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 = 3.5204258 3.5204258 3.5204258 Created orthogonal box = (0.0000000 -62.183118 0.0000000) to (35.901440 62.183118 6.0975564) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5232985 5.5805362 6.0975564 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -62.183118 0.0000000) to (35.901440 62.183118 6.0975564) create_atoms CPU = 0.003 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5232985 5.5805362 6.0975564 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -62.183118 0.0000000) to (35.901440 62.183118 6.0975564) create_atoms CPU = 0.003 seconds 1251 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 13 43 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 2495 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_913991514986_000#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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.206 | 5.206 | 5.206 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14211.321 0 -14211.321 11443.535 122 0 -14387.491 0 -14387.491 7034.8014 Loop time of 156.81 on 1 procs for 122 steps with 2495 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14211.3205071064 -14387.4774016213 -14387.4905601778 Force two-norm initial, final = 133.38421 0.40523215 Force max component initial, final = 30.361401 0.11002131 Final line search alpha, max atom move = 0.43532247 0.047894749 Iterations, force evaluations = 122 214 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 156.72 | 156.72 | 156.72 | 0.0 | 99.94 Neigh | 0.040781 | 0.040781 | 0.040781 | 0.0 | 0.03 Comm | 0.021358 | 0.021358 | 0.021358 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03046 | | | 0.02 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7365.00 ave 7365 max 7365 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: 193566.0 ave 193566 max 193566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193566 Ave neighs/atom = 77.581563 Neighbor list builds = 3 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.228 | 5.228 | 5.228 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -14387.491 0 -14387.491 7034.8014 27225.144 126 0 -14387.847 0 -14387.847 298.332 27316.544 Loop time of 3.90184 on 1 procs for 4 steps with 2495 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 = -14387.4905601778 -14387.8422489579 -14387.8466130479 Force two-norm initial, final = 234.47582 11.515180 Force max component initial, final = 203.04673 11.124568 Final line search alpha, max atom move = 5.8346690e-05 0.00064908171 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8991 | 3.8991 | 3.8991 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039928 | 0.00039928 | 0.00039928 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002366 | | | 0.06 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8274.00 ave 8274 max 8274 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: 193514.0 ave 193514 max 193514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193514 Ave neighs/atom = 77.560721 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.366 | 5.366 | 5.366 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14387.847 0 -14387.847 298.332 Loop time of 2.203e-06 on 1 procs for 0 steps with 2495 atoms 181.6% 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 | | 2.203e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8287.00 ave 8287 max 8287 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: 193432.0 ave 193432 max 193432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193432 Ave neighs/atom = 77.527856 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.366 | 5.366 | 5.366 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 -14387.847 -14387.847 35.925896 124.75123 6.0949944 298.332 298.332 100.96492 654.50066 139.53043 2.263837 1023.4816 Loop time of 2.213e-06 on 1 procs for 0 steps with 2495 atoms 225.9% 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 | | 2.213e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8287.00 ave 8287 max 8287 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96716.0 ave 96716 max 96716 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193432.0 ave 193432 max 193432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193432 Ave neighs/atom = 77.527856 Neighbor list builds = 0 Dangerous builds = 0 2495 -6067.51701131093 eV 2.26383697465347 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:43