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 = 3.61473 3.61473 3.61473 Created orthogonal box = (0 -39.1029 0) to (13.0331 39.1029 3.61473) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.01273 5.01273 3.61473 Created 158 atoms create_atoms CPU = 0.000205994 secs 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.01273 5.01273 3.61473 Created 158 atoms create_atoms CPU = 7.20024e-05 secs 158 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 5 29 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 304 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.418 | 4.418 | 4.418 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1065.0183 0 -1065.0183 -6173.885 36 0 -1069.6482 0 -1069.6482 -22059.78 Loop time of 0.0755441 on 1 procs for 36 steps with 304 atoms 79.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -1065.01832214 -1069.64816947 -1069.64816947 Force two-norm initial, final = 2.47887 0.379305 Force max component initial, final = 0.711565 0.108036 Final line search alpha, max atom move = 5.5171e-08 5.96046e-09 Iterations, force evaluations = 36 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073076 | 0.073076 | 0.073076 | 0.0 | 96.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016406 | 0.0016406 | 0.0016406 | 0.0 | 2.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008278 | | | 1.10 Nlocal: 304 ave 304 max 304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2220 ave 2220 max 2220 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: 16096 ave 16096 max 16096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16096 Ave neighs/atom = 52.9474 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.418 | 4.418 | 4.418 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -1069.6482 0 -1069.6482 -22059.78 3684.362 43 0 -1069.8722 0 -1069.8722 -7154.7132 3642.7398 Loop time of 0.00607514 on 1 procs for 7 steps with 304 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1069.64816947 -1069.87121808 -1069.87218385 Force two-norm initial, final = 55.2394 0.53735 Force max component initial, final = 39.4448 0.308044 Final line search alpha, max atom move = 0.000765407 0.000235779 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0055473 | 0.0055473 | 0.0055473 | 0.0 | 91.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013089 | 0.00013089 | 0.00013089 | 0.0 | 2.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000397 | | | 6.53 Nlocal: 304 ave 304 max 304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2274 ave 2274 max 2274 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: 16348 ave 16348 max 16348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16348 Ave neighs/atom = 53.7763 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.557 | 4.557 | 4.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 1055.0898 0 1055.0898 -7154.7132 Loop time of 9.53674e-07 on 1 procs for 0 steps with 304 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: 304 ave 304 max 304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2292 ave 2292 max 2292 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: 16360 ave 16360 max 16360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16360 Ave neighs/atom = 53.8158 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) = 4.557 | 4.557 | 4.557 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 1055.0898 -1069.8722 12.972729 78.205793 3.5905245 -7154.7132 -7154.7132 -134.85843 -21249.968 -79.313262 2.2747026 115.03543 Loop time of 1.19209e-06 on 1 procs for 0 steps with 304 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: 304 ave 304 max 304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2292 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8180 ave 8180 max 8180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16360 ave 16360 max 16360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16360 Ave neighs/atom = 53.8158 Neighbor list builds = 0 Dangerous builds = 0 304 1055.08976102448 eV 2.27470262222179 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00