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 = 3.7004755 3.7004755 3.7004755 Created orthogonal box = (0.0000000 -59.668375 0.0000000) to (29.834188 59.668375 3.7004755) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0488625 5.0488625 3.7004755 Created 519 atoms using lattice units in orthogonal box = (0.0000000 -59.668375 0.0000000) to (29.834188 59.668375 3.7004755) create_atoms CPU = 0.001 seconds 519 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0488625 5.0488625 3.7004755 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -59.668375 0.0000000) to (29.834188 59.668375 3.7004755) create_atoms CPU = 0.001 seconds 521 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 31 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1040 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.038 | 5.038 | 5.038 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3924.5515 0 -3924.5515 60153.087 335 0 -4156.0631 0 -4156.0631 -9128.514 Loop time of 5.88224 on 1 procs for 335 steps with 1040 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 = -3924.55148401915 -4156.05984195827 -4156.06314082693 Force two-norm initial, final = 315.10025 0.21005032 Force max component initial, final = 61.819753 0.049467244 Final line search alpha, max atom move = 1.0000000 0.049467244 Iterations, force evaluations = 335 658 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.746 | 5.746 | 5.746 | 0.0 | 97.68 Neigh | 0.038206 | 0.038206 | 0.038206 | 0.0 | 0.65 Comm | 0.059101 | 0.059101 | 0.059101 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03893 | | | 0.66 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8827.00 ave 8827 max 8827 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: 154714.0 ave 154714 max 154714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154714 Ave neighs/atom = 148.76346 Neighbor list builds = 4 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 335 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.046 | 5.046 | 5.046 Mbytes Step Temp E_pair E_mol TotEng Press Volume 335 0 -4156.0631 0 -4156.0631 -9128.514 13174.859 402 0 -4169.9098 0 -4169.9098 -406.73695 12931.925 Loop time of 0.71474 on 1 procs for 67 steps with 1040 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 = -4156.06314082695 -4169.9080803116 -4169.90980432782 Force two-norm initial, final = 458.70967 7.1266143 Force max component initial, final = 330.07597 4.6777993 Final line search alpha, max atom move = 0.00035839667 0.0016765077 Iterations, force evaluations = 67 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62404 | 0.62404 | 0.62404 | 0.0 | 87.31 Neigh | 0.060256 | 0.060256 | 0.060256 | 0.0 | 8.43 Comm | 0.0061739 | 0.0061739 | 0.0061739 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02427 | | | 3.40 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8901.00 ave 8901 max 8901 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: 161038.0 ave 161038 max 161038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161038 Ave neighs/atom = 154.84423 Neighbor list builds = 6 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.183 | 5.183 | 5.183 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4169.9098 0 -4169.9098 -406.73695 Loop time of 1.901e-06 on 1 procs for 0 steps with 1040 atoms 105.2% 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 | | 1.901e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8901.00 ave 8901 max 8901 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: 161152.0 ave 161152 max 161152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161152 Ave neighs/atom = 154.95385 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.183 | 5.183 | 5.183 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 -4169.9098 -4169.9098 29.926043 112.69099 3.8346407 -406.73695 -406.73695 -226.75119 -392.90035 -600.5593 2.2396015 411.04999 Loop time of 2.34e-06 on 1 procs for 0 steps with 1040 atoms 213.7% 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 | | 2.34e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8901.00 ave 8901 max 8901 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80576.0 ave 80576 max 80576 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 161152.0 ave 161152 max 161152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161152 Ave neighs/atom = 154.95385 Neighbor list builds = 0 Dangerous builds = 0 1040 -4169.90980432781 eV 2.23960151260786 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07