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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -63.030803 0.0000000) to (25.732218 63.030803 8.9139016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1757322 5.4626696 5.9426011 Created 1197 atoms using lattice units in orthogonal box = (0.0000000 -63.030803 0.0000000) to (25.732218 63.030803 8.9139016) create_atoms CPU = 0.002 seconds 1197 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1757322 5.4626696 5.9426011 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -63.030803 0.0000000) to (25.732218 63.030803 8.9139016) create_atoms CPU = 0.002 seconds 1205 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2400 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_120596890176_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.786 | 7.786 | 7.786 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5942.7988 0 -5942.7988 155907.81 94 0 -7859.0735 0 -7859.0735 4107.6652 Loop time of 6.61759 on 1 procs for 94 steps with 2400 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5942.79878128553 -7859.06716757645 -7859.07354689614 Force two-norm initial, final = 2710.3415 0.20494314 Force max component initial, final = 390.45894 0.0089180803 Final line search alpha, max atom move = 1.0000000 0.0089180803 Iterations, force evaluations = 94 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4843 | 6.4843 | 6.4843 | 0.0 | 97.99 Neigh | 0.081748 | 0.081748 | 0.081748 | 0.0 | 1.24 Comm | 0.028267 | 0.028267 | 0.028267 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0233 | | | 0.35 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12687.0 ave 12687 max 12687 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: 762808.0 ave 762808 max 762808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 762808 Ave neighs/atom = 317.83667 Neighbor list builds = 2 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.786 | 7.786 | 7.786 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -7859.0735 0 -7859.0735 4107.6652 28915.312 99 0 -7859.3353 0 -7859.3353 -11.552673 28998.148 Loop time of 0.29179 on 1 procs for 5 steps with 2400 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 = -7859.07354689614 -7859.33426252356 -7859.33534017904 Force two-norm initial, final = 156.29484 1.6998037 Force max component initial, final = 145.21776 1.3769626 Final line search alpha, max atom move = 8.0016210e-05 0.00011017933 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28722 | 0.28722 | 0.28722 | 0.0 | 98.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000787 | 0.000787 | 0.000787 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003784 | | | 1.30 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12830.0 ave 12830 max 12830 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: 763520.0 ave 763520 max 763520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 763520 Ave neighs/atom = 318.13333 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.924 | 7.924 | 7.924 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7859.3353 0 -7859.3353 -11.552673 Loop time of 2.158e-06 on 1 procs for 0 steps with 2400 atoms 185.4% 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 | | 2.158e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12830.0 ave 12830 max 12830 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: 763328.0 ave 763328 max 763328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 763328 Ave neighs/atom = 318.05333 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.924 | 7.924 | 7.924 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 -7859.3353 -7859.3353 25.711723 126.54553 8.9123509 -11.552673 -11.552673 52.350126 -10.942826 -76.065318 2.3847228 755.02914 Loop time of 2.638e-06 on 1 procs for 0 steps with 2400 atoms 341.2% 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 | | 2.638e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12830.0 ave 12830 max 12830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 381664.0 ave 381664 max 381664 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 763328.0 ave 763328 max 763328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 763328 Ave neighs/atom = 318.05333 Neighbor list builds = 0 Dangerous builds = 0 2400 -7859.33534017904 eV 2.38472279889391 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07