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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -80.842820 0.0000000) to (46.674624 80.842820 6.9837560) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2697256 6.4352493 6.9837560 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -80.842820 0.0000000) to (46.674624 80.842820 6.9837560) create_atoms CPU = 0.003 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2697256 6.4352493 6.9837560 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -80.842820 0.0000000) to (46.674624 80.842820 6.9837560) create_atoms CPU = 0.003 seconds 1610 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 43 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3212 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_020851069572_000#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.629 | 6.629 | 6.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10626.136 0 -10626.136 4527.8482 99 0 -10771.832 0 -10771.832 1546.2493 Loop time of 2.98224 on 1 procs for 99 steps with 3212 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10626.1357014611 -10771.8215802331 -10771.8321307143 Force two-norm initial, final = 55.620126 0.29082653 Force max component initial, final = 7.7032384 0.043767153 Final line search alpha, max atom move = 1.0000000 0.043767153 Iterations, force evaluations = 99 162 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8427 | 2.8427 | 2.8427 | 0.0 | 95.32 Neigh | 0.092037 | 0.092037 | 0.092037 | 0.0 | 3.09 Comm | 0.019553 | 0.019553 | 0.019553 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02795 | | | 0.94 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10852.0 ave 10852 max 10852 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: 423924.0 ave 423924 max 423924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423924 Ave neighs/atom = 131.98132 Neighbor list builds = 4 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.629 | 6.629 | 6.629 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -10771.832 0 -10771.832 1546.2493 52703.727 103 0 -10772.027 0 -10772.027 -167.65366 52814.313 Loop time of 0.114562 on 1 procs for 4 steps with 3212 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 = -10771.8321307143 -10772.0226866178 -10772.0266246651 Force two-norm initial, final = 120.63961 10.382301 Force max component initial, final = 117.78090 7.3760505 Final line search alpha, max atom move = 6.5561647e-05 0.00048358602 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11038 | 0.11038 | 0.11038 | 0.0 | 96.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054837 | 0.00054837 | 0.00054837 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003636 | | | 3.17 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10876.0 ave 10876 max 10876 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: 423876.0 ave 423876 max 423876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423876 Ave neighs/atom = 131.96638 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.767 | 6.767 | 6.767 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10772.027 0 -10772.027 -167.65366 Loop time of 1.88e-06 on 1 procs for 0 steps with 3212 atoms 159.6% 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 | | 1.88e-06 | | |100.00 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10886.0 ave 10886 max 10886 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: 423660.0 ave 423660 max 423660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423660 Ave neighs/atom = 131.89913 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.767 | 6.767 | 6.767 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 -10772.027 -10772.027 46.651108 162.25066 6.9775538 -167.65366 -167.65366 -223.64734 -69.034579 -210.27907 2.5866488 1581.6274 Loop time of 2.167e-06 on 1 procs for 0 steps with 3212 atoms 323.0% 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 | | 2.167e-06 | | |100.00 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10886.0 ave 10886 max 10886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 211830.0 ave 211830 max 211830 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 423660.0 ave 423660 max 423660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423660 Ave neighs/atom = 131.89913 Neighbor list builds = 0 Dangerous builds = 0 3212 -10772.0266246651 eV 2.58664882947156 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03