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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -55.036384 0.0000000) to (27.518192 55.036384 3.6133156) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7445159 4.7445159 3.6133156 Created 463 atoms using lattice units in orthogonal box = (0.0000000 -55.036384 0.0000000) to (27.518192 55.036384 3.6133156) create_atoms CPU = 0.001 seconds 463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7445159 4.7445159 3.6133156 Created 465 atoms using lattice units in orthogonal box = (0.0000000 -55.036384 0.0000000) to (27.518192 55.036384 3.6133156) create_atoms CPU = 0.001 seconds 465 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 ghost atom cutoff = 7 binsize = 3.5, bins = 8 32 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 928 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_122936827583_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3141.7822 0 -3141.7822 49015.103 28 0 -3271.4123 0 -3271.4123 6045.8712 Loop time of 2.78889 on 1 procs for 28 steps with 928 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3141.782203351 -3271.40941943299 -3271.4122571832 Force two-norm initial, final = 470.55493 0.18342495 Force max component initial, final = 314.66148 0.046269766 Final line search alpha, max atom move = 1.0000000 0.046269766 Iterations, force evaluations = 28 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7813 | 2.7813 | 2.7813 | 0.0 | 99.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0039467 | 0.0039467 | 0.0039467 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003689 | | | 0.13 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6967.00 ave 6967 max 6967 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: 123622.0 ave 123622 max 123622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123622 Ave neighs/atom = 133.21336 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -3271.4123 0 -3271.4123 6045.8712 10944.746 33 0 -3271.5607 0 -3271.5607 -33.735394 10998.162 Loop time of 0.42014 on 1 procs for 5 steps with 928 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 = -3271.4122571832 -3271.56061119631 -3271.5606616271 Force two-norm initial, final = 77.378016 0.72173095 Force max component initial, final = 62.901610 0.62589094 Final line search alpha, max atom move = 0.00084964373 0.00053178431 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41788 | 0.41788 | 0.41788 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037063 | 0.00037063 | 0.00037063 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001891 | | | 0.45 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6962.00 ave 6962 max 6962 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: 122922.0 ave 122922 max 122922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122922 Ave neighs/atom = 132.45905 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 ghost atom cutoff = 7 binsize = 3.5, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.127 | 5.127 | 5.127 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3271.5607 0 -3271.5607 -33.735394 Loop time of 1.846e-06 on 1 procs for 0 steps with 928 atoms 162.5% 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 | | 1.846e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6947.00 ave 6947 max 6947 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: 122850.0 ave 122850 max 122850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122850 Ave neighs/atom = 132.38147 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 ghost atom cutoff = 7 binsize = 3.5, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.127 | 5.127 | 5.127 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 -3271.5607 -3271.5607 27.502249 110.51998 3.6183545 -33.735394 -33.735394 -26.498505 16.597233 -91.30491 2.2609407 425.25082 Loop time of 1.711e-06 on 1 procs for 0 steps with 928 atoms 233.8% 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 | | 1.711e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6947.00 ave 6947 max 6947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61425.0 ave 61425 max 61425 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122850.0 ave 122850 max 122850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122850 Ave neighs/atom = 132.38147 Neighbor list builds = 0 Dangerous builds = 0 928 -3271.5606616271 eV 2.26094068887303 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03