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 = 3.5878716 3.5878716 3.5878716 Created orthogonal box = (0.0000000 -58.296013 0.0000000) to (20.610753 58.296013 5.0740167) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6211145 6.1829105 5.0740167 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.296013 0.0000000) to (20.610753 58.296013 5.0740167) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6211145 6.1829105 5.0740167 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.296013 0.0000000) to (20.610753 58.296013 5.0740167) create_atoms CPU = 0.002 seconds 530 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 6 29 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 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_228059236215_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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 5.455 | 5.455 | 5.455 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3539.0221 0 -3539.0221 36789.682 55 0 -3711.8121 0 -3711.8121 3598.7358 Loop time of 2.21711 on 1 procs for 55 steps with 1056 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3539.02208568788 -3711.80888123789 -3711.81206982028 Force two-norm initial, final = 351.60526 0.17681314 Force max component initial, final = 114.58222 0.026247055 Final line search alpha, max atom move = 1.0000000 0.026247055 Iterations, force evaluations = 55 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1887 | 2.1887 | 2.1887 | 0.0 | 98.72 Neigh | 0.011804 | 0.011804 | 0.011804 | 0.0 | 0.53 Comm | 0.0096305 | 0.0096305 | 0.0096305 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006955 | | | 0.31 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8156.00 ave 8156 max 8156 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: 210500.0 ave 210500 max 210500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210500 Ave neighs/atom = 199.33712 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.454 | 5.454 | 5.454 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -3711.8121 0 -3711.8121 3598.7358 12193.113 61 0 -3711.9955 0 -3711.9955 -103.82048 12224.3 Loop time of 0.203691 on 1 procs for 6 steps with 1056 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 = -3711.81206982028 -3711.99526309343 -3711.99546303806 Force two-norm initial, final = 75.135937 1.5508982 Force max component initial, final = 73.671831 1.1074499 Final line search alpha, max atom move = 0.00041838125 0.00046333627 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20021 | 0.20021 | 0.20021 | 0.0 | 98.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059989 | 0.00059989 | 0.00059989 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002883 | | | 1.42 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8108.00 ave 8108 max 8108 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: 210796.0 ave 210796 max 210796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210796 Ave neighs/atom = 199.61742 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 5.591 | 5.591 | 5.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3711.9955 0 -3711.9955 -103.82048 Loop time of 2.455e-06 on 1 procs for 0 steps with 1056 atoms 162.9% 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 | | 2.455e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8126.00 ave 8126 max 8126 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: 210656.0 ave 210656 max 210656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210656 Ave neighs/atom = 199.48485 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 5.591 | 5.591 | 5.591 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 -3711.9955 -3711.9955 20.559682 117.15333 5.075198 -103.82048 -103.82048 -134.72211 -145.84656 -30.892764 2.3545987 400.10263 Loop time of 2.512e-06 on 1 procs for 0 steps with 1056 atoms 238.9% 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 | | 2.512e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8126.00 ave 8126 max 8126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105328.0 ave 105328 max 105328 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 210656.0 ave 210656 max 210656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210656 Ave neighs/atom = 199.48485 Neighbor list builds = 0 Dangerous builds = 0 1056 -3711.99546303806 eV 2.35459873986692 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02