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 = 3.6150000 3.6150000 3.6150000 Created orthogonal box = (0.0000000 -43.978373 0.0000000) to (21.989187 43.978373 3.6150000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1601164 4.1601164 3.6150000 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -43.978373 0.0000000) to (21.989187 43.978373 3.6150000) create_atoms CPU = 0.001 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1601164 4.1601164 3.6150000 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -43.978373 0.0000000) to (21.989187 43.978373 3.6150000) create_atoms CPU = 0.000 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 23 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 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 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_128703483589_005#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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 4.923 | 4.923 | 4.923 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1922.4447 0 -1922.4447 63396.443 55 0 -2073.1831 0 -2073.1831 -3114.4387 Loop time of 0.659727 on 1 procs for 55 steps with 588 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 = -1922.44470578083 -2073.1817801674 -2073.18314265642 Force two-norm initial, final = 464.00609 0.12173818 Force max component initial, final = 158.79725 0.024713641 Final line search alpha, max atom move = 1.0000000 0.024713641 Iterations, force evaluations = 55 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64284 | 0.64284 | 0.64284 | 0.0 | 97.44 Neigh | 0.0067557 | 0.0067557 | 0.0067557 | 0.0 | 1.02 Comm | 0.0063696 | 0.0063696 | 0.0063696 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003762 | | | 0.57 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5992.00 ave 5992 max 5992 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: 104024.0 ave 104024 max 104024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104024 Ave neighs/atom = 176.91156 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.924 | 4.924 | 4.924 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -2073.1831 0 -2073.1831 -3114.4387 6991.7617 58 0 -2073.207 0 -2073.207 339.04561 6974.248 Loop time of 0.0322363 on 1 procs for 3 steps with 588 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 = -2073.18314265642 -2073.20577865612 -2073.20700834416 Force two-norm initial, final = 24.326202 2.6030639 Force max component initial, final = 17.812214 1.8485569 Final line search alpha, max atom move = 0.00054195907 0.0010018422 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030991 | 0.030991 | 0.030991 | 0.0 | 96.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024217 | 0.00024217 | 0.00024217 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001003 | | | 3.11 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6043.00 ave 6043 max 6043 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: 103712.0 ave 103712 max 103712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103712 Ave neighs/atom = 176.38095 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.061 | 5.061 | 5.061 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2073.207 0 -2073.207 339.04561 Loop time of 2.121e-06 on 1 procs for 0 steps with 588 atoms 141.4% 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 | | 2.121e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6043.00 ave 6043 max 6043 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: 103936.0 ave 103936 max 103936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103936 Ave neighs/atom = 176.76190 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.061 | 5.061 | 5.061 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 -2073.207 -2073.207 21.966709 87.728545 3.6190241 339.04561 339.04561 303.31261 288.68715 425.13705 2.3425964 204.64014 Loop time of 2.453e-06 on 1 procs for 0 steps with 588 atoms 163.1% 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 | | 2.453e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6043.00 ave 6043 max 6043 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51968.0 ave 51968 max 51968 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103936.0 ave 103936 max 103936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103936 Ave neighs/atom = 176.76190 Neighbor list builds = 0 Dangerous builds = 0 588 -2073.20689019701 eV 2.34259636472105 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01