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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -47.622613 0.0000000) to (58.325551 47.622613 9.8588175) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6657772 6.1229074 6.5725450 Created 1674 atoms using lattice units in orthogonal box = (0.0000000 -47.622613 0.0000000) to (58.325551 47.622613 9.8588175) create_atoms CPU = 0.003 seconds 1674 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6657772 6.1229074 6.5725450 Created 1698 atoms using lattice units in orthogonal box = (0.0000000 -47.622613 0.0000000) to (58.325551 47.622613 9.8588175) create_atoms CPU = 0.003 seconds 1698 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 14 23 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 3360 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_149316865608_005#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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.585 | 6.585 | 6.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8529.7396 0 -8529.7396 17476.859 79 0 -8861.5574 0 -8861.5574 4963.6265 Loop time of 3.92771 on 1 procs for 79 steps with 3360 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8529.73964400511 -8861.54982374894 -8861.5573783116 Force two-norm initial, final = 209.61876 0.21511579 Force max component initial, final = 18.820513 0.030196845 Final line search alpha, max atom move = 1.0000000 0.030196845 Iterations, force evaluations = 79 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8502 | 3.8502 | 3.8502 | 0.0 | 98.03 Neigh | 0.034207 | 0.034207 | 0.034207 | 0.0 | 0.87 Comm | 0.017614 | 0.017614 | 0.017614 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0257 | | | 0.65 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10636.0 ave 10636 max 10636 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: 472584.0 ave 472584 max 472584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 472584 Ave neighs/atom = 140.65000 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.585 | 6.585 | 6.585 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -8861.5574 0 -8861.5574 4963.6265 54768.001 90 0 -8863.135 0 -8863.135 15.505835 55102.038 Loop time of 0.349919 on 1 procs for 11 steps with 3360 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 = -8861.55737831155 -8863.13342894163 -8863.13502371908 Force two-norm initial, final = 363.89959 1.0896174 Force max component initial, final = 343.17984 0.55847551 Final line search alpha, max atom move = 0.00015937788 8.9008641e-05 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30954 | 0.30954 | 0.30954 | 0.0 | 88.46 Neigh | 0.03197 | 0.03197 | 0.03197 | 0.0 | 9.14 Comm | 0.0013705 | 0.0013705 | 0.0013705 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007041 | | | 2.01 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10502.0 ave 10502 max 10502 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: 469858.0 ave 469858 max 469858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469858 Ave neighs/atom = 139.83869 Neighbor list builds = 1 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 14 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.723 | 6.723 | 6.723 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8863.135 0 -8863.135 15.505835 Loop time of 2.133e-06 on 1 procs for 0 steps with 3360 atoms 187.5% 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 | | 2.133e-06 | | |100.00 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10502.0 ave 10502 max 10502 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: 469842.0 ave 469842 max 469842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469842 Ave neighs/atom = 139.83393 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 14 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.723 | 6.723 | 6.723 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 -8863.135 -8863.135 58.264593 96.228241 9.8278926 15.505835 15.505835 15.601684 14.728224 16.187598 2.6721358 1951.9027 Loop time of 2.659e-06 on 1 procs for 0 steps with 3360 atoms 263.3% 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 | | 2.659e-06 | | |100.00 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10502.0 ave 10502 max 10502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 234921.0 ave 234921 max 234921 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 469842.0 ave 469842 max 469842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469842 Ave neighs/atom = 139.83393 Neighbor list builds = 0 Dangerous builds = 0 3360 -8759.86789968577 eV 2.67213583819952 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04