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 = 3.52152 3.52152 3.52152 Created orthogonal box = (0 -62.206 0) to (35.9126 62.206 6.09945) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.52502 5.58227 6.09945 Created 1250 atoms create_atoms CPU = 0.000808954 secs 1250 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.52502 5.58227 6.09945 Created 1250 atoms create_atoms CPU = 0.000695944 secs 1250 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 41 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 2488 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.711 | 5.711 | 5.711 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14287.529 0 -14287.529 5477.9819 15 0 -14346.027 0 -14346.027 -740.19487 Loop time of 36.8111 on 1 procs for 15 steps with 2488 atoms 84.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14287.5290346 -14346.0127799 -14346.0267906 Force two-norm initial, final = 70.5523 0.408481 Force max component initial, final = 8.32259 0.0393454 Final line search alpha, max atom move = 1 0.0393454 Iterations, force evaluations = 15 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 36.808 | 36.808 | 36.808 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018966 | 0.0018966 | 0.0018966 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001451 | | | 0.00 Nlocal: 2488 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9660 ave 9660 max 9660 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: 213256 ave 213256 max 213256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213256 Ave neighs/atom = 85.7138 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 : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.711 | 5.711 | 5.711 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -14346.027 0 -14346.027 -740.19487 27252.12 17 0 -14346.048 0 -14346.048 808.61549 27231.633 Loop time of 5.79689 on 1 procs for 2 steps with 2488 atoms 93.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14346.0267906 -14346.0459916 -14346.0476696 Force two-norm initial, final = 53.0292 0.414284 Force max component initial, final = 51.5298 0.0788032 Final line search alpha, max atom move = 8.73431e-05 6.88291e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7959 | 5.7959 | 5.7959 | 0.0 | 99.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022912 | 0.00022912 | 0.00022912 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007489 | | | 0.01 Nlocal: 2488 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8976 ave 8976 max 8976 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: 210688 ave 210688 max 210688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210688 Ave neighs/atom = 84.6817 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.845 | 5.845 | 5.845 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14346.048 0 -14346.048 808.61549 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2488 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: 2488 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9231 ave 9231 max 9231 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: 210832 ave 210832 max 210832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210832 Ave neighs/atom = 84.7395 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) = 5.845 | 5.845 | 5.845 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 -14346.048 -14346.048 35.915344 124.41199 6.0944063 808.61549 808.61549 -4.6367467 2431.9359 -1.4526733 2.2490569 896.46759 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2488 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: 2488 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9231 ave 9231 max 9231 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105416 ave 105416 max 105416 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 210832 ave 210832 max 210832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210832 Ave neighs/atom = 84.7395 Neighbor list builds = 0 Dangerous builds = 0 2488 -7146.86320625355 eV 2.2490569340438 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:47