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 = 3.5226425 3.5226425 3.5226425 Created orthogonal box = (0.0000000 -37.446203 0.0000000) to (37.446203 37.446203 3.5226425) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9707350 4.9707350 3.5226425 Created 451 atoms using lattice units in orthogonal box = (0.0000000 -37.446203 0.0000000) to (37.446203 37.446203 3.5226425) create_atoms CPU = 0.002 seconds 451 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9707350 4.9707350 3.5226425 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -37.446203 0.0000000) to (37.446203 37.446203 3.5226425) create_atoms CPU = 0.001 seconds 453 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 7 13 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 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 903 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_381861218831_004#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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 7 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 6.636 | 6.636 | 6.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3271.4749 0 -3271.4749 97191.965 201 0 -3822.3851 0 -3822.3851 11.738311 Loop time of 29.2663 on 1 procs for 201 steps with 903 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 = -3271.47490384857 -3822.38175813201 -3822.38510006031 Force two-norm initial, final = 702.46620 0.32064810 Force max component initial, final = 188.91401 0.12489989 Final line search alpha, max atom move = 1.0000000 0.12489989 Iterations, force evaluations = 201 365 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.857 | 28.857 | 28.857 | 0.0 | 98.60 Neigh | 0.23413 | 0.23413 | 0.23413 | 0.0 | 0.80 Comm | 0.12131 | 0.12131 | 0.12131 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05341 | | | 0.18 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14545.0 ave 14545 max 14545 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: 563740.0 ave 563740 max 563740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 563740 Ave neighs/atom = 624.29679 Neighbor list builds = 4 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 7 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 201 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.644 | 6.644 | 6.644 Mbytes Step Temp E_pair E_mol TotEng Press Volume 201 0 -3822.3851 0 -3822.3851 11.738311 9879.0264 206 0 -3822.473 0 -3822.473 -204.0395 9879.8234 Loop time of 0.567014 on 1 procs for 5 steps with 903 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 = -3822.3851000603 -3822.47151265375 -3822.47296350246 Force two-norm initial, final = 38.346832 4.2188958 Force max component initial, final = 30.954044 4.1898089 Final line search alpha, max atom move = 0.00025994848 0.0010891344 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55858 | 0.55858 | 0.55858 | 0.0 | 98.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022789 | 0.0022789 | 0.0022789 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006157 | | | 1.09 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14521.0 ave 14521 max 14521 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: 559744.0 ave 559744 max 559744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559744 Ave neighs/atom = 619.87154 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 7 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 6.782 | 6.782 | 6.782 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3822.473 0 -3822.473 -204.0395 Loop time of 6.355e-06 on 1 procs for 0 steps with 903 atoms 173.1% 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 | | 6.355e-06 | | |100.00 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14529.0 ave 14529 max 14529 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: 560134.0 ave 560134 max 560134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560134 Ave neighs/atom = 620.30343 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 7 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 6.782 | 6.782 | 6.782 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 -3822.473 -3822.473 37.332788 74.817633 3.5371607 -204.0395 -204.0395 -677.38882 46.576727 18.6936 2.0632175 46.231843 Loop time of 6.575e-06 on 1 procs for 0 steps with 903 atoms 304.2% 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 | | 6.575e-06 | | |100.00 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14529.0 ave 14529 max 14529 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 280067.0 ave 280067 max 280067 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 560134.0 ave 560134 max 560134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560134 Ave neighs/atom = 620.30343 Neighbor list builds = 0 Dangerous builds = 0 903 -3822.47296350246 eV 2.06321750727636 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:30