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 = 3.52 3.52 3.52 Created orthogonal box = (0 -55.4365 0) to (33.9457 55.4365 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4751 5.36449 5.74814 Created 1493 atoms create_atoms CPU = 0.000708103 secs 1493 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4751 5.36449 5.74814 Created 1493 atoms create_atoms CPU = 0.000561953 secs 1493 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 8 27 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 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 2963 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 8 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 7.443 | 7.443 | 7.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13092.873 0 -13092.873 3615.0662 23 0 -13145.648 0 -13145.648 -1250.4323 Loop time of 0.545062 on 1 procs for 23 steps with 2963 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 = -13092.872944 -13145.6354295 -13145.6479016 Force two-norm initial, final = 34.8765 0.380721 Force max component initial, final = 5.30699 0.0446515 Final line search alpha, max atom move = 1 0.0446515 Iterations, force evaluations = 23 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53918 | 0.53918 | 0.53918 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0030713 | 0.0030713 | 0.0030713 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002815 | | | 0.52 Nlocal: 2963 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11988 ave 11988 max 11988 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: 662864 ave 662864 max 662864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 662864 Ave neighs/atom = 223.714 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) = 7.443 | 7.443 | 7.443 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -13145.648 0 -13145.648 -1250.4323 32451.032 25 0 -13145.669 0 -13145.669 -1258.4096 32451.243 Loop time of 0.072475 on 1 procs for 2 steps with 2963 atoms 110.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13145.6479016 -13145.6686595 -13145.6686695 Force two-norm initial, final = 42.4955 0.404234 Force max component initial, final = 30.3708 0.0944298 Final line search alpha, max atom move = 0.00116204 0.000109731 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.070925 | 0.070925 | 0.070925 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035858 | 0.00035858 | 0.00035858 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001191 | | | 1.64 Nlocal: 2963 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11991 ave 11991 max 11991 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: 664982 ave 664982 max 664982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664982 Ave neighs/atom = 224.429 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 8 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 7.581 | 7.581 | 7.581 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13145.669 0 -13145.669 -1258.4096 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2963 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 | | 2.146e-06 | | |100.00 Nlocal: 2963 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11991 ave 11991 max 11991 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: 664984 ave 664984 max 664984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664984 Ave neighs/atom = 224.429 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) = 7.581 | 7.581 | 7.581 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 -13145.669 -13145.669 33.969225 110.87307 8.6162762 -1258.4096 -1258.4096 -4.4368187 -3766.1331 -4.6589648 2.1883527 1096.9117 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2963 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: 2963 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11991 ave 11991 max 11991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 332492 ave 332492 max 332492 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 664984 ave 664984 max 664984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664984 Ave neighs/atom = 224.429 Neighbor list builds = 0 Dangerous builds = 0 2963 -13145.6686695498 eV 2.18835266488364 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00