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 = 3.6800447 3.6800447 3.6800447 Created orthogonal box = (0.0000000 -48.263334 0.0000000) to (34.127331 48.263334 5.2043691) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3492708 6.1732171 5.2043691 Created 687 atoms using lattice units in orthogonal box = (0.0000000 -48.263334 0.0000000) to (34.127331 48.263334 5.2043691) create_atoms CPU = 0.004 seconds 687 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3492708 6.1732171 5.2043691 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -48.263334 0.0000000) to (34.127331 48.263334 5.2043691) create_atoms CPU = 0.004 seconds 695 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1382 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_142799717516_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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.663 | 4.663 | 4.663 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5679.648 0 -5679.648 25587.148 131 0 -5874.2958 0 -5874.2958 -2275.3522 Loop time of 2.0034 on 1 procs for 131 steps with 1382 atoms 86.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5679.64796333467 -5874.29029962224 -5874.29579804399 Force two-norm initial, final = 103.76138 0.24206170 Force max component initial, final = 21.541350 0.049914144 Final line search alpha, max atom move = 1.0000000 0.049914144 Iterations, force evaluations = 131 240 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.882 | 1.882 | 1.882 | 0.0 | 93.94 Neigh | 0.041085 | 0.041085 | 0.041085 | 0.0 | 2.05 Comm | 0.02445 | 0.02445 | 0.02445 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05591 | | | 2.79 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5360.00 ave 5360 max 5360 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: 78242.0 ave 78242 max 78242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78242 Ave neighs/atom = 56.615051 Neighbor list builds = 2 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 131 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.663 | 4.663 | 4.663 Mbytes Step Temp E_pair E_mol TotEng Press Volume 131 0 -5874.2958 0 -5874.2958 -2275.3522 17144.22 136 0 -5874.5006 0 -5874.5006 45.280901 17116.668 Loop time of 0.0698827 on 1 procs for 5 steps with 1382 atoms 79.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5874.29579804398 -5874.50049186158 -5874.50061560005 Force two-norm initial, final = 91.397199 1.1888165 Force max component initial, final = 87.451792 0.79001165 Final line search alpha, max atom move = 0.00036634529 0.00028941704 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065706 | 0.065706 | 0.065706 | 0.0 | 94.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065632 | 0.00065632 | 0.00065632 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00352 | | | 5.04 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5358.00 ave 5358 max 5358 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: 77902.0 ave 77902 max 77902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77902 Ave neighs/atom = 56.369030 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.801 | 4.801 | 4.801 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5874.5006 0 -5874.5006 45.280901 Loop time of 3.172e-06 on 1 procs for 0 steps with 1382 atoms 189.2% 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 | | 3.172e-06 | | |100.00 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5397.00 ave 5397 max 5397 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: 78012.0 ave 78012 max 78012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78012 Ave neighs/atom = 56.448625 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.801 | 4.801 | 4.801 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 -5874.5006 -5874.5006 34.125871 96.139767 5.2171389 45.280901 45.280901 -11.798396 73.511962 74.129137 2.3698043 1248.7124 Loop time of 4.037e-06 on 1 procs for 0 steps with 1382 atoms 198.2% 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 | | 4.037e-06 | | |100.00 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5397.00 ave 5397 max 5397 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39006.0 ave 39006 max 39006 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78012.0 ave 78012 max 78012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78012 Ave neighs/atom = 56.448625 Neighbor list builds = 0 Dangerous builds = 0 1382 -5874.50061560005 eV 2.3698043262366 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02