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 = 3.6583 3.6583 3.6583 Created orthogonal box = (0 -45.1062 0) to (15.9461 45.1062 5.17361) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8749 4.74763 5.17361 Created 306 atoms create_atoms CPU = 0.000267982 secs 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8749 4.74763 5.17361 Created 306 atoms create_atoms CPU = 0.000149012 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 23 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 604 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 ghost atom cutoff = 8 binsize = 4, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2373.2096 0 -2373.2096 43316.851 382 0 -2443.1537 0 -2443.1537 -73661.106 Loop time of 1.84598 on 1 procs for 382 steps with 604 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2373.20955371 -2443.15128379 -2443.1537064 Force two-norm initial, final = 140.275 0.157736 Force max component initial, final = 32.0882 0.0206056 Final line search alpha, max atom move = 1 0.0206056 Iterations, force evaluations = 382 736 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.791 | 1.791 | 1.791 | 0.0 | 97.02 Neigh | 0.018301 | 0.018301 | 0.018301 | 0.0 | 0.99 Comm | 0.024235 | 0.024235 | 0.024235 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0124 | | | 0.67 Nlocal: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5245 ave 5245 max 5245 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: 102064 ave 102064 max 102064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102064 Ave neighs/atom = 168.98 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 : 382 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press Volume 382 0 -2443.1537 0 -2443.1537 -73661.106 7442.4421 418 0 -2455.5006 0 -2455.5006 3155.4534 7055.3314 Loop time of 0.0931799 on 1 procs for 36 steps with 604 atoms 96.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2443.1537064 -2455.49972431 -2455.50056953 Force two-norm initial, final = 597.111 3.9295 Force max component initial, final = 475.031 2.90879 Final line search alpha, max atom move = 0.000434858 0.00126491 Iterations, force evaluations = 36 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.088497 | 0.088497 | 0.088497 | 0.0 | 94.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010891 | 0.0010891 | 0.0010891 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003594 | | | 3.86 Nlocal: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5188 ave 5188 max 5188 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: 102156 ave 102156 max 102156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102156 Ave neighs/atom = 169.132 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 ghost atom cutoff = 8 binsize = 4, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2455.5006 0 -2455.5006 3155.4534 Loop time of 1.19209e-06 on 1 procs for 0 steps with 604 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: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5521 ave 5521 max 5521 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: 105324 ave 105324 max 105324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105324 Ave neighs/atom = 174.377 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) = 5.075 | 5.075 | 5.075 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 -2455.5006 -2455.5006 15.658405 90.212329 4.9946379 3155.4534 3155.4534 -648.6301 10313.32 -198.32921 2.2668136 2165.4277 Loop time of 1.90735e-06 on 1 procs for 0 steps with 604 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: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5521 ave 5521 max 5521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52662 ave 52662 max 52662 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105324 ave 105324 max 105324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105324 Ave neighs/atom = 174.377 Neighbor list builds = 0 Dangerous builds = 0 604 -2455.50056953387 eV 2.26681358590248 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02