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 = 3.52401 3.52401 3.52401 Created orthogonal box = (0 -42.5843 0) to (52.1506 42.5843 8.63203) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.00074 5.24969 5.75469 Created 1757 atoms create_atoms CPU = 0.000675917 secs 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.00074 5.24969 5.75469 Created 1757 atoms create_atoms CPU = 0.000576973 secs 1757 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 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, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 58 atoms, new total = 3456 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 7.408 | 7.408 | 7.408 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15529.669 0 -15529.669 -1739.6939 65 0 -15596.592 0 -15596.592 -13318.584 Loop time of 1.39596 on 1 procs for 65 steps with 3456 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15529.6690957 -15596.5764679 -15596.5920577 Force two-norm initial, final = 39.6729 0.443087 Force max component initial, final = 6.13258 0.103781 Final line search alpha, max atom move = 1 0.103781 Iterations, force evaluations = 65 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3674 | 1.3674 | 1.3674 | 0.0 | 97.95 Neigh | 0.01187 | 0.01187 | 0.01187 | 0.0 | 0.85 Comm | 0.0081174 | 0.0081174 | 0.0081174 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008575 | | | 0.61 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11008 ave 11008 max 11008 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: 598578 ave 598578 max 598578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 598578 Ave neighs/atom = 173.2 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.408 | 7.408 | 7.408 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -15596.592 0 -15596.592 -13318.584 38339.958 70 0 -15597.567 0 -15597.567 -2252.707 38104.072 Loop time of 0.10226 on 1 procs for 5 steps with 3456 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15596.5920577 -15597.5651608 -15597.5673864 Force two-norm initial, final = 436.13 0.580763 Force max component initial, final = 338.659 0.125429 Final line search alpha, max atom move = 7.45832e-05 9.35492e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099592 | 0.099592 | 0.099592 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050759 | 0.00050759 | 0.00050759 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002161 | | | 2.11 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11019 ave 11019 max 11019 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: 599094 ave 599094 max 599094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 599094 Ave neighs/atom = 173.349 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 7.546 | 7.546 | 7.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15597.567 0 -15597.567 -2252.707 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3456 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: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11043 ave 11043 max 11043 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: 599808 ave 599808 max 599808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 599808 Ave neighs/atom = 173.556 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) = 7.546 | 7.546 | 7.546 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 -15597.567 -15597.567 51.948016 85.16861 8.6123736 -2252.707 -2252.707 -0.39253399 -6754.9397 -2.7888229 2.2200517 1589.4074 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3456 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: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11043 ave 11043 max 11043 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 299904 ave 299904 max 299904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 599808 ave 599808 max 599808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 599808 Ave neighs/atom = 173.556 Neighbor list builds = 0 Dangerous builds = 0 3456 -15597.5673863569 eV 2.22005166826855 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01