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 = 3.63909 3.63909 3.63909 Created orthogonal box = (0 -51.4681 0) to (25.7322 51.4681 3.63909) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.11715 4.11715 3.63909 Created 402 atoms create_atoms CPU = 0.000159025 secs 402 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.11715 4.11715 3.63909 Created 402 atoms create_atoms CPU = 7.00951e-05 secs 402 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 22 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.416 | 5.416 | 5.416 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2590.8781 0 -2590.8781 6320.6839 21 0 -2603.6922 0 -2603.6922 -1370.8181 Loop time of 0.189217 on 1 procs for 21 steps with 796 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2590.87806531 -2603.69024845 -2603.69219467 Force two-norm initial, final = 24.6862 0.105201 Force max component initial, final = 6.6482 0.0114332 Final line search alpha, max atom move = 1 0.0114332 Iterations, force evaluations = 21 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18655 | 0.18655 | 0.18655 | 0.0 | 98.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018311 | 0.0018311 | 0.0018311 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008328 | | | 0.44 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9923 ave 9923 max 9923 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: 252344 ave 252344 max 252344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252344 Ave neighs/atom = 317.015 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 : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.416 | 5.416 | 5.416 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -2603.6922 0 -2603.6922 -1370.8181 9639.1189 25 0 -2603.7149 0 -2603.7149 -428.53145 9633.3038 Loop time of 0.0486031 on 1 procs for 4 steps with 796 atoms 82.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2603.69219467 -2603.71293041 -2603.71487257 Force two-norm initial, final = 13.9052 0.128738 Force max component initial, final = 13.7103 0.0217742 Final line search alpha, max atom move = 0.000132293 2.88058e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.047106 | 0.047106 | 0.047106 | 0.0 | 96.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038123 | 0.00038123 | 0.00038123 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001116 | | | 2.30 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9923 ave 9923 max 9923 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: 252824 ave 252824 max 252824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252824 Ave neighs/atom = 317.618 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.554 | 5.554 | 5.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2603.7149 0 -2603.7149 -428.53145 Loop time of 1.19209e-06 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 | | 1.192e-06 | | |100.00 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9923 ave 9923 max 9923 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: 252696 ave 252696 max 252696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252696 Ave neighs/atom = 317.457 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) = 5.554 | 5.554 | 5.554 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 -2603.7149 -2603.7149 25.791257 102.93615 3.6285644 -428.53145 -428.53145 -0.29057961 -1288.9147 3.6109369 2.3147393 199.50646 Loop time of 1.19209e-06 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 | | 1.192e-06 | | |100.00 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9923 ave 9923 max 9923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126348 ave 126348 max 126348 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 252696 ave 252696 max 252696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252696 Ave neighs/atom = 317.457 Neighbor list builds = 0 Dangerous builds = 0 796 -2603.71487256735 eV 2.31473926807112 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00