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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -49.599800 0.0000000) to (20.249034 49.599800 7.0144710) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8597681 4.2986494 4.6763140 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -49.599800 0.0000000) to (20.249034 49.599800 7.0144710) create_atoms CPU = 0.001 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8597681 4.2986494 4.6763140 Created 602 atoms using lattice units in orthogonal box = (0.0000000 -49.599800 0.0000000) to (20.249034 49.599800 7.0144710) create_atoms CPU = 0.001 seconds 602 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 31 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1196 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_179420363944_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4824.0799 0 -4824.0799 43562.017 103 0 -5110.2925 0 -5110.2925 448.94378 Loop time of 17.7373 on 1 procs for 103 steps with 1196 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4824.07993868427 -5110.28821218334 -5110.29253852407 Force two-norm initial, final = 509.01624 0.22865967 Force max component initial, final = 166.44079 0.054761716 Final line search alpha, max atom move = 1.0000000 0.054761716 Iterations, force evaluations = 103 194 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.705 | 17.705 | 17.705 | 0.0 | 99.82 Neigh | 0.008494 | 0.008494 | 0.008494 | 0.0 | 0.05 Comm | 0.010788 | 0.010788 | 0.010788 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01352 | | | 0.08 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5140.00 ave 5140 max 5140 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: 130128.0 ave 130128 max 130128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130128 Ave neighs/atom = 108.80268 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -5110.2925 0 -5110.2925 448.94378 14089.94 105 0 -5110.3178 0 -5110.3178 360.53565 14090.665 Loop time of 0.395619 on 1 procs for 2 steps with 1196 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5110.29253852407 -5110.31432250801 -5110.31784439519 Force two-norm initial, final = 29.728640 5.9658434 Force max component initial, final = 26.951495 4.9352987 Final line search alpha, max atom move = 0.00010754455 0.00053076449 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39446 | 0.39446 | 0.39446 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017131 | 0.00017131 | 0.00017131 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009902 | | | 0.25 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5106.00 ave 5106 max 5106 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: 130860.0 ave 130860 max 130860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130860 Ave neighs/atom = 109.41472 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.165 | 5.165 | 5.165 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5110.3178 0 -5110.3178 360.53565 Loop time of 2.25e-06 on 1 procs for 0 steps with 1196 atoms 177.8% 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 | | 2.25e-06 | | |100.00 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5106.00 ave 5106 max 5106 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: 130828.0 ave 130828 max 130828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130828 Ave neighs/atom = 109.38796 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.165 | 5.165 | 5.165 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 -5110.3178 -5110.3178 20.242166 99.327605 7.0081688 360.53565 360.53565 328.13452 561.89135 191.58108 2.2758664 749.97149 Loop time of 2.323e-06 on 1 procs for 0 steps with 1196 atoms 215.2% 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 | | 2.323e-06 | | |100.00 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5106.00 ave 5106 max 5106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65414.0 ave 65414 max 65414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 130828.0 ave 130828 max 130828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130828 Ave neighs/atom = 109.38796 Neighbor list builds = 0 Dangerous builds = 0 1196 -5110.31784439519 eV 2.27586635478949 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18