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 = 3.56201 3.56201 3.56201 Created orthogonal box = (0 -43.9189 0) to (15.5264 43.9189 5.03744) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.72026 4.62267 5.03744 Created 306 atoms create_atoms CPU = 0.000256062 secs 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.72026 4.62267 5.03744 Created 306 atoms create_atoms CPU = 0.000144005 secs 306 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 5 25 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 606 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2571.9073 0 -2571.9073 65869.62 33 0 -2656.9711 0 -2656.9711 6344.9254 Loop time of 0.122694 on 1 procs for 33 steps with 606 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2571.90730849 -2656.96871824 -2656.97113061 Force two-norm initial, final = 129.454 0.239369 Force max component initial, final = 29.3881 0.0545135 Final line search alpha, max atom move = 1 0.0545135 Iterations, force evaluations = 33 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11984 | 0.11984 | 0.11984 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018764 | 0.0018764 | 0.0018764 | 0.0 | 1.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009799 | | | 0.80 Nlocal: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4866 ave 4866 max 4866 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: 84344 ave 84344 max 84344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84344 Ave neighs/atom = 139.182 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 : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -2656.9711 0 -2656.9711 6344.9254 6870.1044 37 0 -2657.0116 0 -2657.0116 3843.3763 6879.8284 Loop time of 0.014513 on 1 procs for 4 steps with 606 atoms 68.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2656.97113061 -2657.01149461 -2657.01157823 Force two-norm initial, final = 28.4446 0.432506 Force max component initial, final = 28.1986 0.10301 Final line search alpha, max atom move = 0.000860522 8.86427e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.013646 | 0.013646 | 0.013646 | 0.0 | 94.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020099 | 0.00020099 | 0.00020099 | 0.0 | 1.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006664 | | | 4.59 Nlocal: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4858 ave 4858 max 4858 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: 83972 ave 83972 max 83972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83972 Ave neighs/atom = 138.568 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.681 | 4.681 | 4.681 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2657.0116 0 -2657.0116 3843.3763 Loop time of 1.19209e-06 on 1 procs for 0 steps with 606 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: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4858 ave 4858 max 4858 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: 83956 ave 83956 max 83956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83956 Ave neighs/atom = 138.541 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) = 4.681 | 4.681 | 4.681 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 -2657.0116 -2657.0116 15.568439 87.837882 5.030958 3843.3763 3843.3763 14.875086 11491.296 23.95823 2.3814199 352.28218 Loop time of 1.19209e-06 on 1 procs for 0 steps with 606 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: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4858 ave 4858 max 4858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41978 ave 41978 max 41978 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 83956 ave 83956 max 83956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83956 Ave neighs/atom = 138.541 Neighbor list builds = 0 Dangerous builds = 0 606 -2657.0115782287 eV 2.38141992982597 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00