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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -57.612589 0.0000000) to (35.280361 57.612589 8.9612207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6903808 5.5754118 5.9741471 Created 1486 atoms using lattice units in orthogonal box = (0.0000000 -57.612589 0.0000000) to (35.280361 57.612589 8.9612207) create_atoms CPU = 0.002 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6903808 5.5754118 5.9741471 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -57.612589 0.0000000) to (35.280361 57.612589 8.9612207) create_atoms CPU = 0.002 seconds 1492 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 28 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2978 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.405 | 7.405 | 7.405 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11004.606 0 -11004.606 48680.826 1054 0 -11743.012 0 -11743.012 -63314.253 Loop time of 64.4593 on 1 procs for 1054 steps with 2978 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11004.6056457764 -11743.0017590455 -11743.011898538 Force two-norm initial, final = 1064.5897 0.34385214 Force max component initial, final = 314.50539 0.084158592 Final line search alpha, max atom move = 0.84050933 0.070736082 Iterations, force evaluations = 1054 2074 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 63.196 | 63.196 | 63.196 | 0.0 | 98.04 Neigh | 0.75625 | 0.75625 | 0.75625 | 0.0 | 1.17 Comm | 0.22564 | 0.22564 | 0.22564 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2812 | | | 0.44 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11659.0 ave 11659 max 11659 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: 606874.0 ave 606874 max 606874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 606874 Ave neighs/atom = 203.78576 Neighbor list builds = 21 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1054 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.404 | 7.404 | 7.404 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1054 0 -11743.012 0 -11743.012 -63314.253 36429.028 1105 0 -11824.238 0 -11824.238 -21.017844 35084.631 Loop time of 1.83919 on 1 procs for 51 steps with 2978 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11743.0118985381 -11824.2348695725 -11824.2380620357 Force two-norm initial, final = 3088.3815 8.2893651 Force max component initial, final = 2346.6002 4.3396939 Final line search alpha, max atom move = 0.00013446368 0.00058353123 Iterations, force evaluations = 51 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6974 | 1.6974 | 1.6974 | 0.0 | 92.29 Neigh | 0.10688 | 0.10688 | 0.10688 | 0.0 | 5.81 Comm | 0.0054011 | 0.0054011 | 0.0054011 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02956 | | | 1.61 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11770.0 ave 11770 max 11770 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: 643958.0 ave 643958 max 643958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 643958 Ave neighs/atom = 216.23842 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.541 | 7.541 | 7.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11824.238 0 -11824.238 -21.017844 Loop time of 2.052e-06 on 1 procs for 0 steps with 2978 atoms 194.9% 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 | | 2.052e-06 | | |100.00 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11642.0 ave 11642 max 11642 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: 649746.0 ave 649746 max 649746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 649746 Ave neighs/atom = 218.18200 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.541 | 7.541 | 7.541 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 -11824.238 -11824.238 33.901349 111.53564 9.2786819 -21.017844 -21.017844 104.49031 37.653464 -205.19731 2.185543 5136.4336 Loop time of 2.246e-06 on 1 procs for 0 steps with 2978 atoms 222.6% 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 | | 2.246e-06 | | |100.00 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11642.0 ave 11642 max 11642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 324873.0 ave 324873 max 324873 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 649746.0 ave 649746 max 649746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 649746 Ave neighs/atom = 218.18200 Neighbor list builds = 0 Dangerous builds = 0 2978 -11824.2380620357 eV 2.18554299008976 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:07