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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -42.126049 0.0000000) to (51.589303 42.126049 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8959203 5.4157486 5.8134559 Created 1684 atoms using lattice units in orthogonal box = (0.0000000 -42.126049 0.0000000) to (51.589303 42.126049 8.7201838) create_atoms CPU = 0.003 seconds 1684 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8959203 5.4157486 5.8134559 Created 1684 atoms using lattice units in orthogonal box = (0.0000000 -42.126049 0.0000000) to (51.589303 42.126049 8.7201838) create_atoms CPU = 0.003 seconds 1684 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 = 14 22 3 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 56 atoms, new total = 3312 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 = 14 22 3 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) = 6.976 | 6.976 | 6.976 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14340.954 0 -14340.954 -10284.66 74 0 -14514.386 0 -14514.386 -10802.459 Loop time of 3.70546 on 1 procs for 74 steps with 3312 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14340.9535150475 -14514.3735487814 -14514.386210355 Force two-norm initial, final = 65.159532 0.48686165 Force max component initial, final = 5.8924513 0.081330022 Final line search alpha, max atom move = 1.0000000 0.081330022 Iterations, force evaluations = 74 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6363 | 3.6363 | 3.6363 | 0.0 | 98.13 Neigh | 0.033282 | 0.033282 | 0.033282 | 0.0 | 0.90 Comm | 0.01451 | 0.01451 | 0.01451 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02137 | | | 0.58 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10887.0 ave 10887 max 10887 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: 577090.0 ave 577090 max 577090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577090 Ave neighs/atom = 174.24215 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 = 14 22 3 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.981 | 6.981 | 6.981 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -14514.386 0 -14514.386 -10802.459 37902.34 78 0 -14515.123 0 -14515.123 -473.89754 37695.507 Loop time of 0.167249 on 1 procs for 4 steps with 3312 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 = -14514.386210355 -14515.1102548413 -14515.1233278824 Force two-norm initial, final = 373.33181 17.771619 Force max component initial, final = 292.60960 16.955654 Final line search alpha, max atom move = 2.8877583e-05 0.00048963830 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16329 | 0.16329 | 0.16329 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052813 | 0.00052813 | 0.00052813 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003433 | | | 2.05 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11185.0 ave 11185 max 11185 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: 577612.0 ave 577612 max 577612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577612 Ave neighs/atom = 174.39976 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 = 14 22 3 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) = 7.119 | 7.119 | 7.119 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14515.123 0 -14515.123 -473.89754 Loop time of 2.212e-06 on 1 procs for 0 steps with 3312 atoms 180.8% 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 | | 2.212e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11227.0 ave 11227 max 11227 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: 578182.0 ave 578182 max 578182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578182 Ave neighs/atom = 174.57186 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 = 14 22 3 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) = 7.119 | 7.119 | 7.119 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 -14515.123 -14515.123 51.497186 84.252099 8.688111 -473.89754 -473.89754 719.3813 -2364.5545 223.48061 2.3925103 1967.6895 Loop time of 2.687e-06 on 1 procs for 0 steps with 3312 atoms 260.5% 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 | | 2.687e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11227.0 ave 11227 max 11227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 289091.0 ave 289091 max 289091 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 578182.0 ave 578182 max 578182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578182 Ave neighs/atom = 174.57186 Neighbor list builds = 0 Dangerous builds = 0 3312 -14515.1233278824 eV 2.39251034539654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04