LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -51.757199 0.0000000) to (18.297688 51.757199 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7438451 5.7504086 4.9800000 Created 434 atoms create_atoms CPU = 0.001 seconds 434 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7438451 5.7504086 4.9800000 Created 434 atoms create_atoms CPU = 0.001 seconds 434 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 856 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.984 | 4.984 | 4.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3767.5716 0 -3767.5716 9018.1004 56 0 -3792.6533 0 -3792.6533 -4474.4846 Loop time of 2.72039 on 1 procs for 56 steps with 856 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 = -3767.57159342038 -3792.64991823439 -3792.65327686114 Force two-norm initial, final = 45.258504 0.19893974 Force max component initial, final = 15.110908 0.030171371 Final line search alpha, max atom move = 1.0000000 0.030171371 Iterations, force evaluations = 56 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7108 | 2.7108 | 2.7108 | 0.0 | 99.65 Neigh | 0.0034854 | 0.0034854 | 0.0034854 | 0.0 | 0.13 Comm | 0.0036446 | 0.0036446 | 0.0036446 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002511 | | | 0.09 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5502.00 ave 5502 max 5502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113880.0 ave 113880 max 113880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113880 Ave neighs/atom = 133.03738 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -3792.6533 0 -3792.6533 -4474.4846 9432.4894 58 0 -3792.6841 0 -3792.6841 -314.45003 9411.1834 Loop time of 0.101796 on 1 procs for 2 steps with 856 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3792.65327686113 -3792.68066665933 -3792.68405012379 Force two-norm initial, final = 37.825465 5.3599587 Force max component initial, final = 31.871315 5.3474071 Final line search alpha, max atom move = 9.7896760e-05 0.00052349382 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10125 | 0.10125 | 0.10125 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000126 | 0.000126 | 0.000126 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004212 | | | 0.41 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5616.00 ave 5616 max 5616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113940.0 ave 113940 max 113940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113940 Ave neighs/atom = 133.10748 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.123 | 5.123 | 5.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3792.6841 0 -3792.6841 -314.45003 Loop time of 2.29996e-06 on 1 procs for 0 steps with 856 atoms 130.4% 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 | | 2.3e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5616.00 ave 5616 max 5616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113992.0 ave 113992 max 113992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113992 Ave neighs/atom = 133.16822 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) = 5.123 | 5.123 | 5.123 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 -3792.6841 -3792.6841 18.267336 103.5144 4.977007 -314.45003 -314.45003 51.379259 -1904.5342 909.80491 2.283485 448.51057 Loop time of 2.40002e-06 on 1 procs for 0 steps with 856 atoms 166.7% 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 | | 2.4e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5616.00 ave 5616 max 5616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56996.0 ave 56996 max 56996 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113992.0 ave 113992 max 113992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113992 Ave neighs/atom = 133.16822 Neighbor list builds = 0 Dangerous builds = 0 856 -3792.68405012379 eV 2.28348502506818 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03