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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -54.064555 0.0000000) to (44.143524 54.064555 8.9488288) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4423523 5.1842724 5.9658858 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -54.064555 0.0000000) to (44.143524 54.064555 8.9488288) create_atoms CPU = 0.005 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4423523 5.1842724 5.9658858 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -54.064555 0.0000000) to (44.143524 54.064555 8.9488288) create_atoms CPU = 0.005 seconds 1757 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 11 25 3 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3504 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_673777079812_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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 12.20 | 12.20 | 12.20 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10220.077 0 -10220.077 48102.687 62 0 -11401.405 0 -11401.405 3566.6571 Loop time of 4.8351 on 1 procs for 62 steps with 3504 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10220.0771274834 -11401.3953351114 -11401.4052877406 Force two-norm initial, final = 897.13755 0.38046405 Force max component initial, final = 123.88758 0.057386295 Final line search alpha, max atom move = 1.0000000 0.057386295 Iterations, force evaluations = 62 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7227 | 4.7227 | 4.7227 | 0.0 | 97.67 Neigh | 0.046481 | 0.046481 | 0.046481 | 0.0 | 0.96 Comm | 0.028677 | 0.028677 | 0.028677 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03729 | | | 0.77 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13512.0 ave 13512 max 13512 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: 785100.0 ave 785100 max 785100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 785100 Ave neighs/atom = 224.05822 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.81 | 11.81 | 11.81 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -11401.405 0 -11401.405 3566.6571 42714.549 66 0 -11401.654 0 -11401.654 -78.890805 42832.049 Loop time of 0.336095 on 1 procs for 4 steps with 3504 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 = -11401.4052877405 -11401.6533828474 -11401.6542727235 Force two-norm initial, final = 194.30025 5.0081533 Force max component initial, final = 176.28869 4.4766664 Final line search alpha, max atom move = 0.00012837968 0.00057471300 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32572 | 0.32572 | 0.32572 | 0.0 | 96.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014786 | 0.0014786 | 0.0014786 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008893 | | | 2.65 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13590.0 ave 13590 max 13590 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: 784388.0 ave 784388 max 784388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 784388 Ave neighs/atom = 223.85502 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 11.33 | 11.33 | 11.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11401.654 0 -11401.654 -78.890805 Loop time of 4.148e-06 on 1 procs for 0 steps with 3504 atoms 168.8% 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 | | 4.148e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13590.0 ave 13590 max 13590 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: 783976.0 ave 783976 max 783976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 783976 Ave neighs/atom = 223.73744 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 11.33 | 11.33 | 11.33 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 -11401.654 -11401.654 44.149075 108.44069 8.9465371 -78.890805 -78.890805 -167.47533 -81.250703 12.053621 2.2765106 1544.6375 Loop time of 4.418e-06 on 1 procs for 0 steps with 3504 atoms 226.3% 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 | | 4.418e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13590.0 ave 13590 max 13590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 391988.0 ave 391988 max 391988 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 783976.0 ave 783976 max 783976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 783976 Ave neighs/atom = 223.73744 Neighbor list builds = 0 Dangerous builds = 0 3504 -11401.6542727235 eV 2.27651056903832 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06