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 = 3.52 3.52 3.52 Created orthogonal box = (0 -67.3451 0) to (38.8797 67.3451 6.09682) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.73634 5.15181 6.09682 Created 1466 atoms create_atoms CPU = 0.00061202 secs 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.73634 5.15181 6.09682 Created 1466 atoms create_atoms CPU = 0.00048089 secs 1466 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.90187, bins = 10 35 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2904 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.90187, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12838.845 0 -12838.845 -2169.4608 56 0 -12877.216 0 -12877.216 -8382.516 Loop time of 1.18878 on 1 procs for 56 steps with 2904 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12838.8453688 -12877.2041201 -12877.215884 Force two-norm initial, final = 27.5694 0.485983 Force max component initial, final = 4.68019 0.12909 Final line search alpha, max atom move = 0.724491 0.0935248 Iterations, force evaluations = 56 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1617 | 1.1617 | 1.1617 | 0.0 | 97.72 Neigh | 0.010555 | 0.010555 | 0.010555 | 0.0 | 0.89 Comm | 0.009712 | 0.009712 | 0.009712 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006825 | | | 0.57 Nlocal: 2904 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12224 ave 12224 max 12224 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: 511444 ave 511444 max 511444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 511444 Ave neighs/atom = 176.117 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -12877.216 0 -12877.216 -8382.516 31927.254 59 0 -12877.376 0 -12877.376 -3481.716 31843.508 Loop time of 0.0559781 on 1 procs for 3 steps with 2904 atoms 107.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12877.215884 -12877.3752712 -12877.3764547 Force two-norm initial, final = 165.628 0.519171 Force max component initial, final = 134.177 0.116404 Final line search alpha, max atom move = 0.00010733 1.24937e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.054283 | 0.054283 | 0.054283 | 0.0 | 96.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037384 | 0.00037384 | 0.00037384 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001321 | | | 2.36 Nlocal: 2904 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12232 ave 12232 max 12232 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: 511228 ave 511228 max 511228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 511228 Ave neighs/atom = 176.043 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.90187, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.139 | 7.139 | 7.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12877.376 0 -12877.376 -3481.716 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2904 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: 2904 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12232 ave 12232 max 12232 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: 511516 ave 511516 max 511516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 511516 Ave neighs/atom = 176.142 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) = 7.139 | 7.139 | 7.139 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 -12877.376 -12877.376 38.810617 134.69015 6.0916441 -3481.716 -3481.716 -1.3996829 -10440.785 -2.9631851 2.2655786 860.45303 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2904 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: 2904 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12232 ave 12232 max 12232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 255758 ave 255758 max 255758 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 511516 ave 511516 max 511516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 511516 Ave neighs/atom = 176.142 Neighbor list builds = 0 Dangerous builds = 0 2904 -12877.3764546024 eV 2.26557860839911 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01