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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -39.242342 0.0000000) to (9.2487821 39.242342 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1382123 4.3599177 4.3599177 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -39.242342 0.0000000) to (9.2487821 39.242342 4.3599177) create_atoms CPU = 0.001 seconds 110 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1382123 4.3599177 4.3599177 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -39.242342 0.0000000) to (9.2487821 39.242342 4.3599177) create_atoms CPU = 0.000 seconds 110 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 216 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_152208847456_001#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.792 | 4.792 | 4.792 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1334.1091 0 -1334.1091 82298.055 36 0 -1399.7775 0 -1399.7775 6446.0586 Loop time of 3.74959 on 1 procs for 36 steps with 216 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 = -1334.10914045363 -1399.77626980398 -1399.77746254749 Force two-norm initial, final = 134.05391 0.17021936 Force max component initial, final = 35.106220 0.031297862 Final line search alpha, max atom move = 1.0000000 0.031297862 Iterations, force evaluations = 36 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7361 | 3.7361 | 3.7361 | 0.0 | 99.64 Neigh | 0.011009 | 0.011009 | 0.011009 | 0.0 | 0.29 Comm | 0.0013239 | 0.0013239 | 0.0013239 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00112 | | | 0.03 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2277.00 ave 2277 max 2277 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: 15608.0 ave 15608 max 15608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15608 Ave neighs/atom = 72.259259 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard 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) = 4.792 | 4.792 | 4.792 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -1399.7775 0 -1399.7775 6446.0586 3164.8108 51 0 -1400.467 0 -1400.467 -10728.994 3187.7997 Loop time of 0.97394 on 1 procs for 15 steps with 216 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 = -1399.77746254749 -1400.46670502116 -1400.46696961226 Force two-norm initial, final = 89.712278 1.0962788 Force max component initial, final = 86.224028 0.54787642 Final line search alpha, max atom move = 0.0012729535 0.00069742120 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9724 | 0.9724 | 0.9724 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003115 | 0.0003115 | 0.0003115 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001229 | | | 0.13 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2274.00 ave 2274 max 2274 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: 15548.0 ave 15548 max 15548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15548 Ave neighs/atom = 71.981481 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.930 | 4.930 | 4.930 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1400.467 0 -1400.467 -10728.994 Loop time of 1.485e-06 on 1 procs for 0 steps with 216 atoms 134.7% 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 | | 1.485e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2272.00 ave 2272 max 2272 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: 15616.0 ave 15616 max 15616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15616 Ave neighs/atom = 72.296296 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.930 | 4.930 | 4.930 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 -1400.467 -1400.467 9.1850535 78.484685 4.4220578 -10728.994 -10728.994 222.78703 -32130.483 -279.28529 2.4761447 491.18326 Loop time of 1.387e-06 on 1 procs for 0 steps with 216 atoms 216.3% 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 | | 1.387e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2272.00 ave 2272 max 2272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7808.00 ave 7808 max 7808 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15616.0 ave 15616 max 15616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15616 Ave neighs/atom = 72.296296 Neighbor list builds = 0 Dangerous builds = 0 216 -1400.46696961226 eV 2.47614466009573 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05