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 = 0.002 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 = 0.001 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 12 atoms, new total = 840 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_196726067688_000#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) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3515.484 0 -3515.484 536.12858 37 0 -3537.7671 0 -3537.7671 9593.489 Loop time of 3.93013 on 1 procs for 37 steps with 840 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 = -3515.48397812985 -3537.76650117101 -3537.76712098884 Force two-norm initial, final = 25.520821 0.90012437 Force max component initial, final = 6.3980958 0.30580099 Final line search alpha, max atom move = 0.58067533 0.17757109 Iterations, force evaluations = 37 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9054 | 3.9054 | 3.9054 | 0.0 | 99.37 Neigh | 0.0092829 | 0.0092829 | 0.0092829 | 0.0 | 0.24 Comm | 0.0076205 | 0.0076205 | 0.0076205 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007798 | | | 0.20 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4444.00 ave 4444 max 4444 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: 46660.0 ave 46660 max 46660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46660 Ave neighs/atom = 55.547619 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 = 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.545 | 4.545 | 4.545 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -3537.7671 0 -3537.7671 9593.489 9624.828 74 0 -3540.8338 0 -3540.8338 -6153.0143 9855.6937 Loop time of 2.25253 on 1 procs for 37 steps with 840 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 = -3537.76712098884 -3540.83216766352 -3540.83378674891 Force two-norm initial, final = 115.55098 6.3099663 Force max component initial, final = 99.478868 5.9215495 Final line search alpha, max atom move = 0.00013342248 0.00079006785 Iterations, force evaluations = 37 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2309 | 2.2309 | 2.2309 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041285 | 0.0041285 | 0.0041285 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01746 | | | 0.77 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4448.00 ave 4448 max 4448 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: 46860.0 ave 46860 max 46860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46860 Ave neighs/atom = 55.785714 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) = 4.682 | 4.682 | 4.682 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3540.8338 0 -3540.8338 -6153.0143 Loop time of 8.851e-06 on 1 procs for 0 steps with 840 atoms 158.2% 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 | | 8.851e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4420.00 ave 4420 max 4420 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: 48604.0 ave 48604 max 48604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48604 Ave neighs/atom = 57.861905 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) = 4.682 | 4.682 | 4.682 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 -3540.8338 -3540.8338 26.857581 103.88915 3.5322394 -6153.0143 -6153.0143 213.67001 -17719.552 -953.1609 2.2723183 368.6898 Loop time of 1.0044e-05 on 1 procs for 0 steps with 840 atoms 199.1% 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 | | 1.004e-05 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4420.00 ave 4420 max 4420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24302.0 ave 24302 max 24302 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48604.0 ave 48604 max 48604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48604 Ave neighs/atom = 57.861905 Neighbor list builds = 0 Dangerous builds = 0 840 -3540.83378674891 eV 2.27231834881892 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06