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 -51.576803 0.0000000) to (36.470307 51.576803 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7208325 4.5508944 5.1068645 Created 816 atoms using lattice units in orthogonal box = (0.0000000 -51.576803 0.0000000) to (36.470307 51.576803 5.1068645) create_atoms CPU = 0.002 seconds 816 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7208325 4.5508944 5.1068645 Created 824 atoms using lattice units in orthogonal box = (0.0000000 -51.576803 0.0000000) to (36.470307 51.576803 5.1068645) create_atoms CPU = 0.002 seconds 824 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1640 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_179420363944_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.130 | 5.130 | 5.130 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6143.8571 0 -6143.8571 97896.861 363 0 -6956.7339 0 -6956.7339 13728.808 Loop time of 72.4549 on 1 procs for 363 steps with 1640 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6143.85709824016 -6956.72731182409 -6956.73392325946 Force two-norm initial, final = 821.80366 0.26321050 Force max component initial, final = 128.71254 0.052540091 Final line search alpha, max atom move = 1.0000000 0.052540091 Iterations, force evaluations = 363 684 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 72.177 | 72.177 | 72.177 | 0.0 | 99.62 Neigh | 0.10851 | 0.10851 | 0.10851 | 0.0 | 0.15 Comm | 0.077013 | 0.077013 | 0.077013 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09266 | | | 0.13 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7212.00 ave 7212 max 7212 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: 156032.0 ave 156032 max 156032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156032 Ave neighs/atom = 95.141463 Neighbor list builds = 9 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 363 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.128 | 5.128 | 5.128 Mbytes Step Temp E_pair E_mol TotEng Press Volume 363 0 -6956.7339 0 -6956.7339 13728.808 19212.247 388 0 -6960.9241 0 -6960.9241 301.06431 19354.566 Loop time of 3.44768 on 1 procs for 25 steps with 1640 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6956.73392325946 -6960.92120005423 -6960.92409560109 Force two-norm initial, final = 411.51256 7.9124123 Force max component initial, final = 386.18911 6.6333457 Final line search alpha, max atom move = 7.2649448e-05 0.00048190891 Iterations, force evaluations = 25 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3976 | 3.3976 | 3.3976 | 0.0 | 98.55 Neigh | 0.02351 | 0.02351 | 0.02351 | 0.0 | 0.68 Comm | 0.0022499 | 0.0022499 | 0.0022499 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02434 | | | 0.71 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7237.00 ave 7237 max 7237 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: 155068.0 ave 155068 max 155068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155068 Ave neighs/atom = 94.553659 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.267 | 5.267 | 5.267 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6960.9241 0 -6960.9241 301.06431 Loop time of 2.319e-06 on 1 procs for 0 steps with 1640 atoms 215.6% 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 | | 2.319e-06 | | |100.00 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7218.00 ave 7218 max 7218 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: 155144.0 ave 155144 max 155144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155144 Ave neighs/atom = 94.600000 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.267 | 5.267 | 5.267 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 -6960.9241 -6960.9241 36.333234 105.37428 5.0552746 301.06431 301.06431 547.04643 345.58627 10.560244 2.3219114 4117.7312 Loop time of 2.6e-06 on 1 procs for 0 steps with 1640 atoms 269.2% 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 | | 2.6e-06 | | |100.00 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7218.00 ave 7218 max 7218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77572.0 ave 77572 max 77572 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 155144.0 ave 155144 max 155144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155144 Ave neighs/atom = 94.600000 Neighbor list builds = 0 Dangerous builds = 0 1640 -6960.92409560108 eV 2.32191140645665 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:16