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 -42.112283 0.0000000) to (14.888941 42.112283 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1307402 6.1929829 5.1068645 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.112283 0.0000000) to (14.888941 42.112283 5.1068645) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1307402 6.1929829 5.1068645 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.112283 0.0000000) to (14.888941 42.112283 5.1068645) create_atoms CPU = 0.001 seconds 274 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 = 5 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 4 atoms, new total = 542 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_115454747503_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 = 5 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) = 4.506 | 4.506 | 4.506 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2222.4748 0 -2222.4748 32188.821 391 0 -2302.3267 0 -2302.3267 -1576.9483 Loop time of 27.8399 on 1 procs for 391 steps with 542 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2222.47480976775 -2302.3244631835 -2302.32673731844 Force two-norm initial, final = 147.85752 0.15336585 Force max component initial, final = 47.139974 0.038181033 Final line search alpha, max atom move = 1.0000000 0.038181033 Iterations, force evaluations = 391 756 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.743 | 27.743 | 27.743 | 0.0 | 99.65 Neigh | 0.03662 | 0.03662 | 0.03662 | 0.0 | 0.13 Comm | 0.033233 | 0.033233 | 0.033233 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0273 | | | 0.10 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3643.00 ave 3643 max 3643 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: 51760.0 ave 51760 max 51760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51760 Ave neighs/atom = 95.498155 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 = 5 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 : 391 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 391 0 -2302.3267 0 -2302.3267 -1576.9483 6404.0825 410 0 -2304.4369 0 -2304.4369 -5.1229509 6394.7152 Loop time of 0.884981 on 1 procs for 19 steps with 542 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2302.32673731844 -2304.43663491104 -2304.43691688669 Force two-norm initial, final = 170.40255 0.65911931 Force max component initial, final = 130.41549 0.19160040 Final line search alpha, max atom move = 0.00067914452 0.00013012436 Iterations, force evaluations = 19 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8806 | 0.8806 | 0.8806 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007156 | 0.0007156 | 0.0007156 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003662 | | | 0.41 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3586.00 ave 3586 max 3586 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: 52308.0 ave 52308 max 52308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52308 Ave neighs/atom = 96.509225 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 = 5 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) = 4.643 | 4.643 | 4.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2304.4369 0 -2304.4369 -5.1229509 Loop time of 1.844e-06 on 1 procs for 0 steps with 542 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 | | 1.844e-06 | | |100.00 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3617.00 ave 3617 max 3617 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: 52860.0 ave 52860 max 52860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52860 Ave neighs/atom = 97.527675 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 = 5 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) = 4.643 | 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 -2304.4369 -2304.4369 15.135783 84.233752 5.0156839 -5.1229509 -5.1229509 -48.80077 1.3430974 32.08882 2.3486291 849.96536 Loop time of 1.965e-06 on 1 procs for 0 steps with 542 atoms 203.6% 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 | | 1.965e-06 | | |100.00 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3617.00 ave 3617 max 3617 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26430.0 ave 26430 max 26430 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52860.0 ave 52860 max 52860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52860 Ave neighs/atom = 97.527675 Neighbor list builds = 0 Dangerous builds = 0 542 -2304.43691688669 eV 2.34862913772913 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:29