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 = 2.85528 2.85528 2.85528 Created orthogonal box = (0 -29.6758 0) to (20.9819 29.6758 4.03798) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.66265 3.84649 4.03798 Created 218 atoms create_atoms CPU = 0.000146866 secs 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.66265 3.84649 4.03798 Created 218 atoms create_atoms CPU = 9.29832e-05 secs 218 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 6 16 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 428 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 6 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 4.47 | 4.47 | 4.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1720.5244 0 -1720.5244 34223.445 18 0 -1749.9367 0 -1749.9367 -5509.2525 Loop time of 0.0595291 on 1 procs for 18 steps with 428 atoms 100.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1720.52441175 -1749.93560364 -1749.93667788 Force two-norm initial, final = 80.1652 0.108618 Force max component initial, final = 19.9477 0.0230882 Final line search alpha, max atom move = 1 0.0230882 Iterations, force evaluations = 18 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.058331 | 0.058331 | 0.058331 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075436 | 0.00075436 | 0.00075436 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004442 | | | 0.75 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3847 ave 3847 max 3847 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: 71432 ave 71432 max 71432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71432 Ave neighs/atom = 166.897 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.47 | 4.47 | 4.47 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -1749.9367 0 -1749.9367 -5509.2525 5028.5355 21 0 -1749.9622 0 -1749.9622 -803.16593 5014.9632 Loop time of 0.0124788 on 1 procs for 3 steps with 428 atoms 80.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1749.93667788 -1749.96194033 -1749.96221305 Force two-norm initial, final = 24.175 0.14026 Force max component initial, final = 21.2126 0.0217044 Final line search alpha, max atom move = 0.000547973 1.18934e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011841 | 0.011841 | 0.011841 | 0.0 | 94.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015092 | 0.00015092 | 0.00015092 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004871 | | | 3.90 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3847 ave 3847 max 3847 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: 71424 ave 71424 max 71424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71424 Ave neighs/atom = 166.879 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 6 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1749.9622 0 -1749.9622 -803.16593 Loop time of 9.53674e-07 on 1 procs for 0 steps with 428 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: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3847 ave 3847 max 3847 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: 71464 ave 71464 max 71464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71464 Ave neighs/atom = 166.972 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) = 4.608 | 4.608 | 4.608 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 -1749.9622 -1749.9622 20.968534 59.351585 4.0296504 -803.16593 -803.16593 -2.5088036 -2410.3826 3.3936463 2.2699755 327.09771 Loop time of 1.19209e-06 on 1 procs for 0 steps with 428 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: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3847 ave 3847 max 3847 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35732 ave 35732 max 35732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71464 ave 71464 max 71464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71464 Ave neighs/atom = 166.972 Neighbor list builds = 0 Dangerous builds = 0 428 -1749.96221305087 eV 2.26997546413056 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00