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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -58.227214 0.0000000) to (29.113607 58.227214 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9269181 4.9269181 3.6110985 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.227214 0.0000000) to (29.113607 58.227214 3.6110985) create_atoms CPU = 0.001 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9269181 4.9269181 3.6110985 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.227214 0.0000000) to (29.113607 58.227214 3.6110985) create_atoms CPU = 0.001 seconds 522 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 = 9 36 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1042 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_924736622203_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 = 9 36 2 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) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4109.9275 0 -4109.9275 60572.751 83 0 -4406.3232 0 -4406.3232 9286.7753 Loop time of 7.66591 on 1 procs for 83 steps with 1042 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 = -4109.92746531799 -4406.31947744713 -4406.32316535205 Force two-norm initial, final = 483.92699 0.20835564 Force max component initial, final = 170.42732 0.062416630 Final line search alpha, max atom move = 1.0000000 0.062416630 Iterations, force evaluations = 83 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6412 | 7.6412 | 7.6412 | 0.0 | 99.68 Neigh | 0.0069842 | 0.0069842 | 0.0069842 | 0.0 | 0.09 Comm | 0.009408 | 0.009408 | 0.009408 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008371 | | | 0.11 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6524.00 ave 6524 max 6524 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: 90324.0 ave 90324 max 90324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90324 Ave neighs/atom = 86.683301 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 36 2 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -4406.3232 0 -4406.3232 9286.7753 12243.099 94 0 -4406.7282 0 -4406.7282 -92.635841 12309.41 Loop time of 0.733807 on 1 procs for 11 steps with 1042 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4406.32316535205 -4406.7270593604 -4406.72819041995 Force two-norm initial, final = 130.04674 3.2677616 Force max component initial, final = 98.256380 2.0163114 Final line search alpha, max atom move = 0.00013617704 0.00027457530 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72934 | 0.72934 | 0.72934 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074337 | 0.00074337 | 0.00074337 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003725 | | | 0.51 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7318.00 ave 7318 max 7318 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: 90056.0 ave 90056 max 90056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90056 Ave neighs/atom = 86.426104 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 = 9 36 2 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) = 4.765 | 4.765 | 4.765 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4406.7282 0 -4406.7282 -92.635841 Loop time of 1.705e-06 on 1 procs for 0 steps with 1042 atoms 176.0% 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 | | 1.705e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7328.00 ave 7328 max 7328 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: 90028.0 ave 90028 max 90028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90028 Ave neighs/atom = 86.399232 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 = 9 36 2 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) = 4.765 | 4.765 | 4.765 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 -4406.7282 -4406.7282 28.997581 116.41425 3.6464421 -92.635841 -92.635841 -240.1367 -262.34987 224.57905 2.3026063 380.46041 Loop time of 1.861e-06 on 1 procs for 0 steps with 1042 atoms 214.9% 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 | | 1.861e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7328.00 ave 7328 max 7328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45014.0 ave 45014 max 45014 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90028.0 ave 90028 max 90028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90028 Ave neighs/atom = 86.399232 Neighbor list builds = 0 Dangerous builds = 0 1042 -4406.72819041995 eV 2.30260633901153 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08