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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -64.620282 0.0000000) to (37.308537 64.620282 6.3365399) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7397749 5.7992560 6.3365399 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -64.620282 0.0000000) to (37.308537 64.620282 6.3365399) create_atoms CPU = 0.003 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7397749 5.7992560 6.3365399 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -64.620282 0.0000000) to (37.308537 64.620282 6.3365399) create_atoms CPU = 0.002 seconds 1249 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 31 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2494 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.83 | 10.83 | 10.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9305.3625 0 -9305.3625 39751.939 559 0 -9813.6016 0 -9813.6016 -54777.028 Loop time of 33.4331 on 1 procs for 559 steps with 2494 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9305.36254220431 -9813.59362864805 -9813.60158868157 Force two-norm initial, final = 748.16113 0.44409642 Force max component initial, final = 174.15934 0.21792687 Final line search alpha, max atom move = 0.69549981 0.15156810 Iterations, force evaluations = 559 1090 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32.711 | 32.711 | 32.711 | 0.0 | 97.84 Neigh | 0.3772 | 0.3772 | 0.3772 | 0.0 | 1.13 Comm | 0.1915 | 0.1915 | 0.1915 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1537 | | | 0.46 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12617.0 ave 12617 max 12617 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: 509684.0 ave 509684 max 509684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509684 Ave neighs/atom = 204.36407 Neighbor list builds = 11 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 559 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.82 | 10.82 | 10.82 Mbytes Step Temp E_pair E_mol TotEng Press Volume 559 0 -9813.6016 0 -9813.6016 -54777.028 30553.378 585 0 -9839.6442 0 -9839.6442 1.1180704 29381.668 Loop time of 0.939288 on 1 procs for 26 steps with 2494 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 = -9813.60158868165 -9839.63801563118 -9839.64424775109 Force two-norm initial, final = 1876.7489 5.0820782 Force max component initial, final = 1309.2034 1.0728353 Final line search alpha, max atom move = 7.3919773e-05 7.9303743e-05 Iterations, force evaluations = 26 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85067 | 0.85067 | 0.85067 | 0.0 | 90.57 Neigh | 0.067802 | 0.067802 | 0.067802 | 0.0 | 7.22 Comm | 0.0036408 | 0.0036408 | 0.0036408 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01717 | | | 1.83 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12801.0 ave 12801 max 12801 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: 541850.0 ave 541850 max 541850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 541850 Ave neighs/atom = 217.26143 Neighbor list builds = 2 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.33 | 10.33 | 10.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9839.6442 0 -9839.6442 1.1180704 Loop time of 2.71e-06 on 1 procs for 0 steps with 2494 atoms 184.5% 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 | | 2.71e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12760.0 ave 12760 max 12760 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: 542810.0 ave 542810 max 542810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 542810 Ave neighs/atom = 217.64635 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.33 | 10.33 | 10.33 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 -9839.6442 -9839.6442 36.411363 126.86548 6.3605703 1.1180704 1.1180704 50.785448 11.292117 -58.723354 2.2089778 6475.4054 Loop time of 2.735e-06 on 1 procs for 0 steps with 2494 atoms 292.5% 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 | | 2.735e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12760.0 ave 12760 max 12760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271405.0 ave 271405 max 271405 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 542810.0 ave 542810 max 542810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 542810 Ave neighs/atom = 217.64635 Neighbor list builds = 0 Dangerous builds = 0 2494 -9839.64424775108 eV 2.20897781179763 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35