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 = 4.0499994 4.0499994 4.0499994 Created orthogonal box = (0.0000000 -51.548077 0.0000000) to (36.449995 51.548077 5.7275641) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7499991 7.0003562 5.7275641 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -51.548077 0.0000000) to (36.449995 51.548077 5.7275641) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7499991 7.0003562 5.7275641 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.548077 0.0000000) to (36.449995 51.548077 5.7275641) create_atoms CPU = 0.002 seconds 650 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_117656786760_005#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.470 | 5.470 | 5.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4314.2404 0 -4314.2404 5808.0302 59 0 -4354.2187 0 -4354.2187 3766.7105 Loop time of 1.35154 on 1 procs for 59 steps with 1298 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4314.24035677248 -4354.21483699158 -4354.21868088165 Force two-norm initial, final = 28.710755 0.13101085 Force max component initial, final = 6.9283952 0.015186602 Final line search alpha, max atom move = 1.0000000 0.015186602 Iterations, force evaluations = 59 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3351 | 1.3351 | 1.3351 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0089564 | 0.0089564 | 0.0089564 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007504 | | | 0.56 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8258.00 ave 8258 max 8258 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: 227760.0 ave 227760 max 227760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227760 Ave neighs/atom = 175.46995 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.470 | 5.470 | 5.470 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -4354.2187 0 -4354.2187 3766.7105 21523.352 66 0 -4354.4873 0 -4354.4873 -70.116154 21627.775 Loop time of 0.114766 on 1 procs for 7 steps with 1298 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4354.21868088165 -4354.48646365136 -4354.48729630839 Force two-norm initial, final = 101.44088 1.6711128 Force max component initial, final = 92.150869 1.0736721 Final line search alpha, max atom move = 0.00028198751 0.00030276211 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11146 | 0.11146 | 0.11146 | 0.0 | 97.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056911 | 0.00056911 | 0.00056911 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002742 | | | 2.39 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8230.00 ave 8230 max 8230 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: 225624.0 ave 225624 max 225624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225624 Ave neighs/atom = 173.82435 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.608 | 5.608 | 5.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4354.4873 0 -4354.4873 -70.116154 Loop time of 1.853e-06 on 1 procs for 0 steps with 1298 atoms 215.9% 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 | | 1.853e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8221.00 ave 8221 max 8221 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: 225200.0 ave 225200 max 225200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225200 Ave neighs/atom = 173.49769 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.608 | 5.608 | 5.608 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 -4354.4873 -4354.4873 36.409584 103.75448 5.7251815 -70.116154 -70.116154 -79.448996 -52.794451 -78.105013 2.6247197 604.39713 Loop time of 2.729e-06 on 1 procs for 0 steps with 1298 atoms 183.2% 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 | | 2.729e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8221.00 ave 8221 max 8221 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112600.0 ave 112600 max 112600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225200.0 ave 225200 max 225200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225200 Ave neighs/atom = 173.49769 Neighbor list builds = 0 Dangerous builds = 0 1298 -4275.00593019901 eV 2.62471965873493 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01