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 = 3.17012 3.17012 3.17012 Created orthogonal box = (0 -46.1608 0) to (23.0788 46.1608 3.17012) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.91905 3.91905 3.17012 Created 213 atoms create_atoms CPU = 0.00019908 secs 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.91905 3.91905 3.17012 Created 213 atoms create_atoms CPU = 6.19888e-05 secs 213 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 7 26 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 7.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 420 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 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) = 4.463 | 4.463 | 4.463 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4510.5959 0 -4510.5959 -1226.7171 58 0 -4537.0387 0 -4537.0387 -11814.58 Loop time of 6.87006 on 1 procs for 58 steps with 420 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4510.59585855 -4537.03506083 -4537.03868407 Force two-norm initial, final = 63.4716 0.1912 Force max component initial, final = 24.5088 0.0480664 Final line search alpha, max atom move = 1 0.0480664 Iterations, force evaluations = 58 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8638 | 6.8638 | 6.8638 | 0.0 | 99.91 Neigh | 0.0022132 | 0.0022132 | 0.0022132 | 0.0 | 0.03 Comm | 0.0027499 | 0.0027499 | 0.0027499 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001294 | | | 0.02 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3922 ave 3922 max 3922 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: 45962 ave 45962 max 45962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45962 Ave neighs/atom = 109.433 Neighbor list builds = 2 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.463 | 4.463 | 4.463 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -4537.0387 0 -4537.0387 -11814.58 6754.5042 61 0 -4537.1312 0 -4537.1312 -2057.9482 6728.1439 Loop time of 0.344596 on 1 procs for 3 steps with 420 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4537.03868407 -4537.1308115 -4537.13119323 Force two-norm initial, final = 67.0852 1.30154 Force max component initial, final = 50.6493 1.25156 Final line search alpha, max atom move = 0.000260652 0.000326222 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34419 | 0.34419 | 0.34419 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010729 | 0.00010729 | 0.00010729 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002966 | | | 0.09 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3918 ave 3918 max 3918 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: 46084 ave 46084 max 46084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46084 Ave neighs/atom = 109.724 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 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) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4537.1312 0 -4537.1312 -2057.9482 Loop time of 1.90735e-06 on 1 procs for 0 steps with 420 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: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940 ave 3940 max 3940 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: 46118 ave 46118 max 46118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46118 Ave neighs/atom = 109.805 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) = 4.601 | 4.601 | 4.601 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 -4537.1312 -4537.1312 23.039228 92.321676 3.1631782 -2057.9482 -2057.9482 297.52419 -6415.2078 -56.161066 2.5118307 248.25557 Loop time of 9.53674e-07 on 1 procs for 0 steps with 420 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: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940 ave 3940 max 3940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23059 ave 23059 max 23059 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46118 ave 46118 max 46118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46118 Ave neighs/atom = 109.805 Neighbor list builds = 0 Dangerous builds = 0 420 -2762.44384977468 eV 2.51183070303281 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07