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 = 3.5618363 3.5618363 3.5618363 Created orthogonal box = (0.0000000 -45.613761 0.0000000) to (32.253800 45.613761 5.0371973) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5067463 6.1189192 5.0371973 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -45.613761 0.0000000) to (32.253800 45.613761 5.0371973) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5067463 6.1189192 5.0371973 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.613761 0.0000000) to (32.253800 45.613761 5.0371973) create_atoms CPU = 0.005 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 8 22 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 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_322509103239_004#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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.496 | 5.496 | 5.496 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4789.42 0 -4789.42 39514.172 79 0 -5113.3181 0 -5113.3181 -7479.3054 Loop time of 3.98295 on 1 procs for 79 steps with 1304 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4789.41995917557 -5113.31382239391 -5113.31812412542 Force two-norm initial, final = 452.26782 0.30018417 Force max component initial, final = 109.06052 0.029082797 Final line search alpha, max atom move = 1.0000000 0.029082797 Iterations, force evaluations = 79 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8932 | 3.8932 | 3.8932 | 0.0 | 97.75 Neigh | 0.037385 | 0.037385 | 0.037385 | 0.0 | 0.94 Comm | 0.028609 | 0.028609 | 0.028609 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02377 | | | 0.60 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8790.00 ave 8790 max 8790 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: 290792.0 ave 290792 max 290792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290792 Ave neighs/atom = 223.00000 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.497 | 5.497 | 5.497 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -5113.3181 0 -5113.3181 -7479.3054 14821.622 86 0 -5113.8574 0 -5113.8574 -102.1793 14758.679 Loop time of 0.247622 on 1 procs for 7 steps with 1304 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5113.31812412539 -5113.8545439978 -5113.8574488629 Force two-norm initial, final = 173.25508 1.7105677 Force max component initial, final = 164.11734 0.97176460 Final line search alpha, max atom move = 0.00013114239 0.00012743954 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24033 | 0.24033 | 0.24033 | 0.0 | 97.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016869 | 0.0016869 | 0.0016869 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005603 | | | 2.26 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8797.00 ave 8797 max 8797 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: 290720.0 ave 290720 max 290720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290720 Ave neighs/atom = 222.94479 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.635 | 5.635 | 5.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5113.8574 0 -5113.8574 -102.1793 Loop time of 6.485e-06 on 1 procs for 0 steps with 1304 atoms 185.0% 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 | | 6.485e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8797.00 ave 8797 max 8797 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: 291072.0 ave 291072 max 291072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291072 Ave neighs/atom = 223.21472 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.635 | 5.635 | 5.635 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 -5113.8574 -5113.8574 32.047155 91.407181 5.0382267 -102.1793 -102.1793 -104.81719 -100.4355 -101.2852 2.3489864 740.80194 Loop time of 6.876e-06 on 1 procs for 0 steps with 1304 atoms 320.0% 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 | | 6.876e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8797.00 ave 8797 max 8797 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145536.0 ave 145536 max 145536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 291072.0 ave 291072 max 291072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291072 Ave neighs/atom = 223.21472 Neighbor list builds = 0 Dangerous builds = 0 1304 -5113.8574488629 eV 2.34898640114045 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04