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 = 2.6534432 2.6534432 2.6534432 Created orthogonal box = (0.0000000 -29.067014 0.0000000) to (5.9332794 29.067014 6.4995819) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5599676 3.8756019 4.3330546 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -29.067014 0.0000000) to (5.9332794 29.067014 6.4995819) create_atoms CPU = 0.001 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5599676 3.8756019 4.3330546 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -29.067014 0.0000000) to (5.9332794 29.067014 6.4995819) create_atoms CPU = 0.000 seconds 122 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 2 16 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_201919462778_001#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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.487 | 4.487 | 4.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1582.716 0 -1582.716 547575.08 63 0 -1993.6476 0 -1993.6476 74518.895 Loop time of 1.15192 on 1 procs for 63 steps with 240 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 = -1582.71602068506 -1993.64562485144 -1993.64760175083 Force two-norm initial, final = 1395.1994 0.29667310 Force max component initial, final = 436.81978 0.038086348 Final line search alpha, max atom move = 1.0000000 0.038086348 Iterations, force evaluations = 63 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1424 | 1.1424 | 1.1424 | 0.0 | 99.17 Neigh | 0.0032229 | 0.0032229 | 0.0032229 | 0.0 | 0.28 Comm | 0.0040205 | 0.0040205 | 0.0040205 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002263 | | | 0.20 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3303.00 ave 3303 max 3303 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: 42852.0 ave 42852 max 42852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42852 Ave neighs/atom = 178.55000 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.487 | 4.487 | 4.487 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -1993.6476 0 -1993.6476 74518.895 2241.8711 76 0 -1994.735 0 -1994.735 -420.71215 2266.9312 Loop time of 0.145277 on 1 procs for 13 steps with 240 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 = -1993.64760175083 -1994.73483864987 -1994.73502956711 Force two-norm initial, final = 208.16812 1.7790440 Force max component initial, final = 187.19991 1.3202545 Final line search alpha, max atom move = 0.0010560241 0.0013942206 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14301 | 0.14301 | 0.14301 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044108 | 0.00044108 | 0.00044108 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00183 | | | 1.26 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3315.00 ave 3315 max 3315 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: 42944.0 ave 42944 max 42944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42944 Ave neighs/atom = 178.93333 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.625 | 4.625 | 4.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1994.735 0 -1994.735 -420.71215 Loop time of 1.907e-06 on 1 procs for 0 steps with 240 atoms 209.8% 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 | | 1.907e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3315.00 ave 3315 max 3315 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: 42796.0 ave 42796 max 42796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42796 Ave neighs/atom = 178.31667 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.625 | 4.625 | 4.625 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 -1994.735 -1994.735 5.9331928 58.833244 6.4942213 -420.71215 -420.71215 -50.25804 -279.54479 -932.33364 2.2065328 228.05137 Loop time of 1.877e-06 on 1 procs for 0 steps with 240 atoms 159.8% 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 | | 1.877e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3315.00 ave 3315 max 3315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21398.0 ave 21398 max 21398 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42796.0 ave 42796 max 42796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42796 Ave neighs/atom = 178.31667 Neighbor list builds = 0 Dangerous builds = 0 240 -1994.73502956711 eV 2.206532786632 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01