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 -40.4452 0) to (28.5966 40.4452 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.33282 5.51478 4.97803 Created 532 atoms create_atoms CPU = 0.000386 secs 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.33282 5.51478 4.97803 Created 532 atoms create_atoms CPU = 0.000249863 secs 532 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 7 20 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.426 | 5.426 | 5.426 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4618.793 0 -4618.793 4615.1373 34 0 -4642.7758 0 -4642.7758 -1051.7921 Loop time of 0.275111 on 1 procs for 34 steps with 1048 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4618.79299626 -4642.77124284 -4642.77579916 Force two-norm initial, final = 24.9637 0.221981 Force max component initial, final = 4.12293 0.0162786 Final line search alpha, max atom move = 1 0.0162786 Iterations, force evaluations = 34 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26425 | 0.26425 | 0.26425 | 0.0 | 96.05 Neigh | 0.0063989 | 0.0063989 | 0.0063989 | 0.0 | 2.33 Comm | 0.0027151 | 0.0027151 | 0.0027151 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001749 | | | 0.64 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7404 ave 7404 max 7404 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: 229728 ave 229728 max 229728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229728 Ave neighs/atom = 219.206 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 : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.428 | 5.428 | 5.428 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -4642.7758 0 -4642.7758 -1051.7921 11515.154 36 0 -4642.7905 0 -4642.7905 1417.0752 11499.192 Loop time of 0.0290151 on 1 procs for 2 steps with 1048 atoms 68.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4642.77579916 -4642.78977355 -4642.79047824 Force two-norm initial, final = 29.1673 0.231257 Force max component initial, final = 21.7975 0.0442154 Final line search alpha, max atom move = 0.000355822 1.57328e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028108 | 0.028108 | 0.028108 | 0.0 | 96.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022554 | 0.00022554 | 0.00022554 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006816 | | | 2.35 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7372 ave 7372 max 7372 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: 230960 ave 230960 max 230960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230960 Ave neighs/atom = 220.382 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.565 | 5.565 | 5.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4642.7905 0 -4642.7905 1417.0752 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7372 ave 7372 max 7372 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: 230992 ave 230992 max 230992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230992 Ave neighs/atom = 220.412 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) = 5.565 | 5.565 | 5.565 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 -4642.7905 -4642.7905 28.567927 80.890483 4.9761235 1417.0752 1417.0752 -1.0087624 4258.3926 -6.1581515 2.2513995 517.47531 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7372 ave 7372 max 7372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115496 ave 115496 max 115496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 230992 ave 230992 max 230992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230992 Ave neighs/atom = 220.412 Neighbor list builds = 0 Dangerous builds = 0 1048 -4619.16181261689 eV 2.25139946640416 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00