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 = 3.6385685 3.6385685 3.6385685 Created orthogonal box = (0.0000000 -39.357135 0.0000000) to (13.119045 39.357135 3.6385685) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0457866 5.0457866 3.6385685 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -39.357135 0.0000000) to (13.119045 39.357135 3.6385685) create_atoms CPU = 0.002 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0457866 5.0457866 3.6385685 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.357135 0.0000000) to (13.119045 39.357135 3.6385685) create_atoms CPU = 0.001 seconds 158 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 17 1 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_097471813275_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 4.874 | 4.874 | 4.874 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1017.4743 0 -1017.4743 51265.859 15 0 -1057.8474 0 -1057.8474 3195.5033 Loop time of 0.350002 on 1 procs for 15 steps with 312 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 = -1017.47431889147 -1057.84663223942 -1057.84741831079 Force two-norm initial, final = 159.96863 0.065144500 Force max component initial, final = 56.568091 0.010185232 Final line search alpha, max atom move = 1.0000000 0.010185232 Iterations, force evaluations = 15 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34413 | 0.34413 | 0.34413 | 0.0 | 98.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0036737 | 0.0036737 | 0.0036737 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002203 | | | 0.63 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5538.00 ave 5538 max 5538 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: 99368.0 ave 99368 max 99368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99368 Ave neighs/atom = 318.48718 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.873 | 4.873 | 4.873 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -1057.8474 0 -1057.8474 3195.5033 3757.3898 20 0 -1057.8987 0 -1057.8987 -413.77888 3766.8719 Loop time of 0.0941617 on 1 procs for 5 steps with 312 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1057.8474183108 -1057.89796179691 -1057.89865721771 Force two-norm initial, final = 21.424490 1.9729503 Force max component initial, final = 18.523775 1.6581709 Final line search alpha, max atom move = 0.00067312595 0.0011161578 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091097 | 0.091097 | 0.091097 | 0.0 | 96.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081308 | 0.00081308 | 0.00081308 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002251 | | | 2.39 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5442.00 ave 5442 max 5442 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: 99128.0 ave 99128 max 99128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99128 Ave neighs/atom = 317.71795 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.011 | 5.011 | 5.011 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1057.8987 0 -1057.8987 -413.77888 Loop time of 6.886e-06 on 1 procs for 0 steps with 312 atoms 174.3% 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 | | 6.886e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5460.00 ave 5460 max 5460 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: 99096.0 ave 99096 max 99096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99096 Ave neighs/atom = 317.61538 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.011 | 5.011 | 5.011 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 -1057.8987 -1057.8987 13.075959 79.004359 3.6463323 -413.77888 -413.77888 -440.26502 -707.87466 -93.19696 2.2439419 152.21556 Loop time of 7.017e-06 on 1 procs for 0 steps with 312 atoms 256.5% 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 | | 7.017e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5460.00 ave 5460 max 5460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49548.0 ave 49548 max 49548 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 99096.0 ave 99096 max 99096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99096 Ave neighs/atom = 317.61538 Neighbor list builds = 0 Dangerous builds = 0 312 -1057.89865721771 eV 2.24394192164831 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01