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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -44.365372 0.0000000) to (9.0560436 44.365372 9.9203987) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4336262 5.9153829 6.6135992 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -44.365372 0.0000000) to (9.0560436 44.365372 9.9203987) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4336262 5.9153829 6.6135992 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.365372 0.0000000) to (9.0560436 44.365372 9.9203987) create_atoms CPU = 0.001 seconds 242 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 ghost atom cutoff = 6 binsize = 3, bins = 4 30 4 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_022920256108_001#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 ghost atom cutoff = 6 binsize = 3, bins = 4 30 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.431 | 4.431 | 4.431 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1564.5484 0 -1564.5484 14685.181 50 0 -1602.9122 0 -1602.9122 4623.3068 Loop time of 0.810962 on 1 procs for 50 steps with 480 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1564.54840632667 -1602.91183167439 -1602.91220685052 Force two-norm initial, final = 76.902610 0.31704768 Force max component initial, final = 24.763678 0.077077441 Final line search alpha, max atom move = 1.0000000 0.077077441 Iterations, force evaluations = 50 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80691 | 0.80691 | 0.80691 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019152 | 0.0019152 | 0.0019152 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002136 | | | 0.26 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2350.00 ave 2350 max 2350 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: 25896.0 ave 25896 max 25896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25896 Ave neighs/atom = 53.950000 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 ghost atom cutoff = 6 binsize = 3, bins = 4 30 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.431 | 4.431 | 4.431 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -1602.9122 0 -1602.9122 4623.3068 7971.5313 63 0 -1603.1689 0 -1603.1689 -36.303002 8027.5074 Loop time of 0.141032 on 1 procs for 13 steps with 480 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1602.91220685052 -1603.16867924108 -1603.16892993902 Force two-norm initial, final = 50.092263 1.1601284 Force max component initial, final = 47.650258 0.95578930 Final line search alpha, max atom move = 0.0066355800 0.0063422164 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13614 | 0.13614 | 0.13614 | 0.0 | 96.53 Neigh | 0.0024544 | 0.0024544 | 0.0024544 | 0.0 | 1.74 Comm | 0.00043396 | 0.00043396 | 0.00043396 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002002 | | | 1.42 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2327.00 ave 2327 max 2327 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: 25740.0 ave 25740 max 25740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25740 Ave neighs/atom = 53.625000 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 30 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1603.1689 0 -1603.1689 -36.303002 Loop time of 2.176e-06 on 1 procs for 0 steps with 480 atoms 137.9% 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 | | 2.176e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2327.00 ave 2327 max 2327 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: 25740.0 ave 25740 max 25740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25740 Ave neighs/atom = 53.625000 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 ghost atom cutoff = 6 binsize = 3, bins = 4 30 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.569 | 4.569 | 4.569 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 -1603.1689 -1603.1689 9.0318806 89.793201 9.8982649 -36.303002 -36.303002 96.517874 -15.090524 -190.33636 2.5068829 346.78085 Loop time of 2.288e-06 on 1 procs for 0 steps with 480 atoms 131.1% 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 | | 2.288e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2327.00 ave 2327 max 2327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12870.0 ave 12870 max 12870 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25740.0 ave 25740 max 25740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25740 Ave neighs/atom = 53.625000 Neighbor list builds = 0 Dangerous builds = 0 480 -1603.16892993902 eV 2.50688292553185 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01