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 = 3.65836 3.65836 3.65836 Created orthogonal box = (0 -39.0643 0) to (22.5517 39.0643 6.33647) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.93465 5.4822 6.33647 Created 458 atoms create_atoms CPU = 0.000340939 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.93465 5.4822 6.33647 Created 458 atoms create_atoms CPU = 0.000241041 secs 458 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 22 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 900 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3560.7377 0 -3560.7377 711.61328 260 0 -3624.902 0 -3624.902 -64384.048 Loop time of 1.50514 on 1 procs for 260 steps with 900 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3560.73771624 -3624.89912215 -3624.90196718 Force two-norm initial, final = 23.9848 0.171361 Force max component initial, final = 6.51783 0.0297045 Final line search alpha, max atom move = 1 0.0297045 Iterations, force evaluations = 260 500 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4555 | 1.4555 | 1.4555 | 0.0 | 96.70 Neigh | 0.020065 | 0.020065 | 0.020065 | 0.0 | 1.33 Comm | 0.017759 | 0.017759 | 0.017759 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01178 | | | 0.78 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4940 ave 4940 max 4940 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: 121304 ave 121304 max 121304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121304 Ave neighs/atom = 134.782 Neighbor list builds = 6 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 : 260 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 260 0 -3624.902 0 -3624.902 -64384.048 11164.43 292 0 -3633.6443 0 -3633.6443 -15903.637 10748.833 Loop time of 0.0783 on 1 procs for 32 steps with 900 atoms 102.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3624.90196718 -3633.64280643 -3633.64429737 Force two-norm initial, final = 573.704 2.27591 Force max component initial, final = 483.11 1.32859 Final line search alpha, max atom move = 0.000149785 0.000199003 Iterations, force evaluations = 32 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.074487 | 0.074487 | 0.074487 | 0.0 | 95.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085235 | 0.00085235 | 0.00085235 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00296 | | | 3.78 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4932 ave 4932 max 4932 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: 121116 ave 121116 max 121116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121116 Ave neighs/atom = 134.573 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.126 | 5.126 | 5.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3633.6443 0 -3633.6443 -15903.637 Loop time of 9.53674e-07 on 1 procs for 0 steps with 900 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: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5013 ave 5013 max 5013 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: 127108 ave 127108 max 127108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127108 Ave neighs/atom = 141.231 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) = 5.126 | 5.126 | 5.126 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 -3633.6443 -3633.6443 21.877433 78.128611 6.288613 -15903.637 -15903.637 32.643084 -47547.015 -196.53798 2.2588603 2664.8775 Loop time of 1.19209e-06 on 1 procs for 0 steps with 900 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: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5013 ave 5013 max 5013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63554 ave 63554 max 63554 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127108 ave 127108 max 127108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127108 Ave neighs/atom = 141.231 Neighbor list builds = 0 Dangerous builds = 0 900 -3633.64429736576 eV 2.25886031080769 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01