LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8553126 2.8553126 2.8553126 Created orthogonal box = (0.0000000 -46.393338 0.0000000) to (9.4700005 46.393338 6.9940589) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3045457 4.2175762 4.6627059 Created 263 atoms using lattice units in orthogonal box = (0.0000000 -46.393338 0.0000000) to (9.4700005 46.393338 6.9940589) create_atoms CPU = 0.001 seconds 263 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3045457 4.2175762 4.6627059 Created 265 atoms using lattice units in orthogonal box = (0.0000000 -46.393338 0.0000000) to (9.4700005 46.393338 6.9940589) create_atoms CPU = 0.000 seconds 265 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 528 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_577453891941_005#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.980 | 4.980 | 4.980 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1147.4483 0 -1147.4483 347053.74 117 0 -2108.0845 0 -2108.0845 7666.2189 Loop time of 1.6365 on 1 procs for 117 steps with 528 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1147.4482892596 -2108.08259223214 -2108.0844877716 Force two-norm initial, final = 2952.9924 0.15864947 Force max component initial, final = 878.82891 0.026742845 Final line search alpha, max atom move = 1.0000000 0.026742845 Iterations, force evaluations = 117 223 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6096 | 1.6096 | 1.6096 | 0.0 | 98.35 Neigh | 0.0077192 | 0.0077192 | 0.0077192 | 0.0 | 0.47 Comm | 0.011725 | 0.011725 | 0.011725 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007498 | | | 0.46 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5527.00 ave 5527 max 5527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119068.0 ave 119068 max 119068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119068 Ave neighs/atom = 225.50758 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.978 | 4.978 | 4.978 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -2108.0845 0 -2108.0845 7666.2189 6145.6087 124 0 -2108.2562 0 -2108.2562 -88.356985 6173.3227 Loop time of 0.0673018 on 1 procs for 7 steps with 528 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 = -2108.0844877716 -2108.25616666102 -2108.25624664324 Force two-norm initial, final = 63.603014 0.81273483 Force max component initial, final = 59.781669 0.73627780 Final line search alpha, max atom move = 0.00090317506 0.00066498774 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065259 | 0.065259 | 0.065259 | 0.0 | 96.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036442 | 0.00036442 | 0.00036442 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001678 | | | 2.49 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5214.00 ave 5214 max 5214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119370.0 ave 119370 max 119370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119370 Ave neighs/atom = 226.07955 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.116 | 5.116 | 5.116 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2108.2562 0 -2108.2562 -88.356985 Loop time of 1.792e-06 on 1 procs for 0 steps with 528 atoms 111.6% 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 | | 1.792e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5214.00 ave 5214 max 5214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119042.0 ave 119042 max 119042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119042 Ave neighs/atom = 225.45833 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.116 | 5.116 | 5.116 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 -2108.2562 -2108.2562 9.4667327 93.349269 6.985668 -88.356985 -88.356985 -191.02192 -45.803234 -28.245803 2.272076 329.68595 Loop time of 2.27e-06 on 1 procs for 0 steps with 528 atoms 220.3% 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 | | 2.27e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5214.00 ave 5214 max 5214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59521.0 ave 59521 max 59521 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119042.0 ave 119042 max 119042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119042 Ave neighs/atom = 225.45833 Neighbor list builds = 0 Dangerous builds = 0 528 -2108.25624664324 eV 2.27207603911257 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02