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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -68.305646 0.0000000) to (34.151013 68.305646 3.6200001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9883502 4.9883502 3.6200001 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -68.305646 0.0000000) to (34.151013 68.305646 3.6200001) create_atoms CPU = 0.001 seconds 714 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9883502 4.9883502 3.6200001 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -68.305646 0.0000000) to (34.151013 68.305646 3.6200001) create_atoms CPU = 0.001 seconds 714 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 36 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1416 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_657255834688_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.543 | 5.543 | 5.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4974.9691 0 -4974.9691 3064.0657 40 0 -5000.9437 0 -5000.9437 -3344.0807 Loop time of 0.841466 on 1 procs for 40 steps with 1416 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 = -4974.96907905106 -5000.93889037051 -5000.94372181592 Force two-norm initial, final = 24.126492 0.25988085 Force max component initial, final = 5.8170929 0.062340957 Final line search alpha, max atom move = 0.80178520 0.049984057 Iterations, force evaluations = 40 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81709 | 0.81709 | 0.81709 | 0.0 | 97.10 Neigh | 0.013543 | 0.013543 | 0.013543 | 0.0 | 1.61 Comm | 0.0060076 | 0.0060076 | 0.0060076 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004823 | | | 0.57 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11209.0 ave 11209 max 11209 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: 246596.0 ave 246596 max 246596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 246596 Ave neighs/atom = 174.14972 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.544 | 5.544 | 5.544 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -5000.9437 0 -5000.9437 -3344.0807 16888.799 44 0 -5000.9984 0 -5000.9984 2.8753643 16846.888 Loop time of 0.104276 on 1 procs for 4 steps with 1416 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 = -5000.94372181595 -5000.99837645893 -5000.99840068468 Force two-norm initial, final = 52.293295 1.1283410 Force max component initial, final = 43.740872 0.86668893 Final line search alpha, max atom move = 0.012012979 0.010411516 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.101 | 0.101 | 0.101 | 0.0 | 96.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063988 | 0.00063988 | 0.00063988 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002636 | | | 2.53 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11220.0 ave 11220 max 11220 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: 246916.0 ave 246916 max 246916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 246916 Ave neighs/atom = 174.37571 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.682 | 5.682 | 5.682 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5000.9984 0 -5000.9984 2.8753643 Loop time of 1.516e-06 on 1 procs for 0 steps with 1416 atoms 197.9% 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 | | 1.516e-06 | | |100.00 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11220.0 ave 11220 max 11220 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: 246948.0 ave 246948 max 246948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 246948 Ave neighs/atom = 174.39831 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.682 | 5.682 | 5.682 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 -5000.9984 -5000.9984 34.158399 136.61129 3.610236 2.8753643 2.8753643 63.566467 -137.1421 82.201723 2.3077161 409.90635 Loop time of 2.195e-06 on 1 procs for 0 steps with 1416 atoms 227.8% 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 | | 2.195e-06 | | |100.00 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11220.0 ave 11220 max 11220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123474.0 ave 123474 max 123474 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 246948.0 ave 246948 max 246948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 246948 Ave neighs/atom = 174.39831 Neighbor list builds = 0 Dangerous builds = 0 1416 -5000.99840068468 eV 2.30771605155471 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01