (38.8167 54.8988 5.1414) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.12896 6.25998 5.1414 Created 916 atoms create_atoms CPU = 0.000492096 secs 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.12896 6.25998 5.1414 Created 916 atoms create_atoms CPU = 0.000363111 secs 916 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 38 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1816 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.155 | 5.155 | 5.155 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7385.9568 0 -7385.9568 9412.0805 31 0 -7433.976 0 -7433.976 -1674.5113 Loop time of 8.07987 on 1 procs for 31 steps with 1816 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7385.95678183 -7433.96896986 -7433.97602909 Force two-norm initial, final = 60.7287 0.249493 Force max component initial, final = 15.438 0.026142 Final line search alpha, max atom move = 1 0.026142 Iterations, force evaluations = 31 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.0729 | 8.0729 | 8.0729 | 0.0 | 99.91 Neigh | 0.0032408 | 0.0032408 | 0.0032408 | 0.0 | 0.04 Comm | 0.0020356 | 0.0020356 | 0.0020356 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001658 | | | 0.02 Nlocal: 1816 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7340 ave 7340 max 7340 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: 139664 ave 139664 max 139664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139664 Ave neighs/atom = 76.9075 Neighbor list builds = 1 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 : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.155 | 5.155 | 5.155 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -7433.976 0 -7433.976 -1674.5113 21912.596 33 0 -7433.9848 0 -7433.9848 -538.2873 21895.031 Loop time of 0.852632 on 1 procs for 2 steps with 1816 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7433.97602909 -7433.98437405 -7433.98476245 Force two-norm initial, final = 27.2848 0.25542 Force max component initial, final = 23.5466 0.0518175 Final line search alpha, max atom move = 0.000328518 1.7023e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85189 | 0.85189 | 0.85189 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017858 | 0.00017858 | 0.00017858 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000566 | | | 0.07 Nlocal: 1816 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7354 ave 7354 max 7354 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: 139728 ave 139728 max 139728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139728 Ave neighs/atom = 76.9427 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.293 | 5.293 | 5.293 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7433.9848 0 -7433.9848 -538.2873 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1816 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: 1816 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7354 ave 7354 max 7354 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: 139744 ave 139744 max 139744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139744 Ave neighs/atom = 76.9515 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) = 5.293 | 5.293 | 5.293 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 -7433.9848 -7433.9848 38.791397 109.79762 5.1406404 -538.2873 -538.2873 -1.0907759 -1609.9799 -3.791203 2.3945073 664.5905 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1816 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: 1816 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7354 ave 7354 max 7354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69872 ave 69872 max 69872 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139744 ave 139744 max 139744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139744 Ave neighs/atom = 76.9515 Neighbor list builds = 0 Dangerous builds = 0 1816 -6387.18539487759 eV 2.39450725541892 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09