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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -65.000747 0.0000000) to (45.962469 65.000747 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2418168 6.0185877 5.1069410 Created 1296 atoms using lattice units in orthogonal box = (0.0000000 -65.000747 0.0000000) to (45.962469 65.000747 5.1069410) create_atoms CPU = 0.004 seconds 1296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2418168 6.0185877 5.1069410 Created 1300 atoms using lattice units in orthogonal box = (0.0000000 -65.000747 0.0000000) to (45.962469 65.000747 5.1069410) create_atoms CPU = 0.004 seconds 1300 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 18 49 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 2596 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 18 49 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.444 | 6.444 | 6.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10627.397 0 -10627.397 34314.294 80 0 -11007.227 0 -11007.227 5103.6538 Loop time of 20.3435 on 1 procs for 80 steps with 2596 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10627.3974659057 -11007.2165068919 -11007.2270427449 Force two-norm initial, final = 325.79726 0.38342767 Force max component initial, final = 75.421609 0.037234259 Final line search alpha, max atom move = 1.0000000 0.037234259 Iterations, force evaluations = 80 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.267 | 20.267 | 20.267 | 0.0 | 99.63 Neigh | 0.04198 | 0.04198 | 0.04198 | 0.0 | 0.21 Comm | 0.01395 | 0.01395 | 0.01395 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02032 | | | 0.10 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7811.00 ave 7811 max 7811 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: 140496.0 ave 140496 max 140496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140496 Ave neighs/atom = 54.120185 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 18 49 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.444 | 6.444 | 6.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -11007.227 0 -11007.227 5103.6538 30514.941 84 0 -11007.446 0 -11007.446 4.235232 30608.092 Loop time of 1.15194 on 1 procs for 4 steps with 2596 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 = -11007.2270427449 -11007.4462356586 -11007.4463043254 Force two-norm initial, final = 181.50335 0.46921694 Force max component initial, final = 125.53191 0.17635315 Final line search alpha, max atom move = 0.00060613015 0.00010689296 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1475 | 1.1475 | 1.1475 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055564 | 0.00055564 | 0.00055564 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003853 | | | 0.33 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7799.00 ave 7799 max 7799 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: 140472.0 ave 140472 max 140472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140472 Ave neighs/atom = 54.110940 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 18 49 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 6.582 | 6.582 | 6.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11007.446 0 -11007.446 4.235232 Loop time of 2.212e-06 on 1 procs for 0 steps with 2596 atoms 180.8% 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 | | 2.212e-06 | | |100.00 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7799.00 ave 7799 max 7799 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: 140424.0 ave 140424 max 140424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140424 Ave neighs/atom = 54.092450 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 18 49 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 6.582 | 6.582 | 6.582 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 -11007.446 -11007.446 46.044897 130.25577 5.1033784 4.235232 4.235232 9.2477373 3.7417455 -0.28378693 2.3276208 1103.1307 Loop time of 2.234e-06 on 1 procs for 0 steps with 2596 atoms 223.8% 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 | | 2.234e-06 | | |100.00 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7799.00 ave 7799 max 7799 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70212.0 ave 70212 max 70212 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 140424.0 ave 140424 max 140424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140424 Ave neighs/atom = 54.092450 Neighbor list builds = 0 Dangerous builds = 0 2596 -11007.4463043254 eV 2.32762083559737 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22