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 = 3.5273294 3.5273294 3.5273294 Created orthogonal box = (0.0000000 -46.260491 0.0000000) to (32.711107 46.260491 4.9883971) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0857874 5.9170396 4.9883971 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -46.260491 0.0000000) to (32.711107 46.260491 4.9883971) create_atoms CPU = 0.002 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0857874 5.9170396 4.9883971 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -46.260491 0.0000000) to (32.711107 46.260491 4.9883971) create_atoms CPU = 0.002 seconds 694 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 19 1 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 10.13295 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1380 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_758825945924_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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.742 | 6.742 | 6.742 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5009.3189 0 -5009.3189 94512.108 177 0 -5762.1148 0 -5762.1148 10475.636 Loop time of 7.50392 on 1 procs for 177 steps with 1380 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5009.31893081926 -5762.10934459775 -5762.11476125612 Force two-norm initial, final = 857.69206 0.34092992 Force max component initial, final = 240.16136 0.062716485 Final line search alpha, max atom move = 0.93492345 0.058635112 Iterations, force evaluations = 177 319 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2788 | 7.2788 | 7.2788 | 0.0 | 97.00 Neigh | 0.14848 | 0.14848 | 0.14848 | 0.0 | 1.98 Comm | 0.047435 | 0.047435 | 0.047435 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02921 | | | 0.39 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12896.0 ave 12896 max 12896 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: 530258.0 ave 530258 max 530258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530258 Ave neighs/atom = 384.24493 Neighbor list builds = 5 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 177 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.738 | 6.738 | 6.738 Mbytes Step Temp E_pair E_mol TotEng Press Volume 177 0 -5762.1148 0 -5762.1148 10475.636 15097.203 184 0 -5762.7386 0 -5762.7386 11.616123 15181.237 Loop time of 0.240868 on 1 procs for 7 steps with 1380 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 = -5762.11476125615 -5762.73853343389 -5762.73857090336 Force two-norm initial, final = 225.59968 0.54868453 Force max component initial, final = 217.56632 0.30731040 Final line search alpha, max atom move = 0.00066464090 0.00020425106 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2346 | 0.2346 | 0.2346 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010656 | 0.0010656 | 0.0010656 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005202 | | | 2.16 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12259.0 ave 12259 max 12259 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: 531534.0 ave 531534 max 531534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 531534 Ave neighs/atom = 385.16957 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.875 | 6.875 | 6.875 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5762.7386 0 -5762.7386 11.616123 Loop time of 3.63e-06 on 1 procs for 0 steps with 1380 atoms 192.8% 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 | | 3.63e-06 | | |100.00 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12245.0 ave 12245 max 12245 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: 530530.0 ave 530530 max 530530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530530 Ave neighs/atom = 384.44203 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.875 | 6.875 | 6.875 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 -5762.7386 -5762.7386 32.898602 92.472108 4.9902115 11.616123 11.616123 11.302259 32.41537 -8.8692611 2.3420328 1416.7312 Loop time of 2.519e-06 on 1 procs for 0 steps with 1380 atoms 277.9% 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 | | 2.519e-06 | | |100.00 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12245.0 ave 12245 max 12245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 265265.0 ave 265265 max 265265 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 530530.0 ave 530530 max 530530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530530 Ave neighs/atom = 384.44203 Neighbor list builds = 0 Dangerous builds = 0 1380 -5762.73857090336 eV 2.3420327686328 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08