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 -69.696 0) to (42.6777 69.696 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.93552 4.97803 5.74814 Created 2358 atoms create_atoms CPU = 0.0010941 secs 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.93552 4.97803 5.74814 Created 2358 atoms create_atoms CPU = 0.000951052 secs 2358 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 11 34 3 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 4668 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 13.18 | 13.18 | 13.18 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20678.478 0 -20678.478 -1045.5034 23 0 -20709.355 0 -20709.355 -6221.2737 Loop time of 0.824094 on 1 procs for 23 steps with 4668 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20678.4775936 -20709.3370597 -20709.3547251 Force two-norm initial, final = 23.4859 0.415917 Force max component initial, final = 3.59187 0.0184759 Final line search alpha, max atom move = 1 0.0184759 Iterations, force evaluations = 23 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81534 | 0.81534 | 0.81534 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0044141 | 0.0044141 | 0.0044141 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004338 | | | 0.53 Nlocal: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16404 ave 16404 max 16404 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: 1.0362e+06 ave 1.0362e+06 max 1.0362e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1036200 Ave neighs/atom = 221.979 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 : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.18 | 13.18 | 13.18 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -20709.355 0 -20709.355 -6221.2737 51292.902 25 0 -20709.564 0 -20709.564 -1708.5617 51162.468 Loop time of 0.0693901 on 1 procs for 2 steps with 4668 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20709.3547251 -20709.5528514 -20709.5642841 Force two-norm initial, final = 233.315 8.15372 Force max component initial, final = 168.589 6.75958 Final line search alpha, max atom move = 2.22351e-05 0.0001503 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.067623 | 0.067623 | 0.067623 | 0.0 | 97.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033975 | 0.00033975 | 0.00033975 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001427 | | | 2.06 Nlocal: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16452 ave 16452 max 16452 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: 1.03375e+06 ave 1.03375e+06 max 1.03375e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1033752 Ave neighs/atom = 221.455 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 12.69 | 12.69 | 12.69 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20709.564 0 -20709.564 -1708.5617 Loop time of 1.19209e-06 on 1 procs for 0 steps with 4668 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: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16452 ave 16452 max 16452 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: 1.03459e+06 ave 1.03459e+06 max 1.03459e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1034592 Ave neighs/atom = 221.635 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) = 12.69 | 12.69 | 12.69 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 -20709.564 -20709.564 42.619871 139.39193 8.6119544 -1708.5617 -1708.5617 -141.89461 -5195.2184 211.42777 2.1967203 1699.0208 Loop time of 1.19209e-06 on 1 procs for 0 steps with 4668 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: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16452 ave 16452 max 16452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 517296 ave 517296 max 517296 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.03459e+06 ave 1.03459e+06 max 1.03459e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1034592 Ave neighs/atom = 221.635 Neighbor list builds = 0 Dangerous builds = 0 4668 -20604.3175177325 eV 2.19672032886152 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01