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 -53.2703 0) to (26.6333 53.2703 3.65836) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.52264 4.52264 3.65836 Created 426 atoms create_atoms CPU = 0.000209093 secs 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.52264 4.52264 3.65836 Created 426 atoms create_atoms CPU = 7.98702e-05 secs 426 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 = 8 30 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 6 atoms, new total = 846 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 = 8 30 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) = 4.965 | 4.965 | 4.965 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3336.0562 0 -3336.0562 14797.56 187 0 -3379.6299 0 -3379.6299 -1847.9862 Loop time of 0.936515 on 1 procs for 187 steps with 846 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3336.0562345 -3379.62666907 -3379.62989555 Force two-norm initial, final = 40.9202 0.177162 Force max component initial, final = 9.41244 0.0285111 Final line search alpha, max atom move = 1 0.0285111 Iterations, force evaluations = 187 359 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90969 | 0.90969 | 0.90969 | 0.0 | 97.14 Neigh | 0.0053542 | 0.0053542 | 0.0053542 | 0.0 | 0.57 Comm | 0.013845 | 0.013845 | 0.013845 | 0.0 | 1.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00763 | | | 0.81 Nlocal: 846 ave 846 max 846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6629 ave 6629 max 6629 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: 115192 ave 115192 max 115192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115192 Ave neighs/atom = 136.161 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 : 187 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.965 | 4.965 | 4.965 Mbytes Step Temp E_pair E_mol TotEng Press Volume 187 0 -3379.6299 0 -3379.6299 -1847.9862 10380.702 244 0 -3386.6016 0 -3386.6016 -7826.4238 10380.366 Loop time of 0.147463 on 1 procs for 57 steps with 846 atoms 101.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3379.62989555 -3386.59880137 -3386.60161319 Force two-norm initial, final = 260.859 6.0132 Force max component initial, final = 237.231 5.01651 Final line search alpha, max atom move = 0.00037758 0.00189413 Iterations, force evaluations = 57 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13662 | 0.13662 | 0.13662 | 0.0 | 92.64 Neigh | 0.0022409 | 0.0022409 | 0.0022409 | 0.0 | 1.52 Comm | 0.0020618 | 0.0020618 | 0.0020618 | 0.0 | 1.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006545 | | | 4.44 Nlocal: 846 ave 846 max 846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6729 ave 6729 max 6729 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: 117238 ave 117238 max 117238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117238 Ave neighs/atom = 138.579 Neighbor list builds = 1 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 = 8 30 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) = 5.103 | 5.103 | 5.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3386.6016 0 -3386.6016 -7826.4238 Loop time of 9.53674e-07 on 1 procs for 0 steps with 846 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: 846 ave 846 max 846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6729 ave 6729 max 6729 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: 117252 ave 117252 max 117252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117252 Ave neighs/atom = 138.596 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) = 5.103 | 5.103 | 5.103 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 -3386.6016 -3386.6016 25.652881 106.54051 3.7980595 -7826.4238 -7826.4238 163.5405 -24446.661 803.84908 2.2586273 549.75995 Loop time of 9.53674e-07 on 1 procs for 0 steps with 846 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: 846 ave 846 max 846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6729 ave 6729 max 6729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58626 ave 58626 max 58626 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117252 ave 117252 max 117252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117252 Ave neighs/atom = 138.596 Neighbor list builds = 0 Dangerous builds = 0 846 -3386.60161318745 eV 2.25862727040642 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01