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 = 3.51962 3.51962 3.51962 Created orthogonal box = (0 -35.8967 0) to (31.0844 35.8967 6.09616) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.57926 5.52203 6.09616 Created 628 atoms create_atoms CPU = 0.000394106 secs 628 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.57926 5.52203 6.09616 Created 630 atoms create_atoms CPU = 0.000269175 secs 630 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 = 7.56501 ghost atom cutoff = 7.56501 binsize = 3.7825, bins = 9 19 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 7.56501 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 25 atoms, new total = 1233 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 = 7.56501 ghost atom cutoff = 7.56501 binsize = 3.7825, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.56501 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) = 5.447 | 5.447 | 5.447 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5403.8513 0 -5403.8513 13856.58 84 0 -5456.6857 0 -5456.6857 -6258.0939 Loop time of 0.685872 on 1 procs for 84 steps with 1233 atoms 100.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5403.85132846 -5456.68069099 -5456.68565415 Force two-norm initial, final = 65.3122 0.242556 Force max component initial, final = 12.4496 0.0679205 Final line search alpha, max atom move = 1 0.0679205 Iterations, force evaluations = 84 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6631 | 0.6631 | 0.6631 | 0.0 | 96.68 Neigh | 0.011515 | 0.011515 | 0.011515 | 0.0 | 1.68 Comm | 0.0065942 | 0.0065942 | 0.0065942 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00466 | | | 0.68 Nlocal: 1233 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6134 ave 6134 max 6134 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: 211974 ave 211974 max 211974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211974 Ave neighs/atom = 171.917 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.447 | 5.447 | 5.447 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -5456.6857 0 -5456.6857 -6258.0939 13604.541 87 0 -5456.7352 0 -5456.7352 -2785.5682 13577.055 Loop time of 0.0290592 on 1 procs for 3 steps with 1233 atoms 103.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5456.68565415 -5456.73483978 -5456.7351605 Force two-norm initial, final = 55.2437 0.251758 Force max component initial, final = 50.9205 0.0628567 Final line search alpha, max atom move = 0.000213847 1.34417e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028008 | 0.028008 | 0.028008 | 0.0 | 96.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024152 | 0.00024152 | 0.00024152 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008094 | | | 2.79 Nlocal: 1233 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6138 ave 6138 max 6138 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: 212316 ave 212316 max 212316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212316 Ave neighs/atom = 172.195 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 = 7.56501 ghost atom cutoff = 7.56501 binsize = 3.7825, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.56501 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) = 5.585 | 5.585 | 5.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5456.7352 0 -5456.7352 -2785.5682 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1233 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: 1233 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6138 ave 6138 max 6138 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: 212444 ave 212444 max 212444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212444 Ave neighs/atom = 172.298 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) = 5.585 | 5.585 | 5.585 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 -5456.7352 -5456.7352 31.075348 71.79345 6.0856191 -2785.5682 -2785.5682 -4.3313647 -8350.6871 -1.6860643 2.216322 845.52663 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1233 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: 1233 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6138 ave 6138 max 6138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106222 ave 106222 max 106222 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 212444 ave 212444 max 212444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212444 Ave neighs/atom = 172.298 Neighbor list builds = 0 Dangerous builds = 0 1233 -5456.73516050348 eV 2.21632198594119 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00