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 = 3.5192937 3.5192937 3.5192937 Created orthogonal box = (0.0000000 -35.893413 0.0000000) to (31.081560 35.893413 6.0955954) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5787415 5.5215222 6.0955954 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -35.893413 0.0000000) to (31.081560 35.893413 6.0955954) create_atoms CPU = 0.004 seconds 629 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5787415 5.5215222 6.0955954 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -35.893413 0.0000000) to (31.081560 35.893413 6.0955954) create_atoms CPU = 0.004 seconds 628 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 1227 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.456 | 5.456 | 5.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5400.6395 0 -5400.6395 2893.1495 63 0 -5425.2896 0 -5425.2896 -14000.306 Loop time of 2.88861 on 1 procs for 63 steps with 1227 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5400.63950795436 -5425.28439818662 -5425.28960171245 Force two-norm initial, final = 39.870481 0.26078166 Force max component initial, final = 8.5057292 0.023888482 Final line search alpha, max atom move = 1.0000000 0.023888482 Iterations, force evaluations = 63 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7909 | 2.7909 | 2.7909 | 0.0 | 96.62 Neigh | 0.058194 | 0.058194 | 0.058194 | 0.0 | 2.01 Comm | 0.021282 | 0.021282 | 0.021282 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01825 | | | 0.63 Nlocal: 1227.00 ave 1227 max 1227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6887.00 ave 6887 max 6887 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: 211932.0 ave 211932 max 211932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211932 Ave neighs/atom = 172.72372 Neighbor list builds = 2 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.456 | 5.456 | 5.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -5425.2896 0 -5425.2896 -14000.306 13600.776 67 0 -5425.5045 0 -5425.5045 -5435.2046 13533.526 Loop time of 0.168447 on 1 procs for 4 steps with 1227 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 = -5425.28960171246 -5425.50433201631 -5425.50449470741 Force two-norm initial, final = 122.58375 0.33783352 Force max component initial, final = 88.893823 0.035586138 Final line search alpha, max atom move = 0.00054718581 1.9472230e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16399 | 0.16399 | 0.16399 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010039 | 0.0010039 | 0.0010039 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003455 | | | 2.05 Nlocal: 1227.00 ave 1227 max 1227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6887.00 ave 6887 max 6887 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: 211926.0 ave 211926 max 211926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211926 Ave neighs/atom = 172.71883 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.594 | 5.594 | 5.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5425.5045 0 -5425.5045 -5435.2046 Loop time of 6.425e-06 on 1 procs for 0 steps with 1227 atoms 171.2% 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 | | 6.425e-06 | | |100.00 Nlocal: 1227.00 ave 1227 max 1227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6901.00 ave 6901 max 6901 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: 212064.0 ave 212064 max 212064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212064 Ave neighs/atom = 172.83130 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.594 | 5.594 | 5.594 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 -5425.5045 -5425.5045 30.997039 71.786827 6.0819944 -5435.2046 -5435.2046 4.093076 -16306.588 -3.1186007 2.2001261 863.40389 Loop time of 6.836e-06 on 1 procs for 0 steps with 1227 atoms 248.7% 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 | | 6.836e-06 | | |100.00 Nlocal: 1227.00 ave 1227 max 1227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6901.00 ave 6901 max 6901 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106032.0 ave 106032 max 106032 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 212064.0 ave 212064 max 212064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212064 Ave neighs/atom = 172.83130 Neighbor list builds = 0 Dangerous builds = 0 1227 -5425.50449470741 eV 2.20012610668295 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03