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 = 3.51812 3.51812 3.51812 Created orthogonal box = (0 -56.7315 0) to (28.364 56.7315 3.51812) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.80006 4.80006 3.51812 Created 521 atoms create_atoms CPU = 0.000335932 secs 521 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.80006 4.80006 3.51812 Created 521 atoms create_atoms CPU = 0.000181198 secs 521 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 24 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 6 atoms, new total = 1036 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 24 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) = 5.854 | 5.854 | 5.854 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4487.6817 0 -4487.6817 25625.079 35 0 -4527.1527 0 -4527.1527 901.12122 Loop time of 0.45329 on 1 procs for 35 steps with 1036 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4487.68170298 -4527.14833196 -4527.15272097 Force two-norm initial, final = 73.711 0.210864 Force max component initial, final = 23.7706 0.0418334 Final line search alpha, max atom move = 1 0.0418334 Iterations, force evaluations = 35 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44108 | 0.44108 | 0.44108 | 0.0 | 97.31 Neigh | 0.0069499 | 0.0069499 | 0.0069499 | 0.0 | 1.53 Comm | 0.0036232 | 0.0036232 | 0.0036232 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001636 | | | 0.36 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11144 ave 11144 max 11144 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: 334576 ave 334576 max 334576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334576 Ave neighs/atom = 322.95 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.855 | 5.855 | 5.855 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -4527.1527 0 -4527.1527 901.12122 11322.247 36 0 -4527.1528 0 -4527.1528 681.96627 11323.66 Loop time of 0.021786 on 1 procs for 1 steps with 1036 atoms 91.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4527.15272097 -4527.15272097 -4527.15283292 Force two-norm initial, final = 2.37664 0.786686 Force max component initial, final = 2.15441 0.700715 Final line search alpha, max atom move = 0.000464164 0.000325246 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021271 | 0.021271 | 0.021271 | 0.0 | 97.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001719 | 0.0001719 | 0.0001719 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003431 | | | 1.57 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11120 ave 11120 max 11120 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: 334904 ave 334904 max 334904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334904 Ave neighs/atom = 323.266 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 24 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) = 5.992 | 5.992 | 5.992 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4527.1528 0 -4527.1528 681.96627 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1036 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: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11120 ave 11120 max 11120 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: 334880 ave 334880 max 334880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334880 Ave neighs/atom = 323.243 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) = 5.992 | 5.992 | 5.992 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 -4527.1528 -4527.1528 28.365106 113.46303 3.5184227 681.96627 681.96627 -99.1475 2104.1582 40.888135 2.1788432 330.87904 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1036 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: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11120 ave 11120 max 11120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167440 ave 167440 max 167440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 334880 ave 334880 max 334880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334880 Ave neighs/atom = 323.243 Neighbor list builds = 0 Dangerous builds = 0 1036 -4527.15283291673 eV 2.17884319119038 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00