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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -52.542484 0.0000000) to (37.150546 52.542484 5.2021169) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8275366 4.6357770 5.2021169 Created 819 atoms using lattice units in orthogonal box = (0.0000000 -52.542484 0.0000000) to (37.150546 52.542484 5.2021169) create_atoms CPU = 0.001 seconds 819 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8275366 4.6357770 5.2021169 Created 819 atoms using lattice units in orthogonal box = (0.0000000 -52.542484 0.0000000) to (37.150546 52.542484 5.2021169) create_atoms CPU = 0.001 seconds 819 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 35 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 1607 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6731.7123 0 -6731.7123 -1786.5349 216 0 -6768.816 0 -6768.816 -23368.48 Loop time of 1.66485 on 1 procs for 216 steps with 1607 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 = -6731.71227335682 -6768.80946591265 -6768.8160140537 Force two-norm initial, final = 11.115926 0.25186196 Force max component initial, final = 2.1380770 0.028749174 Final line search alpha, max atom move = 1.0000000 0.028749174 Iterations, force evaluations = 216 387 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5862 | 1.5862 | 1.5862 | 0.0 | 95.28 Neigh | 0.034188 | 0.034188 | 0.034188 | 0.0 | 2.05 Comm | 0.021084 | 0.021084 | 0.021084 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02334 | | | 1.40 Nlocal: 1607.00 ave 1607 max 1607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6434.00 ave 6434 max 6434 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: 123900.0 ave 123900 max 123900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123900 Ave neighs/atom = 77.100187 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 216 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.113 | 5.113 | 5.113 Mbytes Step Temp E_pair E_mol TotEng Press Volume 216 0 -6768.816 0 -6768.816 -23368.48 20308.877 231 0 -6772.6702 0 -6772.6702 795.95451 19857.761 Loop time of 0.0773389 on 1 procs for 15 steps with 1607 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 = -6768.81601405368 -6772.66885044804 -6772.67015260168 Force two-norm initial, final = 468.19470 1.5831837 Force max component initial, final = 390.90069 1.2977927 Final line search alpha, max atom move = 0.00012435747 0.00016139021 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071779 | 0.071779 | 0.071779 | 0.0 | 92.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010239 | 0.0010239 | 0.0010239 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004535 | | | 5.86 Nlocal: 1607.00 ave 1607 max 1607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6415.00 ave 6415 max 6415 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: 123094.0 ave 123094 max 123094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123094 Ave neighs/atom = 76.598631 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.250 | 5.250 | 5.250 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6772.6702 0 -6772.6702 795.95451 Loop time of 1.817e-06 on 1 procs for 0 steps with 1607 atoms 165.1% 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 | | 1.817e-06 | | |100.00 Nlocal: 1607.00 ave 1607 max 1607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6517.00 ave 6517 max 6517 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: 124020.0 ave 124020 max 124020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124020 Ave neighs/atom = 77.174860 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 12 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.250 | 5.250 | 5.250 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 -6772.6702 -6772.6702 36.618605 105.08497 5.1604537 795.95451 795.95451 11.285792 2272.707 103.87073 2.393405 1373.9207 Loop time of 1.667e-06 on 1 procs for 0 steps with 1607 atoms 120.0% 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 | | 1.667e-06 | | |100.00 Nlocal: 1607.00 ave 1607 max 1607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6517.00 ave 6517 max 6517 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62010.0 ave 62010 max 62010 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 124020.0 ave 124020 max 124020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124020 Ave neighs/atom = 77.174860 Neighbor list builds = 0 Dangerous builds = 0 1607 -6772.66999190168 eV 2.39340504687298 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02