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 -42.5358 0) to (52.0912 42.5358 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.99505 5.24371 5.74814 Created 1756 atoms create_atoms CPU = 0.00068903 secs 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.99505 5.24371 5.74814 Created 1756 atoms create_atoms CPU = 0.000566006 secs 1756 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 = 13 21 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 56 atoms, new total = 3456 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 = 13 21 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) = 7.908 | 7.908 | 7.908 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15261.934 0 -15261.934 -1512.4342 60 0 -15322.985 0 -15322.985 -15136.21 Loop time of 1.8459 on 1 procs for 60 steps with 3456 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15261.9338464 -15322.9703087 -15322.9850191 Force two-norm initial, final = 27.156 0.403873 Force max component initial, final = 3.49287 0.0619204 Final line search alpha, max atom move = 1 0.0619204 Iterations, force evaluations = 60 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7847 | 1.7847 | 1.7847 | 0.0 | 96.68 Neigh | 0.043411 | 0.043411 | 0.043411 | 0.0 | 2.35 Comm | 0.0091474 | 0.0091474 | 0.0091474 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008658 | | | 0.47 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12605 ave 12605 max 12605 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: 773410 ave 773410 max 773410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 773410 Ave neighs/atom = 223.788 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.909 | 7.909 | 7.909 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -15322.985 0 -15322.985 -15136.21 38209.209 65 0 -15324.102 0 -15324.102 -3360.7648 37951.326 Loop time of 0.107634 on 1 procs for 5 steps with 3456 atoms 102.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15322.9850191 -15324.0991422 -15324.1016559 Force two-norm initial, final = 459.012 0.577691 Force max component initial, final = 348.07 0.0840527 Final line search alpha, max atom move = 7.8629e-05 6.60898e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1052 | 0.1052 | 0.1052 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050068 | 0.00050068 | 0.00050068 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001933 | | | 1.80 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12562 ave 12562 max 12562 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: 773164 ave 773164 max 773164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 773164 Ave neighs/atom = 223.716 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 = 13 21 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) = 8.047 | 8.047 | 8.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15324.102 0 -15324.102 -3360.7648 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3456 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: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12612 ave 12612 max 12612 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: 774318 ave 774318 max 774318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774318 Ave neighs/atom = 224.05 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) = 8.047 | 8.047 | 8.047 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 -15324.102 -15324.102 51.877766 85.071684 8.5992516 -3360.7648 -3360.7648 0.58111321 -10081.281 -1.5941259 2.2152895 1568.8636 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3456 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: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12612 ave 12612 max 12612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387159 ave 387159 max 387159 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 774318 ave 774318 max 774318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774318 Ave neighs/atom = 224.05 Neighbor list builds = 0 Dangerous builds = 0 3456 -15324.1016559352 eV 2.21528948572096 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02