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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -41.830000 0.0000000) to (29.575507 41.830000 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7075539 6.6041183 5.5400000 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -41.830000 0.0000000) to (29.575507 41.830000 5.5400000) create_atoms CPU = 0.004 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7075539 6.6041183 5.5400000 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -41.830000 0.0000000) to (29.575507 41.830000 5.5400000) create_atoms CPU = 0.003 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 26 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 8 atoms, new total = 908 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_020840179467_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 = 10 26 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) = 4.565 | 4.565 | 4.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5141.4961 0 -5141.4961 21817.593 34 0 -5207.931 0 -5207.931 7143.1256 Loop time of 2.13103 on 1 procs for 34 steps with 908 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5141.49606134201 -5207.92598765153 -5207.93102028279 Force two-norm initial, final = 82.988896 0.28124764 Force max component initial, final = 18.369368 0.051925064 Final line search alpha, max atom move = 1.0000000 0.051925064 Iterations, force evaluations = 34 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1053 | 2.1053 | 2.1053 | 0.0 | 98.79 Neigh | 0.01153 | 0.01153 | 0.01153 | 0.0 | 0.54 Comm | 0.006965 | 0.006965 | 0.006965 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007278 | | | 0.34 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4349.00 ave 4349 max 4349 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: 69956.0 ave 69956 max 69956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69956 Ave neighs/atom = 77.044053 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 26 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 : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.565 | 4.565 | 4.565 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -5207.931 0 -5207.931 7143.1256 13707.549 36 0 -5207.9591 0 -5207.9591 4338.0211 13729.49 Loop time of 0.140058 on 1 procs for 2 steps with 908 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5207.93102028279 -5207.95661757042 -5207.95909511391 Force two-norm initial, final = 41.996758 0.67274180 Force max component initial, final = 36.383569 0.43084171 Final line search alpha, max atom move = 0.00016374333 7.0547457e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13829 | 0.13829 | 0.13829 | 0.0 | 98.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041227 | 0.00041227 | 0.00041227 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001357 | | | 0.97 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4349.00 ave 4349 max 4349 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: 69984.0 ave 69984 max 69984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69984 Ave neighs/atom = 77.074890 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 = 10 26 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) = 4.703 | 4.703 | 4.703 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5207.9591 0 -5207.9591 4338.0211 Loop time of 6.385e-06 on 1 procs for 0 steps with 908 atoms 172.3% 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 | | 6.385e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4349.00 ave 4349 max 4349 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: 69980.0 ave 69980 max 69980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69980 Ave neighs/atom = 77.070485 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 = 10 26 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) = 4.703 | 4.703 | 4.703 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 -5207.9591 -5207.9591 29.617714 83.66 5.5409598 4338.0211 4338.0211 49.42326 12914.354 50.286214 2.5433917 820.94912 Loop time of 6.886e-06 on 1 procs for 0 steps with 908 atoms 261.4% 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 | | 6.886e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4349.00 ave 4349 max 4349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34990.0 ave 34990 max 34990 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69980.0 ave 69980 max 69980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69980 Ave neighs/atom = 77.070485 Neighbor list builds = 0 Dangerous builds = 0 908 -5207.95909511391 eV 2.54339167685689 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02