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 = 3.6131481 3.6131481 3.6131481 Created orthogonal box = (0.0000000 -41.825213 0.0000000) to (29.574892 41.825213 5.1097631) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7384119 6.2425692 5.1097631 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.825213 0.0000000) to (29.574892 41.825213 5.1097631) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7384119 6.2425692 5.1097631 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.825213 0.0000000) to (29.574892 41.825213 5.1097631) create_atoms CPU = 0.001 seconds 538 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 6 16 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 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1070 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_173787283511_004#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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 6 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 6.262 | 6.262 | 6.262 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3529.7562 0 -3529.7562 31730.331 85 0 -3728.0708 0 -3728.0708 -398.35219 Loop time of 4.50308 on 1 procs for 85 steps with 1070 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3529.75621411967 -3728.06724960623 -3728.07076749748 Force two-norm initial, final = 286.51897 0.23511023 Force max component initial, final = 89.486453 0.034507008 Final line search alpha, max atom move = 1.0000000 0.034507008 Iterations, force evaluations = 85 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.411 | 4.411 | 4.411 | 0.0 | 97.95 Neigh | 0.048183 | 0.048183 | 0.048183 | 0.0 | 1.07 Comm | 0.02691 | 0.02691 | 0.02691 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.017 | | | 0.38 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10370.0 ave 10370 max 10370 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: 414904.0 ave 414904 max 414904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 414904 Ave neighs/atom = 387.76075 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 6 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.262 | 6.262 | 6.262 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -3728.0708 0 -3728.0708 -398.35219 12641.31 92 0 -3728.5054 0 -3728.5054 21.163855 12635.622 Loop time of 0.369314 on 1 procs for 7 steps with 1070 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 = -3728.07076749748 -3728.50535136109 -3728.5054252882 Force two-norm initial, final = 117.72939 0.50461067 Force max component initial, final = 84.841478 0.20569602 Final line search alpha, max atom move = 0.00092715265 0.00019071161 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35953 | 0.35953 | 0.35953 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017494 | 0.0017494 | 0.0017494 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008035 | | | 2.18 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10330.0 ave 10330 max 10330 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: 415044.0 ave 415044 max 415044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 415044 Ave neighs/atom = 387.89159 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 6.400 | 6.400 | 6.400 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3728.5054 0 -3728.5054 21.163855 Loop time of 4.006e-06 on 1 procs for 0 steps with 1070 atoms 224.7% 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 | | 4.006e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10350.0 ave 10350 max 10350 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: 414604.0 ave 414604 max 414604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 414604 Ave neighs/atom = 387.48037 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 6.400 | 6.400 | 6.400 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 -3728.5054 -3728.5054 29.410523 84.063096 5.1107952 21.163855 21.163855 22.521067 26.210593 14.759906 2.3453604 611.81411 Loop time of 4.457e-06 on 1 procs for 0 steps with 1070 atoms 201.9% 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 | | 4.457e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10350.0 ave 10350 max 10350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 207302.0 ave 207302 max 207302 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 414604.0 ave 414604 max 414604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 414604 Ave neighs/atom = 387.48037 Neighbor list builds = 0 Dangerous builds = 0 1070 -3728.50542528818 eV 2.34536038905917 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05