LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.16926 3.16926 3.16926 Created orthogonal box = (0 -45.2692 0) to (32.0079 45.2692 4.48201) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.02085 3.99406 4.48201 Created 409 atoms create_atoms CPU = 0.000436068 secs 409 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.02085 3.99406 4.48201 Created 409 atoms create_atoms CPU = 0.000254154 secs 409 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 10 28 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8716.0334 0 -8716.0334 7055.9312 51 0 -8774.3017 0 -8774.3017 -1889.0831 Loop time of 20.0586 on 1 procs for 51 steps with 812 atoms 63.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8716.03342333 -8774.29401599 -8774.3016834 Force two-norm initial, final = 82.6669 0.348789 Force max component initial, final = 19.2817 0.074798 Final line search alpha, max atom move = 1 0.074798 Iterations, force evaluations = 51 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.026 | 20.026 | 20.026 | 0.0 | 99.84 Neigh | 0.015042 | 0.015042 | 0.015042 | 0.0 | 0.07 Comm | 0.0028505 | 0.0028505 | 0.0028505 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01508 | | | 0.08 Nlocal: 812 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3789 ave 3789 max 3789 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: 52196 ave 52196 max 52196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52196 Ave neighs/atom = 64.2808 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -8774.3017 0 -8774.3017 -1889.0831 12988.636 53 0 -8774.3344 0 -8774.3344 2281.1259 12967.856 Loop time of 1.3564 on 1 procs for 2 steps with 812 atoms 50.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8774.3016834 -8774.33407148 -8774.33436024 Force two-norm initial, final = 56.5035 0.352301 Force max component initial, final = 43.7216 0.0628702 Final line search alpha, max atom move = 0.000422596 2.65687e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3558 | 1.3558 | 1.3558 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011086 | 0.00011086 | 0.00011086 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000463 | | | 0.03 Nlocal: 812 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3772 ave 3772 max 3772 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: 52080 ave 52080 max 52080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52080 Ave neighs/atom = 64.1379 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.672 | 4.672 | 4.672 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8774.3344 0 -8774.3344 2281.1259 Loop time of 9.53674e-07 on 1 procs for 0 steps with 812 atoms 209.7% 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: 812 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3772 ave 3772 max 3772 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: 52088 ave 52088 max 52088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52088 Ave neighs/atom = 64.1478 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) = 4.672 | 4.672 | 4.672 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 -8774.3344 -8774.3344 31.988933 90.538469 4.4774966 2281.1259 2281.1259 -5.4919753 6847.4234 1.4464059 2.3821856 527.81886 Loop time of 1.19209e-06 on 1 procs for 0 steps with 812 atoms 251.7% 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: 812 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3772 ave 3772 max 3772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26044 ave 26044 max 26044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52088 ave 52088 max 52088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52088 Ave neighs/atom = 64.1478 Neighbor list builds = 0 Dangerous builds = 0 812 -4426.39453707821 eV 2.38218563884322 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22