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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -71.453723 0.0000000) to (41.253826 71.453723 7.0066140) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3467425 6.4125136 7.0066140 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -71.453723 0.0000000) to (41.253826 71.453723 7.0066140) create_atoms CPU = 0.007 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3467425 6.4125136 7.0066140 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.453723 0.0000000) to (41.253826 71.453723 7.0066140) create_atoms CPU = 0.004 seconds 1251 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 31 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 2495 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_658278549784_005#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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 6.938 | 6.938 | 6.938 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8207.6093 0 -8207.6093 19984.453 107 0 -8489.5014 0 -8489.5014 3823.0068 Loop time of 4.56949 on 1 procs for 107 steps with 2495 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 = -8207.60932475895 -8489.49406661014 -8489.50140827117 Force two-norm initial, final = 303.60447 0.18663680 Force max component initial, final = 66.386593 0.042685984 Final line search alpha, max atom move = 1.0000000 0.042685984 Iterations, force evaluations = 107 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3917 | 4.3917 | 4.3917 | 0.0 | 96.11 Neigh | 0.12526 | 0.12526 | 0.12526 | 0.0 | 2.74 Comm | 0.028287 | 0.028287 | 0.028287 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02424 | | | 0.53 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12602.0 ave 12602 max 12602 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: 548430.0 ave 548430 max 548430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 548430 Ave neighs/atom = 219.81162 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.938 | 6.938 | 6.938 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -8489.5014 0 -8489.5014 3823.0068 41307.345 113 0 -8489.9508 0 -8489.9508 -191.1972 41512.393 Loop time of 0.228693 on 1 procs for 6 steps with 2495 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 = -8489.50140827113 -8489.94493781363 -8489.95083483156 Force two-norm initial, final = 191.66684 8.8876362 Force max component initial, final = 169.27817 6.1973670 Final line search alpha, max atom move = 7.1229636e-05 0.00044143620 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2231 | 0.2231 | 0.2231 | 0.0 | 97.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086396 | 0.00086396 | 0.00086396 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004732 | | | 2.07 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12589.0 ave 12589 max 12589 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: 552096.0 ave 552096 max 552096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 552096 Ave neighs/atom = 221.28096 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 7.076 | 7.076 | 7.076 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8489.9508 0 -8489.9508 -191.1972 Loop time of 2.417e-06 on 1 procs for 0 steps with 2495 atoms 165.5% 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 | | 2.417e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12589.0 ave 12589 max 12589 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: 544248.0 ave 544248 max 544248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 544248 Ave neighs/atom = 218.13547 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 7.076 | 7.076 | 7.076 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 -8489.9508 -8489.9508 41.250094 143.72818 7.0018192 -191.1972 -191.1972 -239.16659 -119.68959 -214.73542 2.5124533 1202.584 Loop time of 2.33e-06 on 1 procs for 0 steps with 2495 atoms 257.5% 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 | | 2.33e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12589.0 ave 12589 max 12589 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 272124.0 ave 272124 max 272124 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 544248.0 ave 544248 max 544248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 544248 Ave neighs/atom = 218.13547 Neighbor list builds = 0 Dangerous builds = 0 2495 -8489.95083483156 eV 2.51245325990733 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05