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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -41.433262 0.0000000) to (29.297741 41.433262 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2146723 5.6499903 5.1000820 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.433262 0.0000000) to (29.297741 41.433262 5.1000820) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2146723 5.6499903 5.1000820 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.433262 0.0000000) to (29.297741 41.433262 5.1000820) create_atoms CPU = 0.001 seconds 532 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1060 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.091 | 7.091 | 7.091 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4079.9336 0 -4079.9336 72193.068 158 0 -4437.9349 0 -4437.9349 11334.642 Loop time of 9.42805 on 1 procs for 158 steps with 1060 atoms 95.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4079.93362737559 -4437.93106227135 -4437.9348788358 Force two-norm initial, final = 271.03536 0.26727808 Force max component initial, final = 59.525565 0.022864168 Final line search alpha, max atom move = 1.0000000 0.022864168 Iterations, force evaluations = 158 292 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.2239 | 9.2239 | 9.2239 | 0.0 | 97.83 Neigh | 0.13198 | 0.13198 | 0.13198 | 0.0 | 1.40 Comm | 0.048817 | 0.048817 | 0.048817 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02338 | | | 0.25 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13159.0 ave 13159 max 13159 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: 654496.0 ave 654496 max 654496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654496 Ave neighs/atom = 617.44906 Neighbor list builds = 4 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 158 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.090 | 7.090 | 7.090 Mbytes Step Temp E_pair E_mol TotEng Press Volume 158 0 -4437.9349 0 -4437.9349 11334.642 12381.989 164 0 -4438.4411 0 -4438.4411 257.61797 12460.604 Loop time of 0.454971 on 1 procs for 6 steps with 1060 atoms 50.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4437.9348788358 -4438.43878751045 -4438.44109748424 Force two-norm initial, final = 182.12318 4.2836495 Force max component initial, final = 158.66788 3.9383028 Final line search alpha, max atom move = 9.6012206e-05 0.00037812514 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45092 | 0.45092 | 0.45092 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082436 | 0.00082436 | 0.00082436 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003228 | | | 0.71 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13110.0 ave 13110 max 13110 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: 655024.0 ave 655024 max 655024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 655024 Ave neighs/atom = 617.94717 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.227 | 7.227 | 7.227 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4438.4411 0 -4438.4411 257.61797 Loop time of 1.9061e-05 on 1 procs for 0 steps with 1060 atoms 110.2% 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 | | 1.906e-05 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13103.0 ave 13103 max 13103 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: 651096.0 ave 651096 max 651096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651096 Ave neighs/atom = 614.24151 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.227 | 7.227 | 7.227 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 -4438.4411 -4438.4411 29.444724 83.077528 5.0938722 257.61797 257.61797 205.10501 507.67386 60.075033 2.4067136 717.16872 Loop time of 3.535e-06 on 1 procs for 0 steps with 1060 atoms 198.0% 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 | | 3.535e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13103.0 ave 13103 max 13103 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325548.0 ave 325548 max 325548 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 651096.0 ave 651096 max 651096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651096 Ave neighs/atom = 614.24151 Neighbor list builds = 0 Dangerous builds = 0 1060 -4438.44109748424 eV 2.40671361727329 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10