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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -37.583315 0.0000000) to (26.575417 37.583315 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1285893 5.9342077 4.9780317 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.583315 0.0000000) to (26.575417 37.583315 4.9780317) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1285893 5.9342077 4.9780317 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.583315 0.0000000) to (26.575417 37.583315 4.9780317) create_atoms CPU = 0.001 seconds 458 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.402 | 5.402 | 5.402 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3982.8247 0 -3982.8247 3032.3007 97 0 -4019.6799 0 -4019.6799 6303.1716 Loop time of 2.3955 on 1 procs for 97 steps with 908 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 = -3982.82472751461 -4019.67603018138 -4019.67989603257 Force two-norm initial, final = 22.768223 0.20347603 Force max component initial, final = 5.0784753 0.041943767 Final line search alpha, max atom move = 1.0000000 0.041943767 Iterations, force evaluations = 97 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3405 | 2.3405 | 2.3405 | 0.0 | 97.70 Neigh | 0.035639 | 0.035639 | 0.035639 | 0.0 | 1.49 Comm | 0.011273 | 0.011273 | 0.011273 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008135 | | | 0.34 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7421.00 ave 7421 max 7421 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: 224188.0 ave 224188 max 224188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224188 Ave neighs/atom = 246.90308 Neighbor list builds = 3 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.403 | 5.403 | 5.403 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -4019.6799 0 -4019.6799 6303.1716 9944.0393 102 0 -4019.8628 0 -4019.8628 263.07164 9978.4005 Loop time of 0.0925691 on 1 procs for 5 steps with 908 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 = -4019.67989603258 -4019.85968631963 -4019.86281342514 Force two-norm initial, final = 88.433534 3.5495383 Force max component initial, final = 85.423878 3.2140010 Final line search alpha, max atom move = 0.00014936652 0.00048006413 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090531 | 0.090531 | 0.090531 | 0.0 | 97.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040667 | 0.00040667 | 0.00040667 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001631 | | | 1.76 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7536.00 ave 7536 max 7536 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: 224148.0 ave 224148 max 224148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224148 Ave neighs/atom = 246.85903 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.541 | 5.541 | 5.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4019.8628 0 -4019.8628 263.07164 Loop time of 1.978e-06 on 1 procs for 0 steps with 908 atoms 151.7% 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 | | 1.978e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7556.00 ave 7556 max 7556 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: 223912.0 ave 223912 max 223912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223912 Ave neighs/atom = 246.59912 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.541 | 5.541 | 5.541 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 -4019.8628 -4019.8628 26.557515 75.500125 4.9765207 263.07164 263.07164 40.800172 232.51704 515.8977 2.2865403 633.9613 Loop time of 1.882e-06 on 1 procs for 0 steps with 908 atoms 159.4% 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 | | 1.882e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7556.00 ave 7556 max 7556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111956.0 ave 111956 max 111956 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223912.0 ave 223912 max 223912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223912 Ave neighs/atom = 246.59912 Neighbor list builds = 0 Dangerous builds = 0 908 -4019.86281342514 eV 2.28654029742797 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03