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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -57.611461 0.0000000) to (35.277431 57.611461 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6899082 5.5749487 5.9736509 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -57.611461 0.0000000) to (35.277431 57.611461 8.9604763) create_atoms CPU = 0.002 seconds 1491 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6899082 5.5749487 5.9736509 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -57.611461 0.0000000) to (35.277431 57.611461 8.9604763) create_atoms CPU = 0.002 seconds 1491 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 42 atoms, new total = 2940 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.106 | 6.106 | 6.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11344.447 0 -11344.447 732.49945 752 0 -11563.955 0 -11563.955 -71273.644 Loop time of 30.5455 on 1 procs for 752 steps with 2940 atoms 95.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11344.4470579162 -11563.9432992057 -11563.9545966936 Force two-norm initial, final = 52.507122 0.32554964 Force max component initial, final = 11.303991 0.030339100 Final line search alpha, max atom move = 0.67428215 0.020457113 Iterations, force evaluations = 752 1462 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.724 | 29.724 | 29.724 | 0.0 | 97.31 Neigh | 0.50833 | 0.50833 | 0.50833 | 0.0 | 1.66 Comm | 0.13402 | 0.13402 | 0.13402 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1795 | | | 0.59 Nlocal: 2940.00 ave 2940 max 2940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9396.00 ave 9396 max 9396 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: 404398.0 ave 404398 max 404398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 404398 Ave neighs/atom = 137.55034 Neighbor list builds = 17 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 752 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 752 0 -11563.955 0 -11563.955 -71273.644 36422.263 806 0 -11629.002 0 -11629.002 -20109.931 35245.89 Loop time of 1.16387 on 1 procs for 54 steps with 2940 atoms 94.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11563.9545966936 -11628.9972070384 -11629.0019669125 Force two-norm initial, final = 2602.4073 8.9822622 Force max component initial, final = 2588.2743 3.9888369 Final line search alpha, max atom move = 0.00010753312 0.00042893209 Iterations, force evaluations = 54 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1038 | 1.1038 | 1.1038 | 0.0 | 94.84 Neigh | 0.026075 | 0.026075 | 0.026075 | 0.0 | 2.24 Comm | 0.0044215 | 0.0044215 | 0.0044215 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02957 | | | 2.54 Nlocal: 2940.00 ave 2940 max 2940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9495.00 ave 9495 max 9495 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: 411416.0 ave 411416 max 411416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411416 Ave neighs/atom = 139.93741 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.628 | 6.628 | 6.628 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11629.002 0 -11629.002 -20109.931 Loop time of 2.103e-06 on 1 procs for 0 steps with 2940 atoms 142.7% 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 | | 2.103e-06 | | |100.00 Nlocal: 2940.00 ave 2940 max 2940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9442.00 ave 9442 max 9442 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: 416246.0 ave 416246 max 416246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416246 Ave neighs/atom = 141.58027 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.628 | 6.628 | 6.628 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 -11629.002 -11629.002 33.459575 115.22292 9.1421674 -20109.931 -20109.931 124.44453 -60269.24 -184.99766 2.3086631 5091.8166 Loop time of 2.904e-06 on 1 procs for 0 steps with 2940 atoms 206.6% 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 | | 2.904e-06 | | |100.00 Nlocal: 2940.00 ave 2940 max 2940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9442.00 ave 9442 max 9442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 208123.0 ave 208123 max 208123 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 416246.0 ave 416246 max 416246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416246 Ave neighs/atom = 141.58027 Neighbor list builds = 0 Dangerous builds = 0 2940 -11213.2223926076 eV 2.30866311567778 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:32