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 = 2.8602 2.8602 2.8602 Created orthogonal box = (0 -34.5627 0) to (42.327 34.5627 7.00602) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.05876 4.26081 4.67068 Created 882 atoms create_atoms CPU = 0.000452995 secs 882 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.05876 4.26081 4.67068 Created 882 atoms create_atoms CPU = 0.000342846 secs 882 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 16 26 3 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 24 atoms, new total = 1740 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.808 | 5.808 | 5.808 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7245.7241 0 -7245.7241 21340.455 58 0 -7401.6845 0 -7401.6845 -3110.0849 Loop time of 5.50449 on 1 procs for 58 steps with 1740 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 = -7245.72414062 -7401.67886746 -7401.68453916 Force two-norm initial, final = 116.95 0.286571 Force max component initial, final = 14.6787 0.018757 Final line search alpha, max atom move = 1 0.018757 Iterations, force evaluations = 58 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4973 | 5.4973 | 5.4973 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0033762 | 0.0033762 | 0.0033762 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003787 | | | 0.07 Nlocal: 1740 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4954 ave 4954 max 4954 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: 99684 ave 99684 max 99684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99684 Ave neighs/atom = 57.2897 Neighbor list builds = 0 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.808 | 5.808 | 5.808 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -7401.6845 0 -7401.6845 -3110.0849 20498.741 61 0 -7401.8525 0 -7401.8525 3244.1259 20425.582 Loop time of 0.260425 on 1 procs for 3 steps with 1740 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 = -7401.68453916 -7401.85045663 -7401.85249572 Force two-norm initial, final = 131.063 4.08594 Force max component initial, final = 107.362 4.00017 Final line search alpha, max atom move = 8.42164e-05 0.00033688 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25969 | 0.25969 | 0.25969 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005891 | | | 0.23 Nlocal: 1740 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4930 ave 4930 max 4930 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: 99912 ave 99912 max 99912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99912 Ave neighs/atom = 57.4207 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.946 | 5.946 | 5.946 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7401.8525 0 -7401.8525 3244.1259 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1740 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: 1740 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4933 ave 4933 max 4933 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: 99972 ave 99972 max 99972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99972 Ave neighs/atom = 57.4552 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) = 5.946 | 5.946 | 5.946 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 -7401.8525 -7401.8525 42.228192 69.125467 6.9973543 3244.1259 3244.1259 47.276814 9371.717 313.38388 2.2649992 1559.3625 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1740 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: 1740 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4933 ave 4933 max 4933 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49986 ave 49986 max 49986 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 99972 ave 99972 max 99972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99972 Ave neighs/atom = 57.4552 Neighbor list builds = 0 Dangerous builds = 0 1740 -7401.85249571944 eV 2.26499921280719 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06