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 = 4.04527 4.04527 4.04527 Created orthogonal box = (0 -46.8314 0) to (33.112 46.8314 5.72088) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.42471 6.98916 5.72088 Created 538 atoms create_atoms CPU = 0.000454903 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.42471 6.98916 5.72088 Created 538 atoms create_atoms CPU = 0.000333071 secs 538 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 20 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1060 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.43 | 5.43 | 5.43 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3598.4186 0 -3598.4186 -378.48075 58 0 -3607.7683 0 -3607.7683 -5279.6195 Loop time of 0.548433 on 1 procs for 58 steps with 1060 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3598.41858231 -3607.76482501 -3607.76833873 Force two-norm initial, final = 10.9304 0.13862 Force max component initial, final = 3.10522 0.025303 Final line search alpha, max atom move = 1 0.025303 Iterations, force evaluations = 58 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52716 | 0.52716 | 0.52716 | 0.0 | 96.12 Neigh | 0.013002 | 0.013002 | 0.013002 | 0.0 | 2.37 Comm | 0.0051756 | 0.0051756 | 0.0051756 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003093 | | | 0.56 Nlocal: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7895 ave 7895 max 7895 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: 224064 ave 224064 max 224064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224064 Ave neighs/atom = 211.381 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.43 | 5.43 | 5.43 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -3607.7683 0 -3607.7683 -5279.6195 17742.508 62 0 -3607.8719 0 -3607.8719 -1760.4601 17662.12 Loop time of 0.029681 on 1 procs for 4 steps with 1060 atoms 101.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3607.76833873 -3607.87166433 -3607.87190934 Force two-norm initial, final = 63.5052 0.153435 Force max component initial, final = 47.6837 0.0335114 Final line search alpha, max atom move = 0.000718431 2.40756e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028627 | 0.028627 | 0.028627 | 0.0 | 96.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027132 | 0.00027132 | 0.00027132 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007827 | | | 2.64 Nlocal: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7913 ave 7913 max 7913 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: 223944 ave 223944 max 223944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223944 Ave neighs/atom = 211.268 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.568 | 5.568 | 5.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3607.8719 0 -3607.8719 -1760.4601 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1060 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: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7913 ave 7913 max 7913 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: 227388 ave 227388 max 227388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227388 Ave neighs/atom = 214.517 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) = 5.568 | 5.568 | 5.568 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 -3607.8719 -3607.8719 33.05132 93.662873 5.7054059 -1760.4601 -1760.4601 -3.0343399 -5276.8399 -1.5061313 2.6517693 593.88997 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1060 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: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7913 ave 7913 max 7913 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113694 ave 113694 max 113694 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227388 ave 227388 max 227388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227388 Ave neighs/atom = 214.517 Neighbor list builds = 0 Dangerous builds = 0 1060 -3607.87190934217 eV 2.65176929949815 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00