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 = 2.8553128 2.8553128 2.8553128 Created orthogonal box = (0.0000000 -34.970297 0.0000000) to (4.9455468 34.970297 4.0380221) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9455468 4.6627062 4.0380221 Created 60 atoms using lattice units in orthogonal box = (0.0000000 -34.970297 0.0000000) to (4.9455468 34.970297 4.0380221) create_atoms CPU = 0.002 seconds 60 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9455468 4.6627062 4.0380221 Created 62 atoms using lattice units in orthogonal box = (0.0000000 -34.970297 0.0000000) to (4.9455468 34.970297 4.0380221) create_atoms CPU = 0.001 seconds 62 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 20 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 120 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_884343146310_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.412 | 4.412 | 4.412 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -480.50336 0 -480.50336 -163.1325 9 0 -480.90763 0 -480.90763 -647.425 Loop time of 0.0420225 on 1 procs for 9 steps with 120 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 = -480.503360314981 -480.907303036381 -480.907627703123 Force two-norm initial, final = 1.9178951 0.047956020 Force max component initial, final = 0.94457717 0.010406728 Final line search alpha, max atom move = 1.0000000 0.010406728 Iterations, force evaluations = 9 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040532 | 0.040532 | 0.040532 | 0.0 | 96.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096099 | 0.00096099 | 0.00096099 | 0.0 | 2.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005298 | | | 1.26 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2504.00 ave 2504 max 2504 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: 16480.0 ave 16480 max 16480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16480 Ave neighs/atom = 137.33333 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 9 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.412 | 4.412 | 4.412 Mbytes Step Temp E_pair E_mol TotEng Press Volume 9 0 -480.90763 0 -480.90763 -647.425 1396.7295 11 0 -480.90905 0 -480.90905 -13.755142 1396.235 Loop time of 0.0125344 on 1 procs for 2 steps with 120 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -480.907627703127 -480.908910849304 -480.909053590333 Force two-norm initial, final = 2.4691265 0.12744460 Force max component initial, final = 2.2130574 0.10649716 Final line search alpha, max atom move = 0.00095103230 0.00010128224 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011543 | 0.011543 | 0.011543 | 0.0 | 92.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002589 | 0.0002589 | 0.0002589 | 0.0 | 2.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007326 | | | 5.84 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2499.00 ave 2499 max 2499 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: 16464.0 ave 16464 max 16464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16464 Ave neighs/atom = 137.20000 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.550 | 4.550 | 4.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -480.90905 0 -480.90905 -13.755142 Loop time of 6.034e-06 on 1 procs for 0 steps with 120 atoms 182.3% 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 | | 6.034e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2499.00 ave 2499 max 2499 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: 16456.0 ave 16456 max 16456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16456 Ave neighs/atom = 137.13333 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.550 | 4.550 | 4.550 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 -480.90905 -480.90905 4.9408418 69.989655 4.0376039 -13.755142 -13.755142 42.800059 38.127113 -122.1926 2.4072693 49.981063 Loop time of 6.365e-06 on 1 procs for 0 steps with 120 atoms 157.1% 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 | | 6.365e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2499.00 ave 2499 max 2499 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8228.00 ave 8228 max 8228 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16456.0 ave 16456 max 16456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16456 Ave neighs/atom = 137.13333 Neighbor list builds = 0 Dangerous builds = 0 120 -480.909053590333 eV 2.40726925626946 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00