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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -33.451527 0.0000000) to (33.448381 33.451527 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4400505 4.4400505 3.1465590 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -33.451527 0.0000000) to (33.448381 33.451527 3.1465590) create_atoms CPU = 0.002 seconds 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4400505 4.4400505 3.1465590 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -33.451527 0.0000000) to (33.448381 33.451527 3.1465590) create_atoms CPU = 0.001 seconds 227 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 21 1 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 450 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_356501945107_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.454 | 4.454 | 4.454 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2802.3927 0 -2802.3927 146773.36 41 0 -3051.132 0 -3051.132 -6001.2462 Loop time of 2.65809 on 1 procs for 41 steps with 450 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 = -2802.39265408967 -3051.12908179524 -3051.13203528685 Force two-norm initial, final = 346.76381 0.31589107 Force max component initial, final = 86.562230 0.067620086 Final line search alpha, max atom move = 1.0000000 0.067620086 Iterations, force evaluations = 41 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6461 | 2.6461 | 2.6461 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0061918 | 0.0061918 | 0.0061918 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005839 | | | 0.22 Nlocal: 450.000 ave 450 max 450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3290.00 ave 3290 max 3290 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: 29104.0 ave 29104 max 29104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29104 Ave neighs/atom = 64.675556 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.454 | 4.454 | 4.454 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -3051.132 0 -3051.132 -6001.2462 7041.366 43 0 -3051.1624 0 -3051.1624 -485.65271 7026.5295 Loop time of 0.130232 on 1 procs for 2 steps with 450 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 = -3051.13203528685 -3051.16075181534 -3051.16244044635 Force two-norm initial, final = 39.691144 2.2143639 Force max component initial, final = 33.338682 2.1144256 Final line search alpha, max atom move = 0.00011593466 0.00024513522 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12898 | 0.12898 | 0.12898 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030669 | 0.00030669 | 0.00030669 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009497 | | | 0.73 Nlocal: 450.000 ave 450 max 450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3345.00 ave 3345 max 3345 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: 28892.0 ave 28892 max 28892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28892 Ave neighs/atom = 64.204444 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3051.1624 0 -3051.1624 -485.65271 Loop time of 6.354e-06 on 1 procs for 0 steps with 450 atoms 173.1% 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 | | 6.354e-06 | | |100.00 Nlocal: 450.000 ave 450 max 450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3349.00 ave 3349 max 3349 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: 28896.0 ave 28896 max 28896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28896 Ave neighs/atom = 64.213333 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.592 | 4.592 | 4.592 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 -3051.1624 -3051.1624 33.423482 66.903054 3.1422681 -485.65271 -485.65271 481.7686 -1807.7035 -131.02323 2.5258562 172.46888 Loop time of 7.006e-06 on 1 procs for 0 steps with 450 atoms 242.6% 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 | | 7.006e-06 | | |100.00 Nlocal: 450.000 ave 450 max 450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3349.00 ave 3349 max 3349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14448.0 ave 14448 max 14448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28896.0 ave 28896 max 28896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28896 Ave neighs/atom = 64.213333 Neighbor list builds = 0 Dangerous builds = 0 450 -3051.16244044635 eV 2.52585619454135 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03