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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -37.990554 0.0000000) to (13.431689 37.990554 4.0498067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8842506 4.3171084 4.0498067 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -37.990554 0.0000000) to (13.431689 37.990554 4.0498067) create_atoms CPU = 0.001 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8842506 4.3171084 4.0498067 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.990554 0.0000000) to (13.431689 37.990554 4.0498067) create_atoms CPU = 0.000 seconds 178 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 24 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 350 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1436.1635 0 -1436.1635 37389.967 62 0 -1494.011 0 -1494.011 -479.17635 Loop time of 2.95067 on 1 procs for 62 steps with 350 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1436.16350530825 -1494.0097879257 -1494.01096941766 Force two-norm initial, final = 142.20718 0.10256626 Force max component initial, final = 48.277772 0.018250012 Final line search alpha, max atom move = 1.0000000 0.018250012 Iterations, force evaluations = 62 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9429 | 2.9429 | 2.9429 | 0.0 | 99.74 Neigh | 0.0022581 | 0.0022581 | 0.0022581 | 0.0 | 0.08 Comm | 0.0031313 | 0.0031313 | 0.0031313 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002416 | | | 0.08 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3205.00 ave 3205 max 3205 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: 34520.0 ave 34520 max 34520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34520 Ave neighs/atom = 98.628571 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -1494.011 0 -1494.011 -479.17635 4133.049 67 0 -1494.068 0 -1494.068 -4.6574589 4131.8051 Loop time of 0.187879 on 1 procs for 5 steps with 350 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 = -1494.01096941766 -1494.06792005405 -1494.06800804705 Force two-norm initial, final = 21.967736 0.18952536 Force max component initial, final = 16.611744 0.055727493 Final line search alpha, max atom move = 0.0015739214 8.7710693e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18704 | 0.18704 | 0.18704 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016256 | 0.00016256 | 0.00016256 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006719 | | | 0.36 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3227.00 ave 3227 max 3227 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: 34228.0 ave 34228 max 34228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34228 Ave neighs/atom = 97.794286 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.582 | 4.582 | 4.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1494.068 0 -1494.068 -4.6574589 Loop time of 1.483e-06 on 1 procs for 0 steps with 350 atoms 134.9% 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 | | 1.483e-06 | | |100.00 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3209.00 ave 3209 max 3209 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: 35208.0 ave 35208 max 35208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35208 Ave neighs/atom = 100.59429 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.582 | 4.582 | 4.582 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 -1494.068 -1494.068 13.405636 76.297204 4.0396504 -4.6574589 -4.6574589 -21.475592 -9.3587919 16.862007 2.290514 275.22716 Loop time of 1.663e-06 on 1 procs for 0 steps with 350 atoms 180.4% 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 | | 1.663e-06 | | |100.00 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3209.00 ave 3209 max 3209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17604.0 ave 17604 max 17604 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35208.0 ave 35208 max 35208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35208 Ave neighs/atom = 100.59429 Neighbor list builds = 0 Dangerous builds = 0 350 -1494.06800804705 eV 2.29051403289759 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03