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 = 4.03299 4.03299 4.03299 Created orthogonal box = (0 -52.7422 0) to (24.861 52.7422 5.70351) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2339 6.47662 5.70351 Created 459 atoms create_atoms CPU = 0.000380039 secs 459 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2339 6.47662 5.70351 Created 459 atoms create_atoms CPU = 0.000223875 secs 459 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 4 16 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 896 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 7.082 | 7.082 | 7.082 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2574.324 0 -2574.324 192.70861 65 0 -2601.9146 0 -2601.9146 -9895.7781 Loop time of 1.7734 on 1 procs for 65 steps with 896 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2574.32400603 -2601.91214028 -2601.91459539 Force two-norm initial, final = 14.6547 0.155505 Force max component initial, final = 2.03186 0.0241699 Final line search alpha, max atom move = 1 0.0241699 Iterations, force evaluations = 65 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.746 | 1.746 | 1.746 | 0.0 | 98.46 Neigh | 0.013318 | 0.013318 | 0.013318 | 0.0 | 0.75 Comm | 0.0105 | 0.0105 | 0.0105 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003537 | | | 0.20 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12798 ave 12798 max 12798 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: 586164 ave 586164 max 586164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586164 Ave neighs/atom = 654.201 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.083 | 7.083 | 7.083 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -2601.9146 0 -2601.9146 -9895.7781 14957.156 81 0 -2602.7033 0 -2602.7033 -3103.5025 14815.594 Loop time of 0.277697 on 1 procs for 16 steps with 896 atoms 100.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2601.91459539 -2602.70316603 -2602.70331037 Force two-norm initial, final = 108.267 0.716393 Force max component initial, final = 107.71 0.442998 Final line search alpha, max atom move = 0.00122121 0.000540993 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27232 | 0.27232 | 0.27232 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013449 | 0.0013449 | 0.0013449 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004035 | | | 1.45 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12904 ave 12904 max 12904 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: 587008 ave 587008 max 587008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 587008 Ave neighs/atom = 655.143 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 6.84 | 6.84 | 6.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2602.7033 0 -2602.7033 -3103.5025 Loop time of 9.53674e-07 on 1 procs for 0 steps with 896 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: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12976 ave 12976 max 12976 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: 586296 ave 586296 max 586296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586296 Ave neighs/atom = 654.348 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) = 6.84 | 6.84 | 6.84 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 -2602.7033 -2602.7033 24.484711 105.4844 5.7363524 -3103.5025 -3103.5025 -33.989925 -9228.3354 -48.182278 2.5877954 568.83026 Loop time of 2.14577e-06 on 1 procs for 0 steps with 896 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 | | 2.146e-06 | | |100.00 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12976 ave 12976 max 12976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 293148 ave 293148 max 293148 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 586296 ave 586296 max 586296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586296 Ave neighs/atom = 654.348 Neighbor list builds = 0 Dangerous builds = 0 896 -2602.70331037 eV 2.5877954084275 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02