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 = 2.8147787 2.8147787 2.8147787 Created orthogonal box = (0.0000000 -30.834356 0.0000000) to (6.2940366 30.834356 6.8947716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7764219 4.1112475 4.5965144 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -30.834356 0.0000000) to (6.2940366 30.834356 6.8947716) create_atoms CPU = 0.000 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7764219 4.1112475 4.5965144 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -30.834356 0.0000000) to (6.2940366 30.834356 6.8947716) create_atoms CPU = 0.000 seconds 122 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 17 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.475 | 4.475 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -635.6664 0 -635.6664 284236.21 75 0 -983.90017 0 -983.90017 16959.073 Loop time of 0.345758 on 1 procs for 75 steps with 240 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -635.666400568793 -983.899425789412 -983.900170716464 Force two-norm initial, final = 941.09576 0.12745765 Force max component initial, final = 315.82301 0.031843123 Final line search alpha, max atom move = 1.0000000 0.031843123 Iterations, force evaluations = 75 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33571 | 0.33571 | 0.33571 | 0.0 | 97.10 Neigh | 0.0028447 | 0.0028447 | 0.0028447 | 0.0 | 0.82 Comm | 0.0043323 | 0.0043323 | 0.0043323 | 0.0 | 1.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002867 | | | 0.83 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3018.00 ave 3018 max 3018 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: 39568.0 ave 39568 max 39568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39568 Ave neighs/atom = 164.86667 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.475 | 4.475 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -983.90017 0 -983.90017 16959.073 2676.172 80 0 -984.03192 0 -984.03192 5.2736147 2699.9128 Loop time of 0.0194078 on 1 procs for 5 steps with 240 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -983.900170716463 -984.031192896978 -984.031919240417 Force two-norm initial, final = 49.540411 0.40109308 Force max component initial, final = 31.636628 0.077018185 Final line search alpha, max atom move = 0.00041869159 3.2246866e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.018363 | 0.018363 | 0.018363 | 0.0 | 94.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020076 | 0.00020076 | 0.00020076 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008441 | | | 4.35 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2969.00 ave 2969 max 2969 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: 39564.0 ave 39564 max 39564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39564 Ave neighs/atom = 164.85000 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.613 | 4.613 | 4.613 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -984.03192 0 -984.03192 5.2736147 Loop time of 1.987e-06 on 1 procs for 0 steps with 240 atoms 151.0% 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 | | 1.987e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2969.00 ave 2969 max 2969 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: 39520.0 ave 39520 max 39520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39520 Ave neighs/atom = 164.66667 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.613 | 4.613 | 4.613 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 -984.03192 -984.03192 6.3166188 61.908012 6.9042771 5.2736147 5.2736147 -24.901088 3.9003021 36.82163 2.278072 278.52373 Loop time of 1.702e-06 on 1 procs for 0 steps with 240 atoms 176.3% 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 | | 1.702e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2969.00 ave 2969 max 2969 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19760.0 ave 19760 max 19760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39520.0 ave 39520 max 39520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39520 Ave neighs/atom = 164.66667 Neighbor list builds = 0 Dangerous builds = 0 240 -984.031919240417 eV 2.27807202696633 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01