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 = 3.61115 3.61115 3.61115 Created orthogonal box = (0 -58.6779 0) to (20.7445 58.6779 5.10694) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.65759 6.22303 5.10694 Created 530 atoms create_atoms CPU = 0.000375986 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.65759 6.22303 5.10694 Created 530 atoms create_atoms CPU = 0.000244141 secs 530 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 44 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 12 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4422.4977 0 -4422.4977 -215.41432 37 0 -4442.3561 0 -4442.3561 -8556.9984 Loop time of 1.5899 on 1 procs for 37 steps with 1048 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4422.49766517 -4442.35212618 -4442.35609392 Force two-norm initial, final = 25.0708 0.231802 Force max component initial, final = 9.07268 0.0393858 Final line search alpha, max atom move = 1 0.0393858 Iterations, force evaluations = 37 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5863 | 1.5863 | 1.5863 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018182 | 0.0018182 | 0.0018182 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001775 | | | 0.11 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4160 ave 4160 max 4160 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: 56236 ave 56236 max 56236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56236 Ave neighs/atom = 53.6603 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -4442.3561 0 -4442.3561 -8556.9984 12432.778 41 0 -4442.4705 0 -4442.4705 -2824.6826 12388.825 Loop time of 0.201461 on 1 procs for 4 steps with 1048 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4442.35609392 -4442.46823683 -4442.47054357 Force two-norm initial, final = 77.7384 0.260678 Force max component initial, final = 67.5653 0.0453572 Final line search alpha, max atom move = 0.00010618 4.81601e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20055 | 0.20055 | 0.20055 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002017 | 0.0002017 | 0.0002017 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007112 | | | 0.35 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4148 ave 4148 max 4148 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: 56452 ave 56452 max 56452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56452 Ave neighs/atom = 53.8664 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.507 | 5.507 | 5.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4442.4705 0 -4442.4705 -2824.6826 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: 4148 ave 4148 max 4148 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: 56468 ave 56468 max 56468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56468 Ave neighs/atom = 53.8817 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) = 5.507 | 5.507 | 5.507 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 -4442.4705 -4442.4705 20.67878 117.35579 5.105058 -2824.6826 -2824.6826 -1.3237517 -8468.0218 -4.7022433 2.3691508 217.0336 Loop time of 1.90735e-06 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 | | 1.907e-06 | | |100.00 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4148 ave 4148 max 4148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28234 ave 28234 max 28234 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56468 ave 56468 max 56468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56468 Ave neighs/atom = 53.8817 Neighbor list builds = 0 Dangerous builds = 0 1048 -4442.47054357002 eV 2.36915079355791 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01