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 -62.305060 0.0000000) to (35.971843 62.305060 6.1095137) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5341297 5.5914797 6.1095137 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -62.305060 0.0000000) to (35.971843 62.305060 6.1095137) create_atoms CPU = 0.002 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5341297 5.5914797 6.1095137 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.305060 0.0000000) to (35.971843 62.305060 6.1095137) create_atoms CPU = 0.002 seconds 1250 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 = 8 25 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 10.13295 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 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_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 = 8 25 2 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) = 12.44 | 12.44 | 12.44 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10105.346 0 -10105.346 28296.668 63 0 -10408.02 0 -10408.02 4459.279 Loop time of 4.50773 on 1 procs for 63 steps with 2494 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10105.34573656 -10408.00996732 -10408.0197146052 Force two-norm initial, final = 360.91587 0.45736489 Force max component initial, final = 97.587763 0.12358105 Final line search alpha, max atom move = 1.0000000 0.12358105 Iterations, force evaluations = 63 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3059 | 4.3059 | 4.3059 | 0.0 | 95.52 Neigh | 0.15582 | 0.15582 | 0.15582 | 0.0 | 3.46 Comm | 0.027087 | 0.027087 | 0.027087 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01897 | | | 0.42 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17085.0 ave 17085 max 17085 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: 949968.0 ave 949968 max 949968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 949968 Ave neighs/atom = 380.90136 Neighbor list builds = 3 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 = 8 25 2 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.44 | 12.44 | 12.44 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -10408.02 0 -10408.02 4459.279 27385.624 66 0 -10408.16 0 -10408.16 15.434269 27451.145 Loop time of 0.227684 on 1 procs for 3 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 = -10408.0197146052 -10408.1579477791 -10408.1604584206 Force two-norm initial, final = 149.60859 3.0103423 Force max component initial, final = 127.07275 2.0434952 Final line search alpha, max atom move = 7.0704878e-05 0.00014448508 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22303 | 0.22303 | 0.22303 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085477 | 0.00085477 | 0.00085477 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003795 | | | 1.67 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17075.0 ave 17075 max 17075 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: 949794.0 ave 949794 max 949794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 949794 Ave neighs/atom = 380.83160 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 = 8 25 2 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) = 11.95 | 11.95 | 11.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10408.16 0 -10408.16 15.434269 Loop time of 2.321e-06 on 1 procs for 0 steps with 2494 atoms 215.4% 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 | | 2.321e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17067.0 ave 17067 max 17067 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: 949400.0 ave 949400 max 949400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 949400 Ave neighs/atom = 380.67362 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 = 8 25 2 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) = 11.95 | 11.95 | 11.95 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 -10408.16 -10408.16 35.994907 124.84373 6.1087543 15.434269 15.434269 -119.34436 50.319138 115.32803 2.2226533 988.62477 Loop time of 2.641e-06 on 1 procs for 0 steps with 2494 atoms 302.9% 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 | | 2.641e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17067.0 ave 17067 max 17067 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 474700.0 ave 474700 max 474700 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 949400.0 ave 949400 max 949400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 949400 Ave neighs/atom = 380.67362 Neighbor list builds = 0 Dangerous builds = 0 2494 -10408.1604584206 eV 2.22265331382378 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06