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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -47.359113 0.0000000) to (33.487950 47.359113 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2303163 6.0575610 5.1068645 Created 683 atoms using lattice units in orthogonal box = (0.0000000 -47.359113 0.0000000) to (33.487950 47.359113 5.1068645) create_atoms CPU = 0.002 seconds 683 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2303163 6.0575610 5.1068645 Created 691 atoms using lattice units in orthogonal box = (0.0000000 -47.359113 0.0000000) to (33.487950 47.359113 5.1068645) create_atoms CPU = 0.002 seconds 691 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 28 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1371 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_110119204723_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5718.3807 0 -5718.3807 17798.03 573 0 -5836.3265 0 -5836.3265 -1310.7996 Loop time of 130.539 on 1 procs for 573 steps with 1371 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 = -5718.38066210037 -5836.32178555029 -5836.32649912693 Force two-norm initial, final = 96.604101 0.23308846 Force max component initial, final = 15.487159 0.085199491 Final line search alpha, max atom move = 0.85861901 0.073153902 Iterations, force evaluations = 573 1108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 130.09 | 130.09 | 130.09 | 0.0 | 99.66 Neigh | 0.25373 | 0.25373 | 0.25373 | 0.0 | 0.19 Comm | 0.10264 | 0.10264 | 0.10264 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09042 | | | 0.07 Nlocal: 1371.00 ave 1371 max 1371 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6705.00 ave 6705 max 6705 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: 154850.0 ave 154850 max 154850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154850 Ave neighs/atom = 112.94675 Neighbor list builds = 22 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 573 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press Volume 573 0 -5836.3265 0 -5836.3265 -1310.7996 16198.562 599 0 -5847.5201 0 -5847.5201 10.962078 16163.242 Loop time of 3.99608 on 1 procs for 26 steps with 1371 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 = -5836.32649912693 -5847.51977172375 -5847.52010181783 Force two-norm initial, final = 666.96896 2.1883681 Force max component initial, final = 505.01203 1.1501125 Final line search alpha, max atom move = 0.00049623364 0.00057072451 Iterations, force evaluations = 26 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9602 | 3.9602 | 3.9602 | 0.0 | 99.10 Neigh | 0.023155 | 0.023155 | 0.023155 | 0.0 | 0.58 Comm | 0.0021607 | 0.0021607 | 0.0021607 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01053 | | | 0.26 Nlocal: 1371.00 ave 1371 max 1371 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6920.00 ave 6920 max 6920 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: 154584.0 ave 154584 max 154584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154584 Ave neighs/atom = 112.75274 Neighbor list builds = 2 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.208 | 5.208 | 5.208 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5847.5201 0 -5847.5201 10.962078 Loop time of 2.37e-06 on 1 procs for 0 steps with 1371 atoms 168.8% 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 | | 2.37e-06 | | |100.00 Nlocal: 1371.00 ave 1371 max 1371 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6919.00 ave 6919 max 6919 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: 154582.0 ave 154582 max 154582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154582 Ave neighs/atom = 112.75128 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.208 | 5.208 | 5.208 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 -5847.5201 -5847.5201 33.495302 96.836006 4.9831931 10.962078 10.962078 114.02958 -29.1855 -51.957849 2.3495761 2791.2148 Loop time of 2.651e-06 on 1 procs for 0 steps with 1371 atoms 188.6% 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 | | 2.651e-06 | | |100.00 Nlocal: 1371.00 ave 1371 max 1371 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6919.00 ave 6919 max 6919 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77291.0 ave 77291 max 77291 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 154582.0 ave 154582 max 154582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154582 Ave neighs/atom = 112.75128 Neighbor list builds = 0 Dangerous builds = 0 1371 -5847.52010181783 eV 2.34957608052184 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:15