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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -56.867637 0.0000000) to (34.824173 56.867637 8.8453489) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6168022 5.5033197 5.8968993 Created 1487 atoms using lattice units in orthogonal box = (0.0000000 -56.867637 0.0000000) to (34.824173 56.867637 8.8453489) create_atoms CPU = 0.002 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6168022 5.5033197 5.8968993 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -56.867637 0.0000000) to (34.824173 56.867637 8.8453489) create_atoms CPU = 0.002 seconds 1493 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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2975 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_321233176498_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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.580 | 5.580 | 5.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12171.38 0 -12171.38 32901.115 369 0 -12612.072 0 -12612.072 3541.3354 Loop time of 131.273 on 1 procs for 369 steps with 2975 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 = -12171.3802484087 -12612.0601199312 -12612.0719058644 Force two-norm initial, final = 473.13876 0.36760173 Force max component initial, final = 90.598236 0.10181595 Final line search alpha, max atom move = 0.60322750 0.061418182 Iterations, force evaluations = 369 712 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 130.75 | 130.75 | 130.75 | 0.0 | 99.60 Neigh | 0.25279 | 0.25279 | 0.25279 | 0.0 | 0.19 Comm | 0.10716 | 0.10716 | 0.10716 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1668 | | | 0.13 Nlocal: 2975.00 ave 2975 max 2975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7431.00 ave 7431 max 7431 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: 220240.0 ave 220240 max 220240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 220240 Ave neighs/atom = 74.030252 Neighbor list builds = 8 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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 369 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.581 | 5.581 | 5.581 Mbytes Step Temp E_pair E_mol TotEng Press Volume 369 0 -12612.072 0 -12612.072 3541.3354 35034.1 374 0 -12612.55 0 -12612.55 330.92364 35099.468 Loop time of 1.28227 on 1 procs for 5 steps with 2975 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 = -12612.0719058644 -12612.5458703377 -12612.5496208016 Force two-norm initial, final = 201.80318 14.028130 Force max component initial, final = 162.85307 10.597268 Final line search alpha, max atom move = 5.5493099e-05 0.00058807523 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.276 | 1.276 | 1.276 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00087408 | 0.00087408 | 0.00087408 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005417 | | | 0.42 Nlocal: 2975.00 ave 2975 max 2975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7464.00 ave 7464 max 7464 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: 219818.0 ave 219818 max 219818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219818 Ave neighs/atom = 73.888403 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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.719 | 5.719 | 5.719 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12612.55 0 -12612.55 330.92364 Loop time of 3.883e-06 on 1 procs for 0 steps with 2975 atoms 154.5% 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 | | 3.883e-06 | | |100.00 Nlocal: 2975.00 ave 2975 max 2975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7454.00 ave 7454 max 7454 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: 219492.0 ave 219492 max 219492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219492 Ave neighs/atom = 73.778824 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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.719 | 5.719 | 5.719 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 -12612.55 -12612.55 34.703142 113.96557 8.8747902 330.92364 330.92364 100.1219 484.71025 407.93878 2.2592324 7645.3569 Loop time of 3.926e-06 on 1 procs for 0 steps with 2975 atoms 203.8% 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 | | 3.926e-06 | | |100.00 Nlocal: 2975.00 ave 2975 max 2975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7454.00 ave 7454 max 7454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109746.0 ave 109746 max 109746 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 219492.0 ave 219492 max 219492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219492 Ave neighs/atom = 73.778824 Neighbor list builds = 0 Dangerous builds = 0 2975 -12612.5496208016 eV 2.25923235972262 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:13