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 = 3.86934 3.86934 3.86934 Created orthogonal box = (0 -55.2691 0) to (39.0784 55.2691 5.47207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.12994 4.87634 5.47207 Created 822 atoms create_atoms CPU = 0.00051403 secs 822 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.12994 4.87634 5.47207 Created 822 atoms create_atoms CPU = 0.000362873 secs 822 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 10 27 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 8.19533 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1624 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 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) = 5.54 | 5.54 | 5.54 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5104.8885 0 -5104.8885 18593.512 40 0 -5188.6736 0 -5188.6736 -1184.9662 Loop time of 0.488659 on 1 procs for 40 steps with 1624 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 = -5104.88848548 -5188.66977333 -5188.67361442 Force two-norm initial, final = 89.7968 0.190269 Force max component initial, final = 17.9207 0.0210784 Final line search alpha, max atom move = 1 0.0210784 Iterations, force evaluations = 40 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47393 | 0.47393 | 0.47393 | 0.0 | 96.99 Neigh | 0.00719 | 0.00719 | 0.00719 | 0.0 | 1.47 Comm | 0.0044403 | 0.0044403 | 0.0044403 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003096 | | | 0.63 Nlocal: 1624 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8229 ave 8229 max 8229 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: 239128 ave 239128 max 239128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239128 Ave neighs/atom = 147.246 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.54 | 5.54 | 5.54 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -5188.6736 0 -5188.6736 -1184.9662 23637.429 42 0 -5188.6822 0 -5188.6822 -361.47307 23623.903 Loop time of 0.034024 on 1 procs for 2 steps with 1624 atoms 88.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5188.67361442 -5188.68029846 -5188.68223467 Force two-norm initial, final = 22.03 0.199324 Force max component initial, final = 21.568 0.0554361 Final line search alpha, max atom move = 0.000129475 7.17758e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.032985 | 0.032985 | 0.032985 | 0.0 | 96.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024891 | 0.00024891 | 0.00024891 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007901 | | | 2.32 Nlocal: 1624 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8245 ave 8245 max 8245 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: 236936 ave 236936 max 236936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236936 Ave neighs/atom = 145.897 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 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) = 5.678 | 5.678 | 5.678 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5188.6822 0 -5188.6822 -361.47307 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1624 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: 1624 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8245 ave 8245 max 8245 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: 237920 ave 237920 max 237920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237920 Ave neighs/atom = 146.502 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) = 5.678 | 5.678 | 5.678 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 -5188.6822 -5188.6822 39.089469 110.53811 5.4673873 -361.47307 -361.47307 -3.7607508 -1079.5874 -1.0710402 2.5767573 655.27493 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1624 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: 1624 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8245 ave 8245 max 8245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118960 ave 118960 max 118960 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237920 ave 237920 max 237920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237920 Ave neighs/atom = 146.502 Neighbor list builds = 0 Dangerous builds = 0 1624 -5188.68223466987 eV 2.57675733047313 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00