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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -45.053935 0.0000000) to (31.857943 45.053935 4.9753748) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4391610 6.0438205 4.9753748 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -45.053935 0.0000000) to (31.857943 45.053935 4.9753748) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4391610 6.0438205 4.9753748 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.053935 0.0000000) to (31.857943 45.053935 4.9753748) create_atoms CPU = 0.001 seconds 660 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1312 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_222110751402_000#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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 5.897 | 5.897 | 5.897 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5059.7522 0 -5059.7522 124391.05 96 0 -5734.8892 0 -5734.8892 5813.5887 Loop time of 3.43913 on 1 procs for 96 steps with 1312 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5059.75222181965 -5734.88475101215 -5734.88923509886 Force two-norm initial, final = 1161.8821 0.20666797 Force max component initial, final = 279.02656 0.036600473 Final line search alpha, max atom move = 1.0000000 0.036600473 Iterations, force evaluations = 96 187 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3934 | 3.3934 | 3.3934 | 0.0 | 98.67 Neigh | 0.017392 | 0.017392 | 0.017392 | 0.0 | 0.51 Comm | 0.016301 | 0.016301 | 0.016301 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01199 | | | 0.35 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9551.00 ave 9551 max 9551 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: 324544.0 ave 324544 max 324544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324544 Ave neighs/atom = 247.36585 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.895 | 5.895 | 5.895 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -5734.8892 0 -5734.8892 5813.5887 14282.566 99 0 -5735.0025 0 -5735.0025 195.62373 14329.167 Loop time of 0.0909277 on 1 procs for 3 steps with 1312 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 = -5734.88923509886 -5734.99878014101 -5735.00245583209 Force two-norm initial, final = 95.533345 3.2336305 Force max component initial, final = 78.266628 2.5470451 Final line search alpha, max atom move = 0.00012201081 0.00031076704 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.08927 | 0.08927 | 0.08927 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032764 | 0.00032764 | 0.00032764 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00133 | | | 1.46 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9410.00 ave 9410 max 9410 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: 325168.0 ave 325168 max 325168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325168 Ave neighs/atom = 247.84146 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.033 | 6.033 | 6.033 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5735.0025 0 -5735.0025 195.62373 Loop time of 1.797e-06 on 1 procs for 0 steps with 1312 atoms 166.9% 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 | | 1.797e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9391.00 ave 9391 max 9391 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: 324904.0 ave 324904 max 324904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324904 Ave neighs/atom = 247.64024 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.033 | 6.033 | 6.033 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 -5735.0025 -5735.0025 31.876533 90.319179 4.9770257 195.62373 195.62373 109.09399 285.45871 192.3185 2.2391565 587.70783 Loop time of 1.941e-06 on 1 procs for 0 steps with 1312 atoms 206.1% 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 | | 1.941e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9391.00 ave 9391 max 9391 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162452.0 ave 162452 max 162452 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 324904.0 ave 324904 max 324904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324904 Ave neighs/atom = 247.64024 Neighbor list builds = 0 Dangerous builds = 0 1312 -5735.00245583209 eV 2.23915652334759 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04