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 = 4.0415970 4.0415970 4.0415970 Created orthogonal box = (0.0000000 -51.441132 0.0000000) to (36.374373 51.441132 5.7156813) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7359950 6.9858327 5.7156813 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -51.441132 0.0000000) to (36.374373 51.441132 5.7156813) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7359950 6.9858327 5.7156813 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.441132 0.0000000) to (36.374373 51.441132 5.7156813) 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 35 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, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/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_992900971352_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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.399 | 5.399 | 5.399 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4298.6358 0 -4298.6358 13572.174 44 0 -4364.3634 0 -4364.3634 12263.089 Loop time of 8.81299 on 1 procs for 44 steps with 1298 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 = -4298.63577309826 -4364.35938668263 -4364.36344258288 Force two-norm initial, final = 59.636516 0.18062297 Force max component initial, final = 13.248312 0.012119296 Final line search alpha, max atom move = 1.0000000 0.012119296 Iterations, force evaluations = 44 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.8054 | 8.8054 | 8.8054 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029282 | 0.0029282 | 0.0029282 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004656 | | | 0.05 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4474.00 ave 4474 max 4474 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: 70380.0 ave 70380 max 70380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70380 Ave neighs/atom = 54.221880 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.399 | 5.399 | 5.399 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -4364.3634 0 -4364.3634 12263.089 21389.668 51 0 -4365.0506 0 -4365.0506 -9.1245438 21564.478 Loop time of 0.840514 on 1 procs for 7 steps with 1298 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 = -4364.36344258288 -4365.04897434291 -4365.05064347734 Force two-norm initial, final = 286.00449 0.43833029 Force max component initial, final = 192.86871 0.22687570 Final line search alpha, max atom move = 0.00010449949 2.3708395e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83818 | 0.83818 | 0.83818 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032895 | 0.00032895 | 0.00032895 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002 | | | 0.24 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4492.00 ave 4492 max 4492 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: 70044.0 ave 70044 max 70044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70044 Ave neighs/atom = 53.963020 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/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) = 5.537 | 5.537 | 5.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4365.0506 0 -4365.0506 -9.1245438 Loop time of 1.74e-06 on 1 procs for 0 steps with 1298 atoms 172.4% 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 | | 1.74e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4486.00 ave 4486 max 4486 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: 70044.0 ave 70044 max 70044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70044 Ave neighs/atom = 53.963020 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/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) = 5.537 | 5.537 | 5.537 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 -4365.0506 -4365.0506 36.388149 103.49939 5.7258663 -9.1245438 -9.1245438 -3.7331625 -6.754244 -16.886225 2.6398995 614.05641 Loop time of 1.408e-06 on 1 procs for 0 steps with 1298 atoms 213.1% 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 | | 1.408e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4486.00 ave 4486 max 4486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35022.0 ave 35022 max 35022 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70044.0 ave 70044 max 70044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70044 Ave neighs/atom = 53.963020 Neighbor list builds = 0 Dangerous builds = 0 1298 -4365.05064347734 eV 2.63989946183777 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10