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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -49.051347 0.0000000) to (40.046954 49.051347 9.9090513) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7209934 5.6721369 6.6060342 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -49.051347 0.0000000) to (40.046954 49.051347 9.9090513) create_atoms CPU = 0.002 seconds 1184 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7209934 5.6721369 6.6060342 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -49.051347 0.0000000) to (40.046954 49.051347 9.9090513) create_atoms CPU = 0.001 seconds 1184 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 32 4 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 2320 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7744.8468 0 -7744.8468 -1654.2677 53 0 -7765.7375 0 -7765.7375 -5196.8452 Loop time of 7.63222 on 1 procs for 53 steps with 2320 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7744.84679866385 -7765.72988801344 -7765.73749264921 Force two-norm initial, final = 15.369839 0.19656425 Force max component initial, final = 2.7788924 0.019509506 Final line search alpha, max atom move = 1.0000000 0.019509506 Iterations, force evaluations = 53 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6122 | 7.6122 | 7.6122 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.006929 | 0.006929 | 0.006929 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01308 | | | 0.17 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5376.00 ave 5376 max 5376 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: 124496.0 ave 124496 max 124496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124496 Ave neighs/atom = 53.662069 Neighbor list builds = 0 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -7765.7375 0 -7765.7375 -5196.8452 38929.829 57 0 -7766.1557 0 -7766.1557 -526.10847 38676.109 Loop time of 0.743848 on 1 procs for 4 steps with 2320 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 = -7765.73749264925 -7766.151715386 -7766.15571151572 Force two-norm initial, final = 180.02927 1.3585159 Force max component initial, final = 128.45962 0.99788871 Final line search alpha, max atom move = 7.2537737e-05 7.2384589e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73982 | 0.73982 | 0.73982 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052818 | 0.00052818 | 0.00052818 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003503 | | | 0.47 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5376.00 ave 5376 max 5376 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: 125632.0 ave 125632 max 125632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125632 Ave neighs/atom = 54.151724 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.227 | 5.227 | 5.227 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7766.1557 0 -7766.1557 -526.10847 Loop time of 3.493e-06 on 1 procs for 0 steps with 2320 atoms 143.1% 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 | | 3.493e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5385.00 ave 5385 max 5385 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: 125712.0 ave 125712 max 125712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125712 Ave neighs/atom = 54.186207 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.227 | 5.227 | 5.227 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 -7766.1557 -7766.1557 39.912838 98.102693 9.87755 -526.10847 -526.10847 -36.396744 -1583.1353 41.206607 2.5347256 1830.8039 Loop time of 3.687e-06 on 1 procs for 0 steps with 2320 atoms 162.7% 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 | | 3.687e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5385.00 ave 5385 max 5385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62856.0 ave 62856 max 62856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 125712.0 ave 125712 max 125712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125712 Ave neighs/atom = 54.186207 Neighbor list builds = 0 Dangerous builds = 0 2320 -7766.15571151572 eV 2.53472558236139 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09