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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -53.472189 0.0000000) to (43.659859 53.472189 8.8507797) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3827224 5.1274702 5.9005198 Created 1746 atoms using lattice units in orthogonal box = (0.0000000 -53.472189 0.0000000) to (43.659859 53.472189 8.8507797) create_atoms CPU = 0.002 seconds 1746 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3827224 5.1274702 5.9005198 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -53.472189 0.0000000) to (43.659859 53.472189 8.8507797) create_atoms CPU = 0.002 seconds 1754 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 33 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 3490 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_353393547686_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.110 | 6.110 | 6.110 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11000.125 0 -11000.125 69847.462 186 0 -12307.839 0 -12307.839 1449.5689 Loop time of 31.4109 on 1 procs for 186 steps with 3490 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 = -11000.1252728973 -12307.8281670087 -12307.8393911446 Force two-norm initial, final = 1047.9088 0.37320100 Force max component initial, final = 129.59247 0.098692223 Final line search alpha, max atom move = 1.0000000 0.098692223 Iterations, force evaluations = 186 348 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.218 | 31.218 | 31.218 | 0.0 | 99.39 Neigh | 0.097997 | 0.097997 | 0.097997 | 0.0 | 0.31 Comm | 0.03842 | 0.03842 | 0.03842 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05634 | | | 0.18 Nlocal: 3490.00 ave 3490 max 3490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9133.00 ave 9133 max 9133 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: 300356.0 ave 300356 max 300356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300356 Ave neighs/atom = 86.061891 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 186 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.110 | 6.110 | 6.110 Mbytes Step Temp E_pair E_mol TotEng Press Volume 186 0 -12307.839 0 -12307.839 1449.5689 41325.852 190 0 -12308.097 0 -12308.097 -317.29106 41377.309 Loop time of 0.537791 on 1 procs for 4 steps with 3490 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 = -12307.8393911446 -12308.088330903 -12308.0966929579 Force two-norm initial, final = 136.17286 14.822155 Force max component initial, final = 134.96736 11.609307 Final line search alpha, max atom move = 4.9193217e-05 0.00057109915 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53426 | 0.53426 | 0.53426 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004449 | 0.0004449 | 0.0004449 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003082 | | | 0.57 Nlocal: 3490.00 ave 3490 max 3490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9131.00 ave 9131 max 9131 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: 300320.0 ave 300320 max 300320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300320 Ave neighs/atom = 86.051576 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.249 | 6.249 | 6.249 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12308.097 0 -12308.097 -317.29106 Loop time of 2.147e-06 on 1 procs for 0 steps with 3490 atoms 186.3% 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 | | 2.147e-06 | | |100.00 Nlocal: 3490.00 ave 3490 max 3490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9162.00 ave 9162 max 9162 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: 300176.0 ave 300176 max 300176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300176 Ave neighs/atom = 86.010315 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.249 | 6.249 | 6.249 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 -12308.097 -12308.097 43.599502 107.33441 8.8418214 -317.29106 -317.29106 -448.90413 -233.38951 -269.57954 2.2652462 1792.4657 Loop time of 2.306e-06 on 1 procs for 0 steps with 3490 atoms 260.2% 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 | | 2.306e-06 | | |100.00 Nlocal: 3490.00 ave 3490 max 3490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9162.00 ave 9162 max 9162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 150088.0 ave 150088 max 150088 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 300176.0 ave 300176 max 300176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300176 Ave neighs/atom = 86.010315 Neighbor list builds = 0 Dangerous builds = 0 3490 -12308.0966929579 eV 2.26524621748485 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:32