LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.86934 3.86934 3.86934 Created orthogonal box = (0 -38.8902 0) to (38.8864 38.8902 3.86934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.23515 4.23515 3.86934 Created 406 atoms create_atoms CPU = 0.000202179 secs 406 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.23515 4.23515 3.86934 Created 406 atoms create_atoms CPU = 5.98431e-05 secs 406 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 10 19 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 8.19533 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 796 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 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) = 4.953 | 4.953 | 4.953 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2514.7702 0 -2514.7702 2289.539 343 0 -2539.2946 0 -2539.2946 -12447 Loop time of 2.00392 on 1 procs for 343 steps with 796 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 = -2514.77021114 -2539.29463478 -2539.29463478 Force two-norm initial, final = 42.573 1.00063e-05 Force max component initial, final = 14.3189 1.69312e-06 Final line search alpha, max atom move = 1 1.69312e-06 Iterations, force evaluations = 343 680 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.964 | 1.964 | 1.964 | 0.0 | 98.01 Neigh | 0.0048051 | 0.0048051 | 0.0048051 | 0.0 | 0.24 Comm | 0.023346 | 0.023346 | 0.023346 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0118 | | | 0.59 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6158 ave 6158 max 6158 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: 116780 ave 116780 max 116780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116780 Ave neighs/atom = 146.709 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 : 343 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press Volume 343 0 -2539.2946 0 -2539.2946 -12447 11703.19 1343 0 -2539.5277 0 -2539.5277 -3290.5217 11628.717 Loop time of 5.96416 on 1 procs for 1000 steps with 796 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2539.29463478 -2539.52769662 -2539.52769663 Force two-norm initial, final = 102.348 0.00684681 Force max component initial, final = 74.3189 0.00555599 Final line search alpha, max atom move = 0.0672245 0.000373499 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6996 | 5.6996 | 5.6996 | 0.0 | 95.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.061811 | 0.061811 | 0.061811 | 0.0 | 1.04 Output | 1.812e-05 | 1.812e-05 | 1.812e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2027 | | | 3.40 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6163 ave 6163 max 6163 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: 116792 ave 116792 max 116792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116792 Ave neighs/atom = 146.724 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 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) = 5.092 | 5.092 | 5.092 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2539.5277 0 -2539.5277 -3290.5217 Loop time of 9.53674e-07 on 1 procs for 0 steps with 796 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: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6173 ave 6173 max 6173 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: 123928 ave 123928 max 123928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123928 Ave neighs/atom = 155.688 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.092 | 5.092 | 5.092 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 -2539.5277 -2539.5277 38.742601 77.78045 3.8589805 -3290.5217 -3290.5217 0.76266138 -9872.373 0.04520613 2.5079826 211.44038 Loop time of 9.53674e-07 on 1 procs for 0 steps with 796 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: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6173 ave 6173 max 6173 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61964 ave 61964 max 61964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 123928 ave 123928 max 123928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123928 Ave neighs/atom = 155.688 Neighbor list builds = 0 Dangerous builds = 0 796 -2539.52769662919 eV 2.5079825832095 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08