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 = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -33.5394 0) to (23.7137 33.5394 4.44199) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4084 5.29521 4.44199 Created 229 atoms create_atoms CPU = 0.000211 secs 229 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4084 5.29521 4.44199 Created 229 atoms create_atoms CPU = 9.799e-05 secs 229 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 5 12 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 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 451 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 5 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 4.925 | 4.925 | 4.925 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2874.3966 0 -2874.3966 58523.777 312 0 -3056.907 0 -3056.907 -27503.093 Loop time of 2.64307 on 1 procs for 312 steps with 451 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2874.39657537 -3056.90492577 -3056.90704765 Force two-norm initial, final = 248.19 0.385786 Force max component initial, final = 78.338 0.189061 Final line search alpha, max atom move = 0.700524 0.132442 Iterations, force evaluations = 312 574 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5632 | 2.5632 | 2.5632 | 0.0 | 96.98 Neigh | 0.048408 | 0.048408 | 0.048408 | 0.0 | 1.83 Comm | 0.023129 | 0.023129 | 0.023129 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00831 | | | 0.31 Nlocal: 451 ave 451 max 451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6743 ave 6743 max 6743 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: 183836 ave 183836 max 183836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183836 Ave neighs/atom = 407.619 Neighbor list builds = 13 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 : 312 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.925 | 4.925 | 4.925 Mbytes Step Temp E_pair E_mol TotEng Press Volume 312 0 -3056.907 0 -3056.907 -27503.093 7065.8417 349 0 -3071.3294 0 -3071.3294 -14465.911 7013.2793 Loop time of 0.167004 on 1 procs for 37 steps with 451 atoms 101.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3056.90704765 -3071.32661777 -3071.32940904 Force two-norm initial, final = 668.01 6.49173 Force max component initial, final = 490.462 4.00161 Final line search alpha, max atom move = 0.000140638 0.000562779 Iterations, force evaluations = 37 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16213 | 0.16213 | 0.16213 | 0.0 | 97.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013077 | 0.0013077 | 0.0013077 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003564 | | | 2.13 Nlocal: 451 ave 451 max 451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6689 ave 6689 max 6689 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: 183742 ave 183742 max 183742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183742 Ave neighs/atom = 407.41 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 5.063 | 5.063 | 5.063 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3071.3294 0 -3071.3294 -14465.911 Loop time of 0 on 1 procs for 0 steps with 451 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 | | 0 | | | 0.00 Nlocal: 451 ave 451 max 451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6839 ave 6839 max 6839 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: 186168 ave 186168 max 186168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186168 Ave neighs/atom = 412.789 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) = 5.063 | 5.063 | 5.063 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 -3071.3294 -3071.3294 22.956094 67.078893 4.5544637 -14465.911 -14465.911 -230.9726 -42229.45 -937.3094 2.3526739 2718.3429 Loop time of 9.53674e-07 on 1 procs for 0 steps with 451 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: 451 ave 451 max 451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6839 ave 6839 max 6839 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93084 ave 93084 max 93084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186168 ave 186168 max 186168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186168 Ave neighs/atom = 412.789 Neighbor list builds = 0 Dangerous builds = 0 451 -3071.32940904431 eV 2.3526739035107 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02