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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -51.913000 0.0000000) to (18.354017 51.913000 5.9548295) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7620063 5.4645263 5.9548295 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -51.913000 0.0000000) to (18.354017 51.913000 5.9548295) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7620063 5.4645263 5.9548295 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -51.913000 0.0000000) to (18.354017 51.913000 5.9548295) create_atoms CPU = 0.001 seconds 306 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 24 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 610 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_878712978062_003#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.932 | 4.932 | 4.932 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1930.4389 0 -1930.4389 127616.81 83 0 -2271.3967 0 -2271.3967 3244.9873 Loop time of 1.27851 on 1 procs for 83 steps with 610 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 = -1930.4389146985 -2271.39453243407 -2271.39672871798 Force two-norm initial, final = 1913.5415 0.087488694 Force max component initial, final = 819.51616 0.018527411 Final line search alpha, max atom move = 1.0000000 0.018527411 Iterations, force evaluations = 83 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.254 | 1.254 | 1.254 | 0.0 | 98.08 Neigh | 0.012027 | 0.012027 | 0.012027 | 0.0 | 0.94 Comm | 0.007033 | 0.007033 | 0.007033 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005467 | | | 0.43 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5094.00 ave 5094 max 5094 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: 105100.0 ave 105100 max 105100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105100 Ave neighs/atom = 172.29508 Neighbor list builds = 2 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.932 | 4.932 | 4.932 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -2271.3967 0 -2271.3967 3244.9873 11347.667 90 0 -2271.5081 0 -2271.5081 -37.492418 11437.191 Loop time of 0.0763076 on 1 procs for 7 steps with 610 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 = -2271.39672871798 -2271.50761809404 -2271.50805385337 Force two-norm initial, final = 40.883516 0.66368951 Force max component initial, final = 30.551152 0.49098972 Final line search alpha, max atom move = 0.00038896867 0.00019097962 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.074235 | 0.074235 | 0.074235 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036522 | 0.00036522 | 0.00036522 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001707 | | | 2.24 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5078.00 ave 5078 max 5078 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: 104708.0 ave 104708 max 104708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104708 Ave neighs/atom = 171.65246 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2271.5081 0 -2271.5081 -37.492418 Loop time of 1.85e-06 on 1 procs for 0 steps with 610 atoms 162.2% 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 | | 1.85e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5078.00 ave 5078 max 5078 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: 104192.0 ave 104192 max 104192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104192 Ave neighs/atom = 170.80656 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.070 | 5.070 | 5.070 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 -2271.5081 -2271.5081 18.359215 104.49059 5.9619465 -37.492418 -37.492418 -57.733983 14.119123 -68.862395 2.7725353 1170.8303 Loop time of 2.088e-06 on 1 procs for 0 steps with 610 atoms 239.5% 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 | | 2.088e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5078.00 ave 5078 max 5078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52096.0 ave 52096 max 52096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 104192.0 ave 104192 max 104192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104192 Ave neighs/atom = 170.80656 Neighbor list builds = 0 Dangerous builds = 0 610 -2271.50805385337 eV 2.77253531903155 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01