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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -37.586844 0.0000000) to (26.575423 37.586844 4.9780328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0610614 5.9342090 4.9780328 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.586844 0.0000000) to (26.575423 37.586844 4.9780328) create_atoms CPU = 0.002 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0610614 5.9342090 4.9780328 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.586844 0.0000000) to (26.575423 37.586844 4.9780328) create_atoms CPU = 0.001 seconds 458 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 904 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3964.0942 0 -3964.0942 5428.0087 59 0 -4003.3373 0 -4003.3373 -8957.1243 Loop time of 0.886875 on 1 procs for 59 steps with 904 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 = -3964.09420773882 -4003.33416189623 -4003.33725322566 Force two-norm initial, final = 35.792455 0.24207966 Force max component initial, final = 8.2570377 0.034421402 Final line search alpha, max atom move = 1.0000000 0.034421402 Iterations, force evaluations = 59 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86424 | 0.86424 | 0.86424 | 0.0 | 97.45 Neigh | 0.01053 | 0.01053 | 0.01053 | 0.0 | 1.19 Comm | 0.0065846 | 0.0065846 | 0.0065846 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005521 | | | 0.62 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6420.00 ave 6420 max 6420 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: 159076.0 ave 159076 max 159076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159076 Ave neighs/atom = 175.96903 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.999 | 4.999 | 4.999 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -4003.3373 0 -4003.3373 -8957.1243 9944.9773 62 0 -4003.3854 0 -4003.3854 -4101.0517 9919.4766 Loop time of 0.0546242 on 1 procs for 3 steps with 904 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 = -4003.33725322565 -4003.38538655071 -4003.38540867875 Force two-norm initial, final = 52.285616 0.29149608 Force max component initial, final = 41.104439 0.096119136 Final line search alpha, max atom move = 0.0018414009 0.00017699387 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052711 | 0.052711 | 0.052711 | 0.0 | 96.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033798 | 0.00033798 | 0.00033798 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001575 | | | 2.88 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6432.00 ave 6432 max 6432 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: 159076.0 ave 159076 max 159076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159076 Ave neighs/atom = 175.96903 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.137 | 5.137 | 5.137 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4003.3854 0 -4003.3854 -4101.0517 Loop time of 2.155e-06 on 1 procs for 0 steps with 904 atoms 185.6% 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 | | 2.155e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6432.00 ave 6432 max 6432 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: 159204.0 ave 159204 max 159204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159204 Ave neighs/atom = 176.11062 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.137 | 5.137 | 5.137 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 -4003.3854 -4003.3854 26.535709 75.173687 4.9726994 -4101.0517 -4101.0517 8.9965521 -12296.643 -15.508361 2.3390805 687.44179 Loop time of 2.365e-06 on 1 procs for 0 steps with 904 atoms 253.7% 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 | | 2.365e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6432.00 ave 6432 max 6432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79602.0 ave 79602 max 79602 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159204.0 ave 159204 max 159204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159204 Ave neighs/atom = 176.11062 Neighbor list builds = 0 Dangerous builds = 0 904 -4003.38540867875 eV 2.3390804829395 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01