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 = 4.04093 4.04093 4.04093 Created orthogonal box = (0 -48.9977 0) to (40.0031 48.9977 9.89821) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.71473 5.66593 6.59881 Created 1183 atoms create_atoms CPU = 0.000319958 secs 1183 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.71473 5.66593 6.59881 Created 1183 atoms create_atoms CPU = 0.000252962 secs 1183 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 47 atoms, new total = 2319 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 6.931 | 6.931 | 6.931 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9005.6246 0 -9005.6246 -442.52753 43 0 -9028.6091 0 -9028.6091 -4741.6179 Loop time of 1.19691 on 1 procs for 43 steps with 2319 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 = -9005.62463472 -9028.60110418 -9028.60905185 Force two-norm initial, final = 21.2592 0.201772 Force max component initial, final = 3.99311 0.0372302 Final line search alpha, max atom move = 1 0.0372302 Iterations, force evaluations = 43 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1704 | 1.1704 | 1.1704 | 0.0 | 97.79 Neigh | 0.015875 | 0.015875 | 0.015875 | 0.0 | 1.33 Comm | 0.006187 | 0.006187 | 0.006187 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004405 | | | 0.37 Nlocal: 2319 ave 2319 max 2319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10565 ave 10565 max 10565 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: 568798 ave 568798 max 568798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 568798 Ave neighs/atom = 245.277 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 : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.931 | 6.931 | 6.931 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -9028.6091 0 -9028.6091 -4741.6179 38802.168 47 0 -9028.8524 0 -9028.8524 -1007.8146 38625.051 Loop time of 0.0898139 on 1 procs for 4 steps with 2319 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9028.60905185 -9028.851875 -9028.8524466 Force two-norm initial, final = 147.186 0.219825 Force max component initial, final = 114.403 0.0422928 Final line search alpha, max atom move = 0.00027986 1.18361e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087982 | 0.087982 | 0.087982 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040412 | 0.00040412 | 0.00040412 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001428 | | | 1.59 Nlocal: 2319 ave 2319 max 2319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10569 ave 10569 max 10569 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: 568620 ave 568620 max 568620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 568620 Ave neighs/atom = 245.201 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 7.069 | 7.069 | 7.069 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9028.8524 0 -9028.8524 -1007.8146 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2319 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: 2319 ave 2319 max 2319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10581 ave 10581 max 10581 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: 569014 ave 569014 max 569014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 569014 Ave neighs/atom = 245.37 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) = 7.069 | 7.069 | 7.069 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 -9028.8524 -9028.8524 39.932824 97.995341 9.8703741 -1007.8146 -1007.8146 -1.7512327 -3020.7479 -0.94470923 2.5668901 1841.2142 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2319 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: 2319 ave 2319 max 2319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10581 ave 10581 max 10581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 284507 ave 284507 max 284507 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 569014 ave 569014 max 569014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 569014 Ave neighs/atom = 245.37 Neighbor list builds = 0 Dangerous builds = 0 2319 -9028.85244659532 eV 2.56689008830252 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01