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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -44.731757 0.0000000) to (22.365879 44.731757 2.8636573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0331912 4.0331912 2.8636573 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -44.731757 0.0000000) to (22.365879 44.731757 2.8636573) create_atoms CPU = 0.001 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0331912 4.0331912 2.8636573 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -44.731757 0.0000000) to (22.365879 44.731757 2.8636573) create_atoms CPU = 0.000 seconds 245 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 ghost atom cutoff = 6 binsize = 3, bins = 8 30 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 489 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_162036141261_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 ghost atom cutoff = 6 binsize = 3, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1994.8456 0 -1994.8456 51350.235 30 0 -2090.9975 0 -2090.9975 7938.8303 Loop time of 0.801136 on 1 procs for 30 steps with 489 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 = -1994.84562649789 -2090.99554860058 -2090.99749636687 Force two-norm initial, final = 205.90690 0.15352963 Force max component initial, final = 82.331843 0.026356942 Final line search alpha, max atom move = 1.0000000 0.026356942 Iterations, force evaluations = 30 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79734 | 0.79734 | 0.79734 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020443 | 0.0020443 | 0.0020443 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00175 | | | 0.22 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3781.00 ave 3781 max 3781 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: 31796.0 ave 31796 max 31796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31796 Ave neighs/atom = 65.022495 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -2090.9975 0 -2090.9975 7938.8303 5729.9782 39 0 -2091.2254 0 -2091.2254 97.491942 5755.5413 Loop time of 0.158428 on 1 procs for 9 steps with 489 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2090.99749636687 -2091.22515436807 -2091.22540837615 Force two-norm initial, final = 65.194852 0.63999227 Force max component initial, final = 62.934771 0.38660683 Final line search alpha, max atom move = 0.00082116561 0.00031746824 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15616 | 0.15616 | 0.15616 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040701 | 0.00040701 | 0.00040701 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001858 | | | 1.17 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3830.00 ave 3830 max 3830 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: 31504.0 ave 31504 max 31504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31504 Ave neighs/atom = 64.425358 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 ghost atom cutoff = 6 binsize = 3, bins = 8 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2091.2254 0 -2091.2254 97.491942 Loop time of 1.912e-06 on 1 procs for 0 steps with 489 atoms 209.2% 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 | | 1.912e-06 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3823.00 ave 3823 max 3823 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: 31478.0 ave 31478 max 31478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31478 Ave neighs/atom = 64.372188 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 ghost atom cutoff = 6 binsize = 3, bins = 8 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.612 | 4.612 | 4.612 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 -2091.2254 -2091.2254 22.403072 90.114488 2.8509131 97.491942 97.491942 97.210967 108.40327 86.86159 2.3175946 126.13015 Loop time of 1.734e-06 on 1 procs for 0 steps with 489 atoms 173.0% 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 | | 1.734e-06 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3823.00 ave 3823 max 3823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15739.0 ave 15739 max 15739 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31478.0 ave 31478 max 31478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31478 Ave neighs/atom = 64.372188 Neighbor list builds = 0 Dangerous builds = 0 489 -2091.22540837615 eV 2.31759455679312 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01