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 = 3.6385685 3.6385685 3.6385685 Created orthogonal box = (0.0000000 -69.609913 0.0000000) to (40.189302 69.609913 6.3021854) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9295692 5.3253486 6.3021854 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.609913 0.0000000) to (40.189302 69.609913 6.3021854) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9295692 5.3253486 6.3021854 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.609913 0.0000000) to (40.189302 69.609913 6.3021854) create_atoms CPU = 0.002 seconds 1466 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2930 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_097471813275_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.50 | 12.50 | 12.50 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9289.6258 0 -9289.6258 63521.478 63 0 -9952.7538 0 -9952.7538 3271.2195 Loop time of 4.46779 on 1 procs for 63 steps with 2930 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 = -9289.62577335461 -9952.74398007555 -9952.75375279507 Force two-norm initial, final = 1303.4862 0.29414144 Force max component initial, final = 324.24704 0.029198910 Final line search alpha, max atom move = 0.77647115 0.022672112 Iterations, force evaluations = 63 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2515 | 4.2515 | 4.2515 | 0.0 | 95.16 Neigh | 0.18204 | 0.18204 | 0.18204 | 0.0 | 4.07 Comm | 0.018679 | 0.018679 | 0.018679 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01561 | | | 0.35 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16788.0 ave 16788 max 16788 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: 932896.0 ave 932896 max 932896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 932896 Ave neighs/atom = 318.39454 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.50 | 12.50 | 12.50 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -9952.7538 0 -9952.7538 3271.2195 35261.658 65 0 -9952.8579 0 -9952.8579 -292.23827 35349.31 Loop time of 0.184823 on 1 procs for 2 steps with 2930 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 = -9952.75375279506 -9952.84801504803 -9952.85786613817 Force two-norm initial, final = 130.69482 12.089208 Force max component initial, final = 100.89151 9.5752884 Final line search alpha, max atom move = 4.1225150e-05 0.00039474270 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18222 | 0.18222 | 0.18222 | 0.0 | 98.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050377 | 0.00050377 | 0.00050377 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002099 | | | 1.14 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16784.0 ave 16784 max 16784 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: 932868.0 ave 932868 max 932868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 932868 Ave neighs/atom = 318.38498 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.01 | 12.01 | 12.01 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9952.8579 0 -9952.8579 -292.23827 Loop time of 2.093e-06 on 1 procs for 0 steps with 2930 atoms 191.1% 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 | | 2.093e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16784.0 ave 16784 max 16784 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: 932564.0 ave 932564 max 932564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 932564 Ave neighs/atom = 318.28123 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.01 | 12.01 | 12.01 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 -9952.8579 -9952.8579 40.218036 139.44875 6.3029732 -292.23827 -292.23827 -434.30185 -137.82865 -304.5843 2.2664095 1221.0677 Loop time of 2.167e-06 on 1 procs for 0 steps with 2930 atoms 323.0% 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 | | 2.167e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16784.0 ave 16784 max 16784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 466282.0 ave 466282 max 466282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 932564.0 ave 932564 max 932564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 932564 Ave neighs/atom = 318.28123 Neighbor list builds = 0 Dangerous builds = 0 2930 -9952.85786613817 eV 2.26640948285836 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05