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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -48.467086 0.0000000) to (29.679907 48.467086 8.9488288) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3963468 5.5076234 5.9658858 Created 1054 atoms using lattice units in orthogonal box = (0.0000000 -48.467086 0.0000000) to (29.679907 48.467086 8.9488288) create_atoms CPU = 0.002 seconds 1054 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3963468 5.5076234 5.9658858 Created 1078 atoms using lattice units in orthogonal box = (0.0000000 -48.467086 0.0000000) to (29.679907 48.467086 8.9488288) create_atoms CPU = 0.001 seconds 1078 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 23 3 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 2112 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_673777079812_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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.468 | 6.468 | 6.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6881.8197 0 -6881.8197 2547.3427 19 0 -6899.337 0 -6899.337 543.98817 Loop time of 0.524715 on 1 procs for 19 steps with 2112 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6881.81971229027 -6899.33202682135 -6899.33695152328 Force two-norm initial, final = 24.887572 0.25039508 Force max component initial, final = 7.2466206 0.013400965 Final line search alpha, max atom move = 1.0000000 0.013400965 Iterations, force evaluations = 19 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51756 | 0.51756 | 0.51756 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032203 | 0.0032203 | 0.0032203 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003936 | | | 0.75 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9363.00 ave 9363 max 9363 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: 474336.0 ave 474336 max 474336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 474336 Ave neighs/atom = 224.59091 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.468 | 6.468 | 6.468 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -6899.337 0 -6899.337 543.98817 25745.755 24 0 -6899.6565 0 -6899.6565 18.461782 25756.561 Loop time of 0.105259 on 1 procs for 5 steps with 2112 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 = -6899.33695152327 -6899.65599890899 -6899.65654028635 Force two-norm initial, final = 117.42273 0.73849657 Force max component initial, final = 93.050678 0.57717912 Final line search alpha, max atom move = 0.00025908051 0.00014953586 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10148 | 0.10148 | 0.10148 | 0.0 | 96.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053636 | 0.00053636 | 0.00053636 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003241 | | | 3.08 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9369.00 ave 9369 max 9369 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: 473232.0 ave 473232 max 473232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 473232 Ave neighs/atom = 224.06818 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.606 | 6.606 | 6.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6899.6565 0 -6899.6565 18.461782 Loop time of 2.18e-06 on 1 procs for 0 steps with 2112 atoms 183.5% 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 | | 2.18e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9381.00 ave 9381 max 9381 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: 473280.0 ave 473280 max 473280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 473280 Ave neighs/atom = 224.09091 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.606 | 6.606 | 6.606 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 -6899.6565 -6899.6565 29.578405 97.33907 8.9459391 18.461782 18.461782 12.156638 7.3371076 35.891601 2.462848 458.76946 Loop time of 2.1919e-05 on 1 procs for 0 steps with 2112 atoms 127.7% 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 | | 2.192e-05 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9381.00 ave 9381 max 9381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 236640.0 ave 236640 max 236640 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 473280.0 ave 473280 max 473280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 473280 Ave neighs/atom = 224.09091 Neighbor list builds = 0 Dangerous builds = 0 2112 -6899.65654028635 eV 2.46284801506845 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01