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 -39.4403 0) to (19.32 39.4403 8.64016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.15199 4.73241 5.7601 Created 612 atoms create_atoms CPU = 0.000235081 secs 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.15199 4.73241 5.7601 Created 612 atoms create_atoms CPU = 0.000128984 secs 612 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 = 4 16 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 10.1329 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 1188 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 = 4 16 2 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) = 6.36 | 6.36 | 6.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4882.396 0 -4882.396 10597.388 64 0 -4937.3735 0 -4937.3735 -7157.4924 Loop time of 1.07797 on 1 procs for 64 steps with 1188 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4882.39601103 -4937.36886744 -4937.37352355 Force two-norm initial, final = 42.3828 0.274411 Force max component initial, final = 7.42159 0.0180214 Final line search alpha, max atom move = 1 0.0180214 Iterations, force evaluations = 64 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0531 | 1.0531 | 1.0531 | 0.0 | 97.69 Neigh | 0.012873 | 0.012873 | 0.012873 | 0.0 | 1.19 Comm | 0.0079186 | 0.0079186 | 0.0079186 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004104 | | | 0.38 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9128 ave 9128 max 9128 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: 450672 ave 450672 max 450672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450672 Ave neighs/atom = 379.354 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.36 | 6.36 | 6.36 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -4937.3735 0 -4937.3735 -7157.4924 13167.343 67 0 -4937.453 0 -4937.453 -1970.4599 13129.76 Loop time of 0.060544 on 1 procs for 3 steps with 1188 atoms 115.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4937.37352355 -4937.45286333 -4937.45304921 Force two-norm initial, final = 74.8695 0.312824 Force max component initial, final = 63.5089 0.0615316 Final line search alpha, max atom move = 0.000455528 2.80294e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.059246 | 0.059246 | 0.059246 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033092 | 0.00033092 | 0.00033092 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000967 | | | 1.60 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9191 ave 9191 max 9191 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: 450696 ave 450696 max 450696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450696 Ave neighs/atom = 379.374 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 = 4 16 2 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) = 6.497 | 6.497 | 6.497 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4937.453 0 -4937.453 -1970.4599 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1188 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: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9191 ave 9191 max 9191 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: 450888 ave 450888 max 450888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450888 Ave neighs/atom = 379.535 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) = 6.497 | 6.497 | 6.497 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 -4937.453 -4937.453 19.301581 78.880538 8.6237082 -1970.4599 -1970.4599 -7.5013261 -5903.4121 -0.46625599 2.211598 678.06519 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1188 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: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9191 ave 9191 max 9191 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 225444 ave 225444 max 225444 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 450888 ave 450888 max 450888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450888 Ave neighs/atom = 379.535 Neighbor list builds = 0 Dangerous builds = 0 1188 -4937.45304921052 eV 2.21159803184181 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01