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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -41.790702 0.0000000) to (20.893916 41.790702 2.8700001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5480235 3.5480235 2.8700001 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.790702 0.0000000) to (20.893916 41.790702 2.8700001) create_atoms CPU = 0.001 seconds 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5480235 3.5480235 2.8700001 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.790702 0.0000000) to (20.893916 41.790702 2.8700001) create_atoms CPU = 0.001 seconds 213 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 28 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 420 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1766.4766 0 -1766.4766 8369.5022 59 0 -1788.5067 0 -1788.5067 -1780.9491 Loop time of 0.393568 on 1 procs for 59 steps with 420 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1766.47656863376 -1788.50523710205 -1788.50674903704 Force two-norm initial, final = 44.930528 0.10594588 Force max component initial, final = 17.680972 0.015483656 Final line search alpha, max atom move = 1.0000000 0.015483656 Iterations, force evaluations = 59 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37264 | 0.37264 | 0.37264 | 0.0 | 94.68 Neigh | 0.0052789 | 0.0052789 | 0.0052789 | 0.0 | 1.34 Comm | 0.00858 | 0.00858 | 0.00858 | 0.0 | 2.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007067 | | | 1.80 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3557.00 ave 3557 max 3557 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: 27338.0 ave 27338 max 27338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27338 Ave neighs/atom = 65.090476 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -1788.5067 0 -1788.5067 -1780.9491 5012.0041 64 0 -1788.5524 0 -1788.5524 3019.2646 4997.6677 Loop time of 0.0270321 on 1 procs for 5 steps with 420 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1788.50674903704 -1788.55213855714 -1788.55241847661 Force two-norm initial, final = 25.821308 0.80445076 Force max component initial, final = 24.803369 0.77877944 Final line search alpha, max atom move = 0.00043838464 0.00034140495 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.024929 | 0.024929 | 0.024929 | 0.0 | 92.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046692 | 0.00046692 | 0.00046692 | 0.0 | 1.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001636 | | | 6.05 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3390.00 ave 3390 max 3390 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: 27220.0 ave 27220 max 27220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27220 Ave neighs/atom = 64.809524 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1788.5524 0 -1788.5524 3019.2646 Loop time of 6.475e-06 on 1 procs for 0 steps with 420 atoms 154.4% 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 | | 6.475e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3390.00 ave 3390 max 3390 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: 27226.0 ave 27226 max 27226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27226 Ave neighs/atom = 64.823810 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.595 | 4.595 | 4.595 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 -1788.5524 -1788.5524 20.915941 83.581404 2.8587772 3019.2646 3019.2646 249.92806 8850.7889 -42.923211 2.3651925 253.47712 Loop time of 6.745e-06 on 1 procs for 0 steps with 420 atoms 281.7% 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 | | 6.745e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3390.00 ave 3390 max 3390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13613.0 ave 13613 max 13613 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27226.0 ave 27226 max 27226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27226 Ave neighs/atom = 64.823810 Neighbor list builds = 0 Dangerous builds = 0 420 -1788.55237647661 eV 2.3651925465761 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00