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 = 4.2107 4.2107 4.2107 Created orthogonal box = (0 -84.4285 0) to (48.7424 84.4285 7.29315) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.54748 6.72034 7.29315 Created 1609 atoms create_atoms CPU = 0.00103498 secs 1609 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.54748 6.72034 7.29315 Created 1609 atoms create_atoms CPU = 0.00092411 secs 1609 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 11 38 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 3188 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 7.046 | 7.046 | 7.046 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11849.197 0 -11849.197 524.55234 50 0 -11871.607 0 -11871.607 -1978.4245 Loop time of 1.55565 on 1 procs for 50 steps with 3188 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 = -11849.1967695 -11871.5972521 -11871.6068019 Force two-norm initial, final = 24.7938 0.187567 Force max component initial, final = 4.77666 0.0651542 Final line search alpha, max atom move = 1 0.0651542 Iterations, force evaluations = 50 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4972 | 1.4972 | 1.4972 | 0.0 | 96.24 Neigh | 0.044986 | 0.044986 | 0.044986 | 0.0 | 2.89 Comm | 0.007422 | 0.007422 | 0.007422 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006073 | | | 0.39 Nlocal: 3188 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12911 ave 12911 max 12911 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: 551698 ave 551698 max 551698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551698 Ave neighs/atom = 173.055 Neighbor list builds = 3 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.047 | 7.047 | 7.047 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -11871.607 0 -11871.607 -1978.4245 60026.18 53 0 -11871.729 0 -11871.729 -421.26295 59785.968 Loop time of 0.110153 on 1 procs for 3 steps with 3188 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11871.6068019 -11871.7292075 -11871.7294681 Force two-norm initial, final = 87.901 2.12742 Force max component initial, final = 63.4723 2.04784 Final line search alpha, max atom move = 0.000395943 0.000810828 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10836 | 0.10836 | 0.10836 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040102 | 0.00040102 | 0.00040102 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001388 | | | 1.26 Nlocal: 3188 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12909 ave 12909 max 12909 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: 551760 ave 551760 max 551760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551760 Ave neighs/atom = 173.074 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 7.185 | 7.185 | 7.185 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11871.729 0 -11871.729 -421.26295 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3188 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: 3188 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12959 ave 12959 max 12959 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: 552554 ave 552554 max 552554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 552554 Ave neighs/atom = 173.323 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) = 7.185 | 7.185 | 7.185 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 -11871.729 -11871.729 48.653973 168.85698 7.2771603 -421.26295 -421.26295 54.779564 -1333.0497 14.481305 2.7357205 1995.8464 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3188 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: 3188 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12959 ave 12959 max 12959 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 276277 ave 276277 max 276277 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 552554 ave 552554 max 552554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 552554 Ave neighs/atom = 173.323 Neighbor list builds = 0 Dangerous builds = 0 3188 -11871.7294680883 eV 2.73572050981444 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02