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 -57.275641 0.0000000) to (28.637821 57.275641 4.0499994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5820513 4.5820513 4.0499994 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -57.275641 0.0000000) to (28.637821 57.275641 4.0499994) create_atoms CPU = 0.002 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5820513 4.5820513 4.0499994 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -57.275641 0.0000000) to (28.637821 57.275641 4.0499994) create_atoms CPU = 0.001 seconds 402 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 = 7 27 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 796 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 = 7 27 1 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) = 4.976 | 4.976 | 4.976 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2639.2982 0 -2639.2982 1915.9563 60 0 -2668.2761 0 -2668.2761 89.009964 Loop time of 1.98872 on 1 procs for 60 steps with 796 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 = -2639.29818971405 -2668.27388180347 -2668.27612462157 Force two-norm initial, final = 32.959524 0.10880286 Force max component initial, final = 10.975481 0.0091152082 Final line search alpha, max atom move = 1.0000000 0.0091152082 Iterations, force evaluations = 60 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9369 | 1.9369 | 1.9369 | 0.0 | 97.39 Neigh | 0.018014 | 0.018014 | 0.018014 | 0.0 | 0.91 Comm | 0.020598 | 0.020598 | 0.020598 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01325 | | | 0.67 Nlocal: 796.000 ave 796 max 796 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: 137644.0 ave 137644 max 137644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137644 Ave neighs/atom = 172.91960 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 27 1 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.976 | 4.976 | 4.976 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -2668.2761 0 -2668.2761 89.009964 13286.02 62 0 -2668.2874 0 -2668.2874 248.30817 13283.576 Loop time of 0.0707606 on 1 procs for 2 steps with 796 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 = -2668.27612462157 -2668.28530534274 -2668.28736181585 Force two-norm initial, final = 10.385432 3.7572263 Force max component initial, final = 8.4333866 2.9360763 Final line search alpha, max atom move = 0.00024709228 0.00072548178 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068357 | 0.068357 | 0.068357 | 0.0 | 96.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062606 | 0.00062606 | 0.00062606 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001778 | | | 2.51 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7312.00 ave 7312 max 7312 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: 138024.0 ave 138024 max 138024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138024 Ave neighs/atom = 173.39698 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 = 7 27 1 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2668.2874 0 -2668.2874 248.30817 Loop time of 6.826e-06 on 1 procs for 0 steps with 796 atoms 175.8% 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 | | 6.826e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7312.00 ave 7312 max 7312 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: 138008.0 ave 138008 max 138008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138008 Ave neighs/atom = 173.37688 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 = 7 27 1 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) = 5.114 | 5.114 | 5.114 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 -2668.2874 -2668.2874 28.631109 114.71531 4.0444126 248.30817 248.30817 237.07254 354.63705 153.21493 2.6505796 305.36108 Loop time of 6.575e-06 on 1 procs for 0 steps with 796 atoms 273.8% 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 | | 6.575e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7312.00 ave 7312 max 7312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69004.0 ave 69004 max 69004 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138008.0 ave 138008 max 138008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138008 Ave neighs/atom = 173.37688 Neighbor list builds = 0 Dangerous builds = 0 796 -2619.5453221987 eV 2.65057964242263 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02