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 -51.651466 0.0000000) to (36.523102 51.651466 5.7039502) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2356515 6.9288551 5.7039502 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -51.651466 0.0000000) to (36.523102 51.651466 5.7039502) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2356515 6.9288551 5.7039502 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -51.651466 0.0000000) to (36.523102 51.651466 5.7039502) create_atoms CPU = 0.004 seconds 660 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 = 9 25 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1312 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 = 9 25 2 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) = 5.080 | 5.080 | 5.080 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4279.7211 0 -4279.7211 19237.317 83 0 -4411.2137 0 -4411.2137 3404.6491 Loop time of 3.94421 on 1 procs for 83 steps with 1312 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 = -4279.72112805925 -4411.20954051091 -4411.21365854877 Force two-norm initial, final = 167.06446 0.16360888 Force max component initial, final = 36.688651 0.016130939 Final line search alpha, max atom move = 1.0000000 0.016130939 Iterations, force evaluations = 83 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8614 | 3.8614 | 3.8614 | 0.0 | 97.90 Neigh | 0.028772 | 0.028772 | 0.028772 | 0.0 | 0.73 Comm | 0.028488 | 0.028488 | 0.028488 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0255 | | | 0.65 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7566.00 ave 7566 max 7566 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: 190720.0 ave 190720 max 190720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190720 Ave neighs/atom = 145.36585 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 2 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.076 | 5.076 | 5.076 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -4411.2137 0 -4411.2137 3404.6491 21520.681 89 0 -4411.421 0 -4411.421 -123.55619 21613.464 Loop time of 0.224732 on 1 procs for 6 steps with 1312 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 = -4411.21365854877 -4411.42018279072 -4411.42099590335 Force two-norm initial, final = 91.468715 3.3920970 Force max component initial, final = 82.867664 2.7193084 Final line search alpha, max atom move = 0.00020448275 0.00055605167 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21812 | 0.21812 | 0.21812 | 0.0 | 97.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013254 | 0.0013254 | 0.0013254 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005286 | | | 2.35 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7066.00 ave 7066 max 7066 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: 187608.0 ave 187608 max 187608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187608 Ave neighs/atom = 142.99390 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 = 9 25 2 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) = 5.214 | 5.214 | 5.214 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4411.421 0 -4411.421 -123.55619 Loop time of 6.525e-06 on 1 procs for 0 steps with 1312 atoms 183.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7066.00 ave 7066 max 7066 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: 186568.0 ave 186568 max 186568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186568 Ave neighs/atom = 142.20122 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 = 9 25 2 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) = 5.214 | 5.214 | 5.214 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 -4411.421 -4411.421 36.488194 103.85246 5.703681 -123.55619 -123.55619 -201.38595 -21.258711 -148.0239 2.6502792 765.05262 Loop time of 7.077e-06 on 1 procs for 0 steps with 1312 atoms 282.6% 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 | | 7.077e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7066.00 ave 7066 max 7066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93284.0 ave 93284 max 93284 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186568.0 ave 186568 max 186568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186568 Ave neighs/atom = 142.20122 Neighbor list builds = 0 Dangerous builds = 0 1312 -4411.42099590335 eV 2.65027921108206 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05