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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -59.610378 0.0000000) to (42.150902 59.610378 4.6834336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7241966 5.5194794 4.6834336 Created 1294 atoms using lattice units in orthogonal box = (0.0000000 -59.610378 0.0000000) to (42.150902 59.610378 4.6834336) create_atoms CPU = 0.003 seconds 1294 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7241966 5.5194794 4.6834336 Created 1298 atoms using lattice units in orthogonal box = (0.0000000 -59.610378 0.0000000) to (42.150902 59.610378 4.6834336) create_atoms CPU = 0.003 seconds 1298 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 12 32 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2578 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_255315407910_000#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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 10.82 | 10.82 | 10.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9303.5001 0 -9303.5001 82180.3 277 0 -10048.733 0 -10048.733 190208.24 Loop time of 14.6163 on 1 procs for 277 steps with 2578 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 = -9303.50013438854 -10048.7229807228 -10048.7325987704 Force two-norm initial, final = 1029.3199 0.62745881 Force max component initial, final = 236.51256 0.075318507 Final line search alpha, max atom move = 0.48876050 0.036812711 Iterations, force evaluations = 277 544 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.397 | 14.397 | 14.397 | 0.0 | 98.50 Neigh | 0.057484 | 0.057484 | 0.057484 | 0.0 | 0.39 Comm | 0.089882 | 0.089882 | 0.089882 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07205 | | | 0.49 Nlocal: 2578.00 ave 2578 max 2578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13922.0 ave 13922 max 13922 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: 495432.0 ave 495432 max 495432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 495432 Ave neighs/atom = 192.17688 Neighbor list builds = 2 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 277 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 277 0 -10048.733 0 -10048.733 190208.24 23535.483 484 0 -10156.064 0 -10156.064 -278.94359 26842.384 Loop time of 5.77926 on 1 procs for 207 steps with 2578 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 = -10048.7325987703 -10156.0547926006 -10156.0641842852 Force two-norm initial, final = 4962.7838 14.430001 Force max component initial, final = 3556.2952 5.3055498 Final line search alpha, max atom move = 6.6916382e-05 0.00035502820 Iterations, force evaluations = 207 227 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4909 | 5.4909 | 5.4909 | 0.0 | 95.01 Neigh | 0.13277 | 0.13277 | 0.13277 | 0.0 | 2.30 Comm | 0.025365 | 0.025365 | 0.025365 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1302 | | | 2.25 Nlocal: 2578.00 ave 2578 max 2578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13293.0 ave 13293 max 13293 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: 447200.0 ave 447200 max 447200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447200 Ave neighs/atom = 173.46780 Neighbor list builds = 5 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 13 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 9.943 | 9.943 | 9.943 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10156.064 0 -10156.064 -278.94359 Loop time of 1.687e-06 on 1 procs for 0 steps with 2578 atoms 237.1% 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 | | 1.687e-06 | | |100.00 Nlocal: 2578.00 ave 2578 max 2578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13203.0 ave 13203 max 13203 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: 436624.0 ave 436624 max 436624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436624 Ave neighs/atom = 169.36540 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 13 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 9.943 | 9.943 | 9.943 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 -10156.064 -10156.064 46.508436 122.08239 4.727552 -278.94359 -278.94359 -232.49986 -284.66848 -319.66245 2.2868187 4100.1211 Loop time of 2.3e-06 on 1 procs for 0 steps with 2578 atoms 304.3% 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 | | 2.3e-06 | | |100.00 Nlocal: 2578.00 ave 2578 max 2578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13203.0 ave 13203 max 13203 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218312.0 ave 218312 max 218312 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 436624.0 ave 436624 max 436624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436624 Ave neighs/atom = 169.36540 Neighbor list builds = 0 Dangerous builds = 0 2578 -10156.0641842852 eV 2.28681869604366 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21