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 = 2.8553126 2.8553126 2.8553126 Created orthogonal box = (0.0000000 -37.880002 0.0000000) to (13.392603 37.880002 4.0380218) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8700375 4.3045457 4.0380218 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -37.880002 0.0000000) to (13.392603 37.880002 4.0380218) create_atoms CPU = 0.002 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8700375 4.3045457 4.0380218 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.880002 0.0000000) to (13.392603 37.880002 4.0380218) create_atoms CPU = 0.001 seconds 178 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 18 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 352 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.490 | 4.490 | 4.490 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1328.8739 0 -1328.8739 72049.08 88 0 -1404.8719 0 -1404.8719 9586.9358 Loop time of 1.96408 on 1 procs for 88 steps with 352 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 = -1328.87385472176 -1404.87074514178 -1404.87194810466 Force two-norm initial, final = 239.52626 0.15378236 Force max component initial, final = 76.974517 0.029878093 Final line search alpha, max atom move = 1.0000000 0.029878093 Iterations, force evaluations = 88 172 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9307 | 1.9307 | 1.9307 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020753 | 0.020753 | 0.020753 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01266 | | | 0.64 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5021.00 ave 5021 max 5021 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: 79872.0 ave 79872 max 79872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79872 Ave neighs/atom = 226.90909 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.490 | 4.490 | 4.490 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -1404.8719 0 -1404.8719 9586.9358 4097.0725 96 0 -1405.0193 0 -1405.0193 4.3160279 4120.2944 Loop time of 0.116237 on 1 procs for 8 steps with 352 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 = -1404.87194810466 -1405.01924773532 -1405.01932256169 Force two-norm initial, final = 48.978184 0.35485506 Force max component initial, final = 44.445286 0.14760579 Final line search alpha, max atom move = 0.0021573106 0.00031843153 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11183 | 0.11183 | 0.11183 | 0.0 | 96.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011533 | 0.0011533 | 0.0011533 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003253 | | | 2.80 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5021.00 ave 5021 max 5021 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: 79556.0 ave 79556 max 79556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79556 Ave neighs/atom = 226.01136 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.628 | 4.628 | 4.628 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1405.0193 0 -1405.0193 4.3160279 Loop time of 6.384e-06 on 1 procs for 0 steps with 352 atoms 188.0% 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 | | 6.384e-06 | | |100.00 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5021.00 ave 5021 max 5021 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: 79140.0 ave 79140 max 79140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79140 Ave neighs/atom = 224.82955 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.628 | 4.628 | 4.628 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 -1405.0193 -1405.0193 13.387793 76.301697 4.0335279 4.3160279 4.3160279 -11.001956 -33.382597 57.332637 2.2653978 280.27168 Loop time of 6.936e-06 on 1 procs for 0 steps with 352 atoms 259.5% 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 | | 6.936e-06 | | |100.00 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5021.00 ave 5021 max 5021 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39570.0 ave 39570 max 39570 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79140.0 ave 79140 max 79140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79140 Ave neighs/atom = 224.82955 Neighbor list builds = 0 Dangerous builds = 0 352 -1405.01932256169 eV 2.2653978136436 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02