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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -48.826700 0.0000000) to (59.800251 48.826700 9.8982079) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7342706 6.0197302 6.5988053 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -48.826700 0.0000000) to (59.800251 48.826700 9.8982079) create_atoms CPU = 0.004 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7342706 6.0197302 6.5988053 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -48.826700 0.0000000) to (59.800251 48.826700 9.8982079) create_atoms CPU = 0.007 seconds 1755 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 3495 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 12.19 | 12.19 | 12.19 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12631.904 0 -12631.904 39872.182 91 0 -13618.407 0 -13618.407 3071.5885 Loop time of 7.64281 on 1 procs for 91 steps with 3495 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12631.9041423079 -13618.3947339125 -13618.4072081409 Force two-norm initial, final = 866.66455 0.27614296 Force max component initial, final = 121.38233 0.063777903 Final line search alpha, max atom move = 1.0000000 0.063777903 Iterations, force evaluations = 91 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3587 | 7.3587 | 7.3587 | 0.0 | 96.28 Neigh | 0.22365 | 0.22365 | 0.22365 | 0.0 | 2.93 Comm | 0.028099 | 0.028099 | 0.028099 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03237 | | | 0.42 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13317.0 ave 13317 max 13317 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: 861008.0 ave 861008 max 861008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 861008 Ave neighs/atom = 246.35422 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.19 | 12.19 | 12.19 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -13618.407 0 -13618.407 3071.5885 57802.544 97 0 -13618.923 0 -13618.923 -75.659918 58023.847 Loop time of 0.399176 on 1 procs for 6 steps with 3495 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 = -13618.407208141 -13618.9222556531 -13618.9230479649 Force two-norm initial, final = 229.17613 5.7870100 Force max component initial, final = 209.30157 4.4995589 Final line search alpha, max atom move = 0.00012055438 0.00054244154 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39329 | 0.39329 | 0.39329 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078914 | 0.00078914 | 0.00078914 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005101 | | | 1.28 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13317.0 ave 13317 max 13317 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: 861082.0 ave 861082 max 861082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 861082 Ave neighs/atom = 246.37539 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 11.70 | 11.70 | 11.70 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13618.923 0 -13618.923 -75.659918 Loop time of 2.012e-06 on 1 procs for 0 steps with 3495 atoms 198.8% 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 | | 2.012e-06 | | |100.00 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13293.0 ave 13293 max 13293 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: 859362.0 ave 859362 max 859362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 859362 Ave neighs/atom = 245.88326 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 11.70 | 11.70 | 11.70 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 -13618.923 -13618.923 59.804052 98.160037 9.8841926 -75.659918 -75.659918 -124.25142 -2.8393934 -99.888937 2.5359661 1970.2544 Loop time of 2.602e-06 on 1 procs for 0 steps with 3495 atoms 230.6% 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 | | 2.602e-06 | | |100.00 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13293.0 ave 13293 max 13293 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 429681.0 ave 429681 max 429681 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 859362.0 ave 859362 max 859362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 859362 Ave neighs/atom = 245.88326 Neighbor list builds = 0 Dangerous builds = 0 3495 -13618.9230479649 eV 2.53596606571052 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09