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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -72.833315 0.0000000) to (44.598862 72.833315 9.0103308) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1576915 5.2021169 6.0068872 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -72.833315 0.0000000) to (44.598862 72.833315 9.0103308) create_atoms CPU = 0.008 seconds 2357 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1576915 5.2021169 6.0068872 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -72.833315 0.0000000) to (44.598862 72.833315 9.0103308) create_atoms CPU = 0.008 seconds 2357 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 = 15 48 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 35 atoms, new total = 4679 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 = 15 48 3 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) = 6.284 | 6.284 | 6.284 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19642.571 0 -19642.571 2217.9669 30 0 -19707.577 0 -19707.577 -4803.287 Loop time of 1.30336 on 1 procs for 30 steps with 4679 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 = -19642.5705309655 -19707.5585984455 -19707.5773629015 Force two-norm initial, final = 55.778047 0.45097432 Force max component initial, final = 8.5164711 0.037619566 Final line search alpha, max atom move = 1.0000000 0.037619566 Iterations, force evaluations = 30 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2694 | 1.2694 | 1.2694 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012566 | 0.012566 | 0.012566 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02141 | | | 1.64 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11001.0 ave 11001 max 11001 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: 363060.0 ave 363060 max 363060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363060 Ave neighs/atom = 77.593503 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 15 48 3 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 : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.284 | 6.284 | 6.284 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -19707.577 0 -19707.577 -4803.287 58536.209 34 0 -19707.872 0 -19707.872 -1202.6384 58336.351 Loop time of 0.186334 on 1 procs for 4 steps with 4679 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 = -19707.5773629014 -19707.8699134185 -19707.8721519838 Force two-norm initial, final = 209.56589 0.48019640 Force max component initial, final = 184.14760 0.043875306 Final line search alpha, max atom move = 5.3901622e-05 2.3649502e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17687 | 0.17687 | 0.17687 | 0.0 | 94.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017039 | 0.0017039 | 0.0017039 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007764 | | | 4.17 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11007.0 ave 11007 max 11007 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: 363802.0 ave 363802 max 363802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363802 Ave neighs/atom = 77.752084 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 = 15 48 3 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) = 6.422 | 6.422 | 6.422 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19707.872 0 -19707.872 -1202.6384 Loop time of 6.235e-06 on 1 procs for 0 steps with 4679 atoms 208.5% 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 | | 6.235e-06 | | |100.00 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11007.0 ave 11007 max 11007 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: 363918.0 ave 363918 max 363918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363918 Ave neighs/atom = 77.776875 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 = 15 48 3 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) = 6.422 | 6.422 | 6.422 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 -19707.872 -19707.872 44.467716 145.66663 9.0060502 -1202.6384 -1202.6384 -0.092275429 -3606.9415 -0.88153523 2.3348791 1775.1225 Loop time of 7.798e-06 on 1 procs for 0 steps with 4679 atoms 705.3% 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 | | 7.798e-06 | | |100.00 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11007.0 ave 11007 max 11007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 181959.0 ave 181959 max 181959 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 363918.0 ave 363918 max 363918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363918 Ave neighs/atom = 77.776875 Neighbor list builds = 0 Dangerous builds = 0 4679 -19707.8716840838 eV 2.33487914311509 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02