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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -46.717631 0.0000000) to (26.972437 46.717631 6.2429061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7798079 5.5616228 6.2429061 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -46.717631 0.0000000) to (26.972437 46.717631 6.2429061) create_atoms CPU = 0.002 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7798079 5.5616228 6.2429061 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.717631 0.0000000) to (26.972437 46.717631 6.2429061) create_atoms CPU = 0.002 seconds 676 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 ghost atom cutoff = 6 binsize = 3, bins = 9 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1348 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 9 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.050 | 5.050 | 5.050 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5453.5984 0 -5453.5984 70629.627 84 0 -5709.1113 0 -5709.1113 8388.1509 Loop time of 7.87188 on 1 procs for 84 steps with 1348 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5453.59839542059 -5709.10661320924 -5709.11125665798 Force two-norm initial, final = 497.65191 0.18879665 Force max component initial, final = 130.07808 0.017552299 Final line search alpha, max atom move = 1.0000000 0.017552299 Iterations, force evaluations = 84 153 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.8319 | 7.8319 | 7.8319 | 0.0 | 99.49 Neigh | 0.016621 | 0.016621 | 0.016621 | 0.0 | 0.21 Comm | 0.010185 | 0.010185 | 0.010185 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01314 | | | 0.17 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5249.00 ave 5249 max 5249 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: 103928.0 ave 103928 max 103928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103928 Ave neighs/atom = 77.097923 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.050 | 5.050 | 5.050 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -5709.1113 0 -5709.1113 8388.1509 15733.227 91 0 -5709.5294 0 -5709.5294 0.079781853 15814.037 Loop time of 0.506418 on 1 procs for 7 steps with 1348 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 = -5709.11125665797 -5709.52889508634 -5709.52943443211 Force two-norm initial, final = 159.75944 0.41711098 Force max component initial, final = 132.70741 0.13196790 Final line search alpha, max atom move = 0.00015637094 2.0635945e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50314 | 0.50314 | 0.50314 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044053 | 0.00044053 | 0.00044053 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00284 | | | 0.56 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5249.00 ave 5249 max 5249 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: 103888.0 ave 103888 max 103888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103888 Ave neighs/atom = 77.068249 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 ghost atom cutoff = 6 binsize = 3, bins = 9 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.188 | 5.188 | 5.188 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5709.5294 0 -5709.5294 0.079781853 Loop time of 2.585e-06 on 1 procs for 0 steps with 1348 atoms 193.4% 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 | | 2.585e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5249.00 ave 5249 max 5249 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: 103720.0 ave 103720 max 103720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103720 Ave neighs/atom = 76.943620 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 ghost atom cutoff = 6 binsize = 3, bins = 9 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.188 | 5.188 | 5.188 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 -5709.5294 -5709.5294 26.907422 93.979855 6.2536836 0.079781853 0.079781853 8.0304199 5.6021457 -13.39322 2.2659851 903.8222 Loop time of 2.678e-06 on 1 procs for 0 steps with 1348 atoms 224.0% 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 | | 2.678e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5249.00 ave 5249 max 5249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51860.0 ave 51860 max 51860 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103720.0 ave 103720 max 103720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103720 Ave neighs/atom = 76.943620 Neighbor list builds = 0 Dangerous builds = 0 1348 -5709.52943443211 eV 2.26598514694154 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09