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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -38.150000 0.0000000) to (31.149345 38.150000 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4499064 4.4119048 5.1383093 Created 588 atoms using lattice units in orthogonal box = (0.0000000 -38.150000 0.0000000) to (31.149345 38.150000 7.7074639) create_atoms CPU = 0.001 seconds 588 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4499064 4.4119048 5.1383093 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -38.150000 0.0000000) to (31.149345 38.150000 7.7074639) create_atoms CPU = 0.001 seconds 590 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 23 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1178 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_486450342170_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.582 | 4.582 | 4.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7196.0419 0 -7196.0419 180984.25 79 0 -7961.4259 0 -7961.4259 19032.9 Loop time of 4.78027 on 1 procs for 79 steps with 1178 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 = -7196.04193430044 -7961.41868185995 -7961.42586306244 Force two-norm initial, final = 613.44921 0.56947492 Force max component initial, final = 110.12324 0.13728629 Final line search alpha, max atom move = 0.57549456 0.079007514 Iterations, force evaluations = 79 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7639 | 4.7639 | 4.7639 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0065152 | 0.0065152 | 0.0065152 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009886 | | | 0.21 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4144.00 ave 4144 max 4144 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: 77584.0 ave 77584 max 77584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77584 Ave neighs/atom = 65.860781 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.582 | 4.582 | 4.582 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -7961.4259 0 -7961.4259 19032.9 18318.291 90 0 -7963.5701 0 -7963.5701 -72.207507 18449.547 Loop time of 0.407465 on 1 procs for 11 steps with 1178 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 = -7961.42586306244 -7963.56889063346 -7963.57011866309 Force two-norm initial, final = 474.38328 2.4166131 Force max component initial, final = 451.60280 1.1452097 Final line search alpha, max atom move = 0.00014698948 0.00016833378 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4045 | 0.4045 | 0.4045 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042553 | 0.00042553 | 0.00042553 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002539 | | | 0.62 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4094.00 ave 4094 max 4094 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: 79468.0 ave 79468 max 79468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79468 Ave neighs/atom = 67.460102 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.720 | 4.720 | 4.720 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7963.5701 0 -7963.5701 -72.207507 Loop time of 1.528e-06 on 1 procs for 0 steps with 1178 atoms 130.9% 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 | | 1.528e-06 | | |100.00 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4100.00 ave 4100 max 4100 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: 78192.0 ave 78192 max 78192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78192 Ave neighs/atom = 66.376910 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.720 | 4.720 | 4.720 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 -7963.5701 -7963.5701 31.088693 77.081873 7.6989408 -72.207507 -72.207507 -37.290379 -100.47023 -78.861915 2.4001031 982.22 Loop time of 1.548e-06 on 1 procs for 0 steps with 1178 atoms 193.8% 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 | | 1.548e-06 | | |100.00 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4100.00 ave 4100 max 4100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39096.0 ave 39096 max 39096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78192.0 ave 78192 max 78192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78192 Ave neighs/atom = 66.376910 Neighbor list builds = 0 Dangerous builds = 0 1178 -7963.57011866309 eV 2.40010314668279 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05