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 = 4.0515263 4.0515263 4.0515263 Created orthogonal box = (0.0000000 -57.297234 0.0000000) to (28.648617 57.297234 4.0515263) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5837787 4.5837787 4.0515263 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -57.297234 0.0000000) to (28.648617 57.297234 4.0515263) create_atoms CPU = 0.003 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5837787 4.5837787 4.0515263 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -57.297234 0.0000000) to (28.648617 57.297234 4.0515263) create_atoms CPU = 0.002 seconds 402 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 29 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 796 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 4.941 | 4.941 | 4.941 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1818.5781 0 -1818.5781 161307.92 68 0 -2665.6524 0 -2665.6524 2735.5154 Loop time of 1.64251 on 1 procs for 68 steps with 796 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1818.5781419741 -2665.64986353908 -2665.65242731941 Force two-norm initial, final = 2075.6673 0.15365538 Force max component initial, final = 707.56193 0.021007318 Final line search alpha, max atom move = 1.0000000 0.021007318 Iterations, force evaluations = 68 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5977 | 1.5977 | 1.5977 | 0.0 | 97.27 Neigh | 0.012439 | 0.012439 | 0.012439 | 0.0 | 0.76 Comm | 0.01743 | 0.01743 | 0.01743 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01493 | | | 0.91 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5546.00 ave 5546 max 5546 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: 105244.0 ave 105244 max 105244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105244 Ave neighs/atom = 132.21608 Neighbor list builds = 1 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.941 | 4.941 | 4.941 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -2665.6524 0 -2665.6524 2735.5154 13301.052 70 0 -2665.687 0 -2665.687 -239.31988 13341.695 Loop time of 0.0510569 on 1 procs for 2 steps with 796 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2665.6524273194 -2665.6850279789 -2665.68699758588 Force two-norm initial, final = 39.888548 4.8084918 Force max component initial, final = 28.117099 3.4779076 Final line search alpha, max atom move = 0.00013351089 0.00046433855 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049171 | 0.049171 | 0.049171 | 0.0 | 96.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047245 | 0.00047245 | 0.00047245 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001414 | | | 2.77 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5516.00 ave 5516 max 5516 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: 105728.0 ave 105728 max 105728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105728 Ave neighs/atom = 132.82412 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.079 | 5.079 | 5.079 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2665.687 0 -2665.687 -239.31988 Loop time of 6.004e-06 on 1 procs for 0 steps with 796 atoms 166.6% 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 | | 6.004e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5516.00 ave 5516 max 5516 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: 105704.0 ave 105704 max 105704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105704 Ave neighs/atom = 132.79397 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.079 | 5.079 | 5.079 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 -2665.687 -2665.687 28.670786 114.76795 4.0546258 -239.31988 -239.31988 -388.65598 88.670578 -417.97424 2.6914482 258.42298 Loop time of 6.956e-06 on 1 procs for 0 steps with 796 atoms 230.0% 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 | | 6.956e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5516.00 ave 5516 max 5516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52852.0 ave 52852 max 52852 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105704.0 ave 105704 max 105704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105704 Ave neighs/atom = 132.79397 Neighbor list builds = 0 Dangerous builds = 0 796 -2665.68699757853 eV 2.69144815093481 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02