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 = 3.52733 3.52733 3.52733 Created orthogonal box = (0 -44.8991 0) to (10.582 44.8991 4.9884) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.87888 4.9884 4.9884 Created 218 atoms create_atoms CPU = 0.000258923 secs 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.87888 4.9884 4.9884 Created 218 atoms create_atoms CPU = 0.000119925 secs 218 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 3 18 1 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 10.1329 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 428 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 3 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 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) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1754.6542 0 -1754.6542 14832.801 189 0 -1785.4366 0 -1785.4366 -10537.554 Loop time of 1.33562 on 1 procs for 189 steps with 428 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1754.65418041 -1785.43484032 -1785.43660491 Force two-norm initial, final = 40.5615 0.179064 Force max component initial, final = 11.912 0.0345664 Final line search alpha, max atom move = 1 0.0345664 Iterations, force evaluations = 189 362 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3065 | 1.3065 | 1.3065 | 0.0 | 97.82 Neigh | 0.0068572 | 0.0068572 | 0.0068572 | 0.0 | 0.51 Comm | 0.016485 | 0.016485 | 0.016485 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005763 | | | 0.43 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7255 ave 7255 max 7255 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: 162764 ave 162764 max 162764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162764 Ave neighs/atom = 380.29 Neighbor list builds = 2 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 : 189 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 189 0 -1785.4366 0 -1785.4366 -10537.554 4740.192 193 0 -1785.5666 0 -1785.5666 1256.7667 4709.5678 Loop time of 0.025439 on 1 procs for 4 steps with 428 atoms 117.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1785.43660491 -1785.56564125 -1785.56658804 Force two-norm initial, final = 56.5806 0.318864 Force max component initial, final = 40.7843 0.18653 Final line search alpha, max atom move = 0.000263704 4.91887e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02454 | 0.02454 | 0.02454 | 0.0 | 96.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024724 | 0.00024724 | 0.00024724 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006521 | | | 2.56 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7289 ave 7289 max 7289 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: 162764 ave 162764 max 162764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162764 Ave neighs/atom = 380.29 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 3 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 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) = 5.124 | 5.124 | 5.124 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1785.5666 0 -1785.5666 1256.7667 Loop time of 1.19209e-06 on 1 procs for 0 steps with 428 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: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7289 ave 7289 max 7289 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: 162932 ave 162932 max 162932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162932 Ave neighs/atom = 380.682 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) = 5.124 | 5.124 | 5.124 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 -1785.5666 -1785.5666 10.547876 89.798202 4.9721978 1256.7667 1256.7667 63.252171 3758.4731 -51.425049 2.3473687 210.09455 Loop time of 9.53674e-07 on 1 procs for 0 steps with 428 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: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7289 ave 7289 max 7289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81466 ave 81466 max 81466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162932 ave 162932 max 162932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162932 Ave neighs/atom = 380.682 Neighbor list builds = 0 Dangerous builds = 0 428 -1785.56658803901 eV 2.34736873657455 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01