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 = 4.05018 4.05018 4.05018 Created orthogonal box = (0 -51.2352 0) to (12.8078 51.2352 4.05018) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.12312 5.12312 4.05018 Created 162 atoms create_atoms CPU = 0.000200987 secs 162 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.12312 5.12312 4.05018 Created 162 atoms create_atoms CPU = 7.08103e-05 secs 162 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 4 25 1 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 8.40393 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 316 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 4 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 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) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1128.4995 0 -1128.4995 -3059.1013 13 0 -1129.4208 0 -1129.4208 -3850.3721 Loop time of 0.026809 on 1 procs for 13 steps with 316 atoms 111.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1128.49945587 -1129.41977332 -1129.42080823 Force two-norm initial, final = 1.70778 0.0575686 Force max component initial, final = 0.446707 0.00772878 Final line search alpha, max atom move = 1 0.00772878 Iterations, force evaluations = 13 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.026 | 0.026 | 0.026 | 0.0 | 96.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055623 | 0.00055623 | 0.00055623 | 0.0 | 2.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002532 | | | 0.94 Nlocal: 316 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4431 ave 4431 max 4431 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: 43816 ave 43816 max 43816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43816 Ave neighs/atom = 138.658 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 : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -1129.4208 0 -1129.4208 -3850.3721 5315.5418 17 0 -1129.4536 0 -1129.4536 -371.80274 5291.4793 Loop time of 0.0100639 on 1 procs for 4 steps with 316 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1129.42080823 -1129.45341111 -1129.45361585 Force two-norm initial, final = 18.1767 0.0719533 Force max component initial, final = 13.7895 0.0157225 Final line search alpha, max atom move = 0.00150872 2.37209e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0093861 | 0.0093861 | 0.0093861 | 0.0 | 93.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018096 | 0.00018096 | 0.00018096 | 0.0 | 1.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004969 | | | 4.94 Nlocal: 316 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4416 ave 4416 max 4416 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: 44008 ave 44008 max 44008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44008 Ave neighs/atom = 139.266 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 4 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 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) = 4.613 | 4.613 | 4.613 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1129.4536 0 -1129.4536 -371.80274 Loop time of 1.90735e-06 on 1 procs for 0 steps with 316 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: 316 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4416 ave 4416 max 4416 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: 44040 ave 44040 max 44040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44040 Ave neighs/atom = 139.367 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) = 4.613 | 4.613 | 4.613 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 -1129.4536 -1129.4536 12.787755 102.47047 4.0381651 -371.80274 -371.80274 -4.7530819 -1108.8441 -1.811089 2.5872297 219.13826 Loop time of 1.19209e-06 on 1 procs for 0 steps with 316 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 | | 1.192e-06 | | |100.00 Nlocal: 316 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4416 ave 4416 max 4416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22020 ave 22020 max 22020 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44040 ave 44040 max 44040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44040 Ave neighs/atom = 139.367 Neighbor list builds = 0 Dangerous builds = 0 316 -1129.45331449016 eV 2.58722967017006 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00