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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -64.999774 0.0000000) to (45.961781 64.999774 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2417233 6.0184975 5.1068645 Created 1295 atoms using lattice units in orthogonal box = (0.0000000 -64.999774 0.0000000) to (45.961781 64.999774 5.1068645) create_atoms CPU = 0.004 seconds 1295 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2417233 6.0184975 5.1068645 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -64.999774 0.0000000) to (45.961781 64.999774 5.1068645) create_atoms CPU = 0.003 seconds 1299 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2594 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_260546967793_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.116 | 6.116 | 6.116 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10498.764 0 -10498.764 41543.428 977 0 -11056.069 0 -11056.069 4786.7002 Loop time of 397.602 on 1 procs for 977 steps with 2594 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 = -10498.7640169477 -11056.0584239485 -11056.0693866782 Force two-norm initial, final = 565.90152 0.36771657 Force max component initial, final = 157.07029 0.095408169 Final line search alpha, max atom move = 0.46480537 0.044346230 Iterations, force evaluations = 977 1843 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 396.32 | 396.32 | 396.32 | 0.0 | 99.68 Neigh | 0.68886 | 0.68886 | 0.68886 | 0.0 | 0.17 Comm | 0.31766 | 0.31766 | 0.31766 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2767 | | | 0.07 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11008.0 ave 11008 max 11008 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: 293160.0 ave 293160 max 293160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293160 Ave neighs/atom = 113.01465 Neighbor list builds = 32 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 977 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.733 Mbytes Step Temp E_pair E_mol TotEng Press Volume 977 0 -11056.069 0 -11056.069 4786.7002 30513.57 1003 0 -11078.266 0 -11078.266 -19.198566 30552.238 Loop time of 6.80349 on 1 procs for 26 steps with 2594 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 = -11056.0693866782 -11078.2613019175 -11078.2658639279 Force two-norm initial, final = 1321.4102 3.1911148 Force max component initial, final = 950.00375 2.0640024 Final line search alpha, max atom move = 6.5928391e-05 0.00013607636 Iterations, force evaluations = 26 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.7459 | 6.7459 | 6.7459 | 0.0 | 99.15 Neigh | 0.039091 | 0.039091 | 0.039091 | 0.0 | 0.57 Comm | 0.0033244 | 0.0033244 | 0.0033244 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01517 | | | 0.22 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11216.0 ave 11216 max 11216 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: 292470.0 ave 292470 max 292470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292470 Ave neighs/atom = 112.74865 Neighbor list builds = 2 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.873 | 5.873 | 5.873 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11078.266 0 -11078.266 -19.198566 Loop time of 2.453e-06 on 1 procs for 0 steps with 2594 atoms 163.1% 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 | | 2.453e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11265.0 ave 11265 max 11265 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: 292448.0 ave 292448 max 292448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292448 Ave neighs/atom = 112.74017 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.873 | 5.873 | 5.873 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 -11078.266 -11078.266 46.277076 132.62778 4.9778594 -19.198566 -19.198566 -108.97994 -4.0748139 55.45906 2.3113565 5332.3604 Loop time of 2.386e-06 on 1 procs for 0 steps with 2594 atoms 251.5% 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 | | 2.386e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11265.0 ave 11265 max 11265 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146224.0 ave 146224 max 146224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 292448.0 ave 292448 max 292448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292448 Ave neighs/atom = 112.74017 Neighbor list builds = 0 Dangerous builds = 0 2594 -11078.2658639279 eV 2.31135646748737 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:06:45