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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -42.301627 0.0000000) to (51.808700 42.301627 9.8795315) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5938346 6.1529639 6.5863543 Created 1318 atoms using lattice units in orthogonal box = (0.0000000 -42.301627 0.0000000) to (51.808700 42.301627 9.8795315) create_atoms CPU = 0.002 seconds 1318 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5938346 6.1529639 6.5863543 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -42.301627 0.0000000) to (51.808700 42.301627 9.8795315) create_atoms CPU = 0.002 seconds 1324 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 = 13 20 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2628 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 = 13 20 3 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) = 6.075 | 6.075 | 6.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8135.6399 0 -8135.6399 37530.316 78 0 -8824.2622 0 -8824.2622 2162.9865 Loop time of 2.87316 on 1 procs for 78 steps with 2628 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8135.63985154039 -8824.25358564413 -8824.2621997083 Force two-norm initial, final = 668.52320 0.23983452 Force max component initial, final = 89.840137 0.063018472 Final line search alpha, max atom move = 1.0000000 0.063018472 Iterations, force evaluations = 78 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7333 | 2.7333 | 2.7333 | 0.0 | 95.13 Neigh | 0.10792 | 0.10792 | 0.10792 | 0.0 | 3.76 Comm | 0.012997 | 0.012997 | 0.012997 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0189 | | | 0.66 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8701.00 ave 8701 max 8701 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: 378290.0 ave 378290 max 378290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 378290 Ave neighs/atom = 143.94597 Neighbor list builds = 4 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 = 13 20 3 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.073 | 6.073 | 6.073 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -8824.2622 0 -8824.2622 2162.9865 43303.81 84 0 -8824.5861 0 -8824.5861 12.82779 43417.951 Loop time of 0.183564 on 1 procs for 6 steps with 2628 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 = -8824.2621997083 -8824.58588086896 -8824.58605932716 Force two-norm initial, final = 137.52312 1.4612651 Force max component initial, final = 130.65422 1.3554063 Final line search alpha, max atom move = 0.00028867844 0.00039127658 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17903 | 0.17903 | 0.17903 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059287 | 0.00059287 | 0.00059287 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003942 | | | 2.15 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8561.00 ave 8561 max 8561 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: 376066.0 ave 376066 max 376066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376066 Ave neighs/atom = 143.09970 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 = 13 21 3 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) = 6.211 | 6.211 | 6.211 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8824.5861 0 -8824.5861 12.82779 Loop time of 2.228e-06 on 1 procs for 0 steps with 2628 atoms 179.5% 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 | | 2.228e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8518.00 ave 8518 max 8518 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: 374834.0 ave 374834 max 374834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374834 Ave neighs/atom = 142.63090 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 = 13 21 3 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) = 6.211 | 6.211 | 6.211 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 -8824.5861 -8824.5861 51.809724 85.02496 9.8562479 12.82779 12.82779 3.5818685 50.265488 -15.363987 2.5845962 1817.3336 Loop time of 2.702e-06 on 1 procs for 0 steps with 2628 atoms 259.1% 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 | | 2.702e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8518.00 ave 8518 max 8518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 187417.0 ave 187417 max 187417 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 374834.0 ave 374834 max 374834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374834 Ave neighs/atom = 142.63090 Neighbor list builds = 0 Dangerous builds = 0 2628 -8824.58605932715 eV 2.58459619115271 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03