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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -51.944574 0.0000000) to (25.970503 51.944574 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4100855 4.4100855 3.5673230 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.944574 0.0000000) to (25.970503 51.944574 3.5673230) create_atoms CPU = 0.003 seconds 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4100855 4.4100855 3.5673230 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.944574 0.0000000) to (25.970503 51.944574 3.5673230) create_atoms CPU = 0.002 seconds 426 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 38 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 836 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3509.0486 0 -3509.0486 -8435.6773 50 0 -3521.7206 0 -3521.7206 6242.0092 Loop time of 5.97308 on 1 procs for 50 steps with 836 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3509.04856349957 -3521.71768775604 -3521.72057761122 Force two-norm initial, final = 7.8203454 0.60482858 Force max component initial, final = 1.8004869 0.16601156 Final line search alpha, max atom move = 0.54910491 0.091157765 Iterations, force evaluations = 50 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9487 | 5.9487 | 5.9487 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012292 | 0.012292 | 0.012292 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01209 | | | 0.20 Nlocal: 836.000 ave 836 max 836 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: 44860.0 ave 44860 max 44860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44860 Ave neighs/atom = 53.660287 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -3521.7206 0 -3521.7206 6242.0092 9624.8283 86 0 -3524.1205 0 -3524.1205 -2882.049 9835.3236 Loop time of 2.47998 on 1 procs for 36 steps with 836 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3521.72057761122 -3524.11903673441 -3524.12052764895 Force two-norm initial, final = 164.70090 5.1470967 Force max component initial, final = 123.74614 4.4114057 Final line search alpha, max atom move = 0.00013472968 0.00059434729 Iterations, force evaluations = 36 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4526 | 2.4526 | 2.4526 | 0.0 | 98.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00522 | 0.00522 | 0.00522 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02212 | | | 0.89 Nlocal: 836.000 ave 836 max 836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5124.00 ave 5124 max 5124 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: 47060.0 ave 47060 max 47060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47060 Ave neighs/atom = 56.291866 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.692 | 4.692 | 4.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3524.1205 0 -3524.1205 -2882.049 Loop time of 7.617e-06 on 1 procs for 0 steps with 836 atoms 183.8% 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 | | 7.617e-06 | | |100.00 Nlocal: 836.000 ave 836 max 836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5042.00 ave 5042 max 5042 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: 49084.0 ave 49084 max 49084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49084 Ave neighs/atom = 58.712919 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.692 | 4.692 | 4.692 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 -3524.1205 -3524.1205 26.838365 103.88915 3.5274625 -2882.049 -2882.049 307.73328 -8243.291 -710.58932 2.2656671 346.07639 Loop time of 1.1327e-05 on 1 procs for 0 steps with 836 atoms 0.0% 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 | | 1.133e-05 | | |100.00 Nlocal: 836.000 ave 836 max 836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5042.00 ave 5042 max 5042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24542.0 ave 24542 max 24542 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49084.0 ave 49084 max 49084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49084 Ave neighs/atom = 58.712919 Neighbor list builds = 0 Dangerous builds = 0 836 -3524.12052764896 eV 2.26566708382279 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09