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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -43.852336 0.0000000) to (21.924366 43.852336 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1478530 4.1478530 3.6043435 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -43.852336 0.0000000) to (21.924366 43.852336 3.6043435) create_atoms CPU = 0.002 seconds 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1478530 4.1478530 3.6043435 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -43.852336 0.0000000) to (21.924366 43.852336 3.6043435) create_atoms CPU = 0.001 seconds 298 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 29 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 588 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.497 | 4.497 | 4.497 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2470.8083 0 -2470.8083 6935.2561 37 0 -2488.0696 0 -2488.0696 -6021.2458 Loop time of 3.38047 on 1 procs for 37 steps with 588 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 = -2470.80830974349 -2488.06735411183 -2488.06960861592 Force two-norm initial, final = 22.822622 0.13084030 Force max component initial, final = 5.9409797 0.016556031 Final line search alpha, max atom move = 1.0000000 0.016556031 Iterations, force evaluations = 37 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.368 | 3.368 | 3.368 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064694 | 0.0064694 | 0.0064694 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006049 | | | 0.18 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4089.00 ave 4089 max 4089 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: 45696.0 ave 45696 max 45696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45696 Ave neighs/atom = 77.714286 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.497 | 4.497 | 4.497 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -2488.0696 0 -2488.0696 -6021.2458 6930.6814 50 0 -2488.2597 0 -2488.2597 -2871.2999 6916.5053 Loop time of 0.76917 on 1 procs for 13 steps with 588 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 = -2488.06960861592 -2488.25833730288 -2488.25970641153 Force two-norm initial, final = 30.438705 2.1782740 Force max component initial, final = 30.400250 1.6768900 Final line search alpha, max atom move = 0.00068472444 0.0011482076 Iterations, force evaluations = 13 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76321 | 0.76321 | 0.76321 | 0.0 | 99.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012475 | 0.0012475 | 0.0012475 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004712 | | | 0.61 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119.00 ave 4119 max 4119 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: 45768.0 ave 45768 max 45768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45768 Ave neighs/atom = 77.836735 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.635 | 4.635 | 4.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2488.2597 0 -2488.2597 -2871.2999 Loop time of 6.405e-06 on 1 procs for 0 steps with 588 atoms 187.4% 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 | | 6.405e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119.00 ave 4119 max 4119 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: 45800.0 ave 45800 max 45800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45800 Ave neighs/atom = 77.891156 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.635 | 4.635 | 4.635 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 -2488.2597 -2488.2597 21.646034 87.704671 3.6432222 -2871.2999 -2871.2999 -383.5125 -7931.9677 -298.41952 2.2904779 203.06161 Loop time of 6.846e-06 on 1 procs for 0 steps with 588 atoms 277.5% 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 | | 6.846e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119.00 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22900.0 ave 22900 max 22900 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 45800.0 ave 45800 max 45800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45800 Ave neighs/atom = 77.891156 Neighbor list builds = 0 Dangerous builds = 0 588 -2488.25970641153 eV 2.2904779046827 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04