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 = 3.3901167 3.3901167 3.3901167 Created orthogonal box = (0.0000000 -34.572542 0.0000000) to (17.286271 34.572542 3.3901167) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9891395 3.9891395 3.3901167 Created 104 atoms using lattice units in orthogonal box = (0.0000000 -34.572542 0.0000000) to (17.286271 34.572542 3.3901167) create_atoms CPU = 0.001 seconds 104 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9891395 3.9891395 3.3901167 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -34.572542 0.0000000) to (17.286271 34.572542 3.3901167) create_atoms CPU = 0.000 seconds 106 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 7 1 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 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 208 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_959249795837_003#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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 7 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 5.794 | 5.794 | 5.794 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4664.6877 0 -4664.6877 4765949.1 65 0 -7403.7364 0 -7403.7364 104785.49 Loop time of 0.594367 on 1 procs for 65 steps with 208 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 = -4664.68773471071 -7403.73034950576 -7403.73638924646 Force two-norm initial, final = 9501.7096 1.3996449 Force max component initial, final = 3204.2378 0.33608821 Final line search alpha, max atom move = 0.24822806 0.083426524 Iterations, force evaluations = 65 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57452 | 0.57452 | 0.57452 | 0.0 | 96.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015394 | 0.015394 | 0.015394 | 0.0 | 2.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004449 | | | 0.75 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14872.0 ave 14872 max 14872 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: 383292.0 ave 383292 max 383292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383292 Ave neighs/atom = 1842.7500 Neighbor list builds = 0 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 7 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.794 | 5.794 | 5.794 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -7403.7364 0 -7403.7364 104785.49 4052.0731 529 0 -7699.0189 0 -7699.0189 -7807.0185 3973.0252 Loop time of 3.08364 on 1 procs for 464 steps with 208 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7403.73638924645 -7699.01133982126 -7699.01888764998 Force two-norm initial, final = 2013.7341 37.948182 Force max component initial, final = 1335.6824 28.636122 Final line search alpha, max atom move = 4.2798692e-05 0.0012255886 Iterations, force evaluations = 464 576 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7414 | 2.7414 | 2.7414 | 0.0 | 88.90 Neigh | 0.052605 | 0.052605 | 0.052605 | 0.0 | 1.71 Comm | 0.060901 | 0.060901 | 0.060901 | 0.0 | 1.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2288 | | | 7.42 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15147.0 ave 15147 max 15147 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: 390424.0 ave 390424 max 390424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390424 Ave neighs/atom = 1877.0385 Neighbor list builds = 3 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 8 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 5.936 | 5.936 | 5.936 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7699.0189 0 -7699.0189 -7807.0185 Loop time of 2.221e-06 on 1 procs for 0 steps with 208 atoms 135.1% 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 | | 2.221e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15087.0 ave 15087 max 15087 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: 391292.0 ave 391292 max 391292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391292 Ave neighs/atom = 1881.2115 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 8 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 5.936 | 5.936 | 5.936 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 -7699.0189 -7699.0189 18.445332 71.872402 2.996903 -7807.0185 -7807.0185 -9684.9936 -12003.395 -1732.6671 2.8619084 1024.539 Loop time of 2.398e-06 on 1 procs for 0 steps with 208 atoms 250.2% 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 | | 2.398e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15087.0 ave 15087 max 15087 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 195646.0 ave 195646 max 195646 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 391292.0 ave 391292 max 391292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391292 Ave neighs/atom = 1881.2115 Neighbor list builds = 0 Dangerous builds = 0 208 -7699.01888764998 eV 2.86190836555648 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04