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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -63.263023 0.0000000) to (31.631512 63.263023 4.0500001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7040431 5.7040431 4.0500001 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -63.263023 0.0000000) to (31.631512 63.263023 4.0500001) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7040431 5.7040431 4.0500001 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -63.263023 0.0000000) to (31.631512 63.263023 4.0500001) create_atoms CPU = 0.001 seconds 490 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 34 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3241.1508 0 -3241.1508 13759.587 73 0 -3282.3641 0 -3282.3641 5397.7001 Loop time of 0.744751 on 1 procs for 73 steps with 978 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 = -3241.15084908502 -3282.36117613429 -3282.36408020787 Force two-norm initial, final = 42.257682 0.10984222 Force max component initial, final = 14.917923 0.031182839 Final line search alpha, max atom move = 1.0000000 0.031182839 Iterations, force evaluations = 73 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72578 | 0.72578 | 0.72578 | 0.0 | 97.45 Neigh | 0.0071523 | 0.0071523 | 0.0071523 | 0.0 | 0.96 Comm | 0.0063991 | 0.0063991 | 0.0063991 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005421 | | | 0.73 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6309.00 ave 6309 max 6309 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: 127684.0 ave 127684 max 127684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127684 Ave neighs/atom = 130.55624 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -3282.3641 0 -3282.3641 5397.7001 16208.951 82 0 -3282.7369 0 -3282.7369 0.37029117 16319.335 Loop time of 0.0744243 on 1 procs for 9 steps with 978 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3282.36408020787 -3282.7338183258 -3282.73686526262 Force two-norm initial, final = 106.17112 0.54269312 Force max component initial, final = 93.975970 0.40235918 Final line search alpha, max atom move = 0.00021227973 8.5412696e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.063924 | 0.063924 | 0.063924 | 0.0 | 85.89 Neigh | 0.0073753 | 0.0073753 | 0.0073753 | 0.0 | 9.91 Comm | 0.00066967 | 0.00066967 | 0.00066967 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002455 | | | 3.30 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6316.00 ave 6316 max 6316 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: 127388.0 ave 127388 max 127388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127388 Ave neighs/atom = 130.25358 Neighbor list builds = 1 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.126 | 5.126 | 5.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3282.7369 0 -3282.7369 0.37029117 Loop time of 9.217e-06 on 1 procs for 0 steps with 978 atoms 130.2% 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 | | 9.217e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6316.00 ave 6316 max 6316 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: 127348.0 ave 127348 max 127348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127348 Ave neighs/atom = 130.21268 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.126 | 5.126 | 5.126 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 -3282.7369 -3282.7369 31.608224 127.64575 4.0447903 0.37029117 0.37029117 39.473164 -8.6223934 -29.739897 2.5919195 275.10545 Loop time of 2.772e-06 on 1 procs for 0 steps with 978 atoms 216.5% 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 | | 2.772e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6316.00 ave 6316 max 6316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63674.0 ave 63674 max 63674 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127348.0 ave 127348 max 127348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127348 Ave neighs/atom = 130.21268 Neighbor list builds = 0 Dangerous builds = 0 978 -3282.73686526262 eV 2.59191949219654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01