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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -43.397484 0.0000000) to (15.343328 43.397484 4.9780328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6528049 4.5681562 4.9780328 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -43.397484 0.0000000) to (15.343328 43.397484 4.9780328) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6528049 4.5681562 4.9780328 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.397484 0.0000000) to (15.343328 43.397484 4.9780328) create_atoms CPU = 0.001 seconds 306 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 = 4 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, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 604 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_820335782779_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 = 4 23 2 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) = 4.934 | 4.934 | 4.934 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2625.6293 0 -2625.6293 14344.927 67 0 -2675.7085 0 -2675.7085 -3247.993 Loop time of 0.798955 on 1 procs for 67 steps with 604 atoms 95.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2625.62927467609 -2675.70606016846 -2675.70851915244 Force two-norm initial, final = 138.79115 0.20236394 Force max component initial, final = 46.868858 0.039269667 Final line search alpha, max atom move = 0.62057901 0.024369931 Iterations, force evaluations = 67 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78077 | 0.78077 | 0.78077 | 0.0 | 97.72 Neigh | 0.0074534 | 0.0074534 | 0.0074534 | 0.0 | 0.93 Comm | 0.0062402 | 0.0062402 | 0.0062402 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004486 | | | 0.56 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5100.00 ave 5100 max 5100 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: 106724.0 ave 106724 max 106724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106724 Ave neighs/atom = 176.69536 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 = 4 23 2 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.932 | 4.932 | 4.932 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -2675.7085 0 -2675.7085 -3247.993 6629.364 70 0 -2675.7271 0 -2675.7271 8.6395696 6617.9936 Loop time of 0.046015 on 1 procs for 3 steps with 604 atoms 97.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2675.70851915244 -2675.72698011876 -2675.72713117642 Force two-norm initial, final = 25.038098 0.23021985 Force max component initial, final = 19.877964 0.056554975 Final line search alpha, max atom move = 0.00073783642 4.1728320e-05 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044075 | 0.044075 | 0.044075 | 0.0 | 95.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033069 | 0.00033069 | 0.00033069 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00161 | | | 3.50 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5092.00 ave 5092 max 5092 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: 106576.0 ave 106576 max 106576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106576 Ave neighs/atom = 176.45033 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 = 4 23 2 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) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2675.7271 0 -2675.7271 8.6395696 Loop time of 1.957e-06 on 1 procs for 0 steps with 604 atoms 153.3% 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 | | 1.957e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5092.00 ave 5092 max 5092 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: 106652.0 ave 106652 max 106652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106652 Ave neighs/atom = 176.57616 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 = 4 23 2 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) = 5.070 | 5.070 | 5.070 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 -2675.7271 -2675.7271 15.338897 86.637311 4.979976 8.6395696 8.6395696 2.9295657 13.66675 9.3223933 2.3588217 278.83123 Loop time of 2.21e-06 on 1 procs for 0 steps with 604 atoms 226.2% 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 | | 2.21e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5092.00 ave 5092 max 5092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53326.0 ave 53326 max 53326 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106652.0 ave 106652 max 106652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106652 Ave neighs/atom = 176.57616 Neighbor list builds = 0 Dangerous builds = 0 604 -2675.72713117642 eV 2.35882173398009 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01