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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -30.709613 0.0000000) to (30.706725 30.709613 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0761139 4.0761139 2.8886457 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -30.709613 0.0000000) to (30.706725 30.709613 2.8886457) create_atoms CPU = 0.002 seconds 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0761139 4.0761139 2.8886457 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -30.709613 0.0000000) to (30.706725 30.709613 2.8886457) create_atoms CPU = 0.001 seconds 227 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 23 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 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 454 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.816 | 4.816 | 4.816 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1797.8835 0 -1797.8835 60115.543 124 0 -1887.935 0 -1887.935 10753.666 Loop time of 21.7803 on 1 procs for 124 steps with 454 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 = -1797.8835290476 -1887.93334055914 -1887.9350252616 Force two-norm initial, final = 125.89017 0.14712480 Force max component initial, final = 42.180929 0.028329261 Final line search alpha, max atom move = 1.0000000 0.028329261 Iterations, force evaluations = 124 241 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.746 | 21.746 | 21.746 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017249 | 0.017249 | 0.017249 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01721 | | | 0.08 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2782.00 ave 2782 max 2782 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: 26252.0 ave 26252 max 26252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26252 Ave neighs/atom = 57.823789 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 124 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.816 | 4.816 | 4.816 Mbytes Step Temp E_pair E_mol TotEng Press Volume 124 0 -1887.935 0 -1887.935 10753.666 5447.9375 127 0 -1887.9643 0 -1887.9643 5677.525 5463.7907 Loop time of 0.484914 on 1 procs for 3 steps with 454 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1887.9350252616 -1887.96240485467 -1887.964255654 Force two-norm initial, final = 26.867745 0.16280225 Force max component initial, final = 20.668062 0.031048769 Final line search alpha, max atom move = 0.00025486415 7.9132181e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48321 | 0.48321 | 0.48321 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036539 | 0.00036539 | 0.00036539 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001334 | | | 0.28 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2821.00 ave 2821 max 2821 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: 26224.0 ave 26224 max 26224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26224 Ave neighs/atom = 57.762115 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1887.9643 0 -1887.9643 5677.525 Loop time of 6.305e-06 on 1 procs for 0 steps with 454 atoms 190.3% 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 | | 6.305e-06 | | |100.00 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2813.00 ave 2813 max 2813 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: 26224.0 ave 26224 max 26224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26224 Ave neighs/atom = 57.762115 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.954 | 4.954 | 4.954 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 -1887.9643 -1887.9643 30.72025 61.419227 2.895776 5677.525 5677.525 3.7398479 17028.766 0.068592267 2.304614 120.31033 Loop time of 7.026e-06 on 1 procs for 0 steps with 454 atoms 298.9% 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 | | 7.026e-06 | | |100.00 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2813.00 ave 2813 max 2813 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13112.0 ave 13112 max 13112 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26224.0 ave 26224 max 26224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26224 Ave neighs/atom = 57.762115 Neighbor list builds = 0 Dangerous builds = 0 454 -1887.964255654 eV 2.30461401314856 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22