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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -46.291129 0.0000000) to (23.145564 46.291129 3.6147299) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0807337 5.0807337 3.6147299 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -46.291129 0.0000000) to (23.145564 46.291129 3.6147299) create_atoms CPU = 0.002 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0807337 5.0807337 3.6147299 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -46.291129 0.0000000) to (23.145564 46.291129 3.6147299) create_atoms CPU = 0.001 seconds 330 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 9 34 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 658 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_887933271505_003#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2219.5925 0 -2219.5925 43554.26 34 0 -2331.9501 0 -2331.9501 5540.323 Loop time of 0.700776 on 1 procs for 34 steps with 658 atoms 44.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2219.59246746033 -2331.94841571909 -2331.95008482214 Force two-norm initial, final = 231.38571 0.10852147 Force max component initial, final = 103.15879 0.022120238 Final line search alpha, max atom move = 1.0000000 0.022120238 Iterations, force evaluations = 34 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68734 | 0.68734 | 0.68734 | 0.0 | 98.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0074056 | 0.0074056 | 0.0074056 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006026 | | | 0.86 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4227.00 ave 4227 max 4227 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: 35776.0 ave 35776 max 35776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35776 Ave neighs/atom = 54.370821 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -2331.9501 0 -2331.9501 5540.323 7745.8912 43 0 -2332.4678 0 -2332.4678 306.66951 7774.0324 Loop time of 0.139907 on 1 procs for 9 steps with 658 atoms 48.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2331.95008482214 -2332.46595848109 -2332.46777674939 Force two-norm initial, final = 64.065839 2.6393685 Force max component initial, final = 51.911361 1.7997188 Final line search alpha, max atom move = 0.00037430430 0.00067364249 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1344 | 0.1344 | 0.1344 | 0.0 | 96.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001237 | 0.001237 | 0.001237 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004274 | | | 3.06 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4218.00 ave 4218 max 4218 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: 36120.0 ave 36120 max 36120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36120 Ave neighs/atom = 54.893617 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.643 | 4.643 | 4.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2332.4678 0 -2332.4678 306.66951 Loop time of 6.124e-06 on 1 procs for 0 steps with 658 atoms 98.0% 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 | | 6.124e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4227.00 ave 4227 max 4227 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: 36172.0 ave 36172 max 36172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36172 Ave neighs/atom = 54.972644 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.643 | 4.643 | 4.643 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 -2332.4678 -2332.4678 23.008626 92.670016 3.645998 306.66951 306.66951 291.62122 254.26875 374.11855 2.3038009 140.20994 Loop time of 6.455e-06 on 1 procs for 0 steps with 658 atoms 170.4% 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 | | 6.455e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4227.00 ave 4227 max 4227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18086.0 ave 18086 max 18086 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36172.0 ave 36172 max 36172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36172 Ave neighs/atom = 54.972644 Neighbor list builds = 0 Dangerous builds = 0 658 -2332.46777674939 eV 2.3038008529874 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01