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 = 4.0515263 4.0515263 4.0515263 Created orthogonal box = (0.0000000 -44.382247 0.0000000) to (9.0594882 44.382247 9.9241721) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4356929 5.9176329 6.6161147 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -44.382247 0.0000000) to (9.0594882 44.382247 9.9241721) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4356929 5.9176329 6.6161147 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.382247 0.0000000) to (9.0594882 44.382247 9.9241721) create_atoms CPU = 0.001 seconds 242 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 3 23 3 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 3 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 4.506 | 4.506 | 4.506 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1171.0422 0 -1171.0422 177770.14 93 0 -1605.1038 0 -1605.1038 10839.97 Loop time of 0.626224 on 1 procs for 93 steps with 480 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 = -1171.04216844938 -1605.10247376419 -1605.10382149975 Force two-norm initial, final = 1170.5463 0.13294087 Force max component initial, final = 338.41319 0.034559634 Final line search alpha, max atom move = 1.0000000 0.034559634 Iterations, force evaluations = 93 174 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60735 | 0.60735 | 0.60735 | 0.0 | 96.99 Neigh | 0.0088322 | 0.0088322 | 0.0088322 | 0.0 | 1.41 Comm | 0.0054572 | 0.0054572 | 0.0054572 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004587 | | | 0.73 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3610.00 ave 3610 max 3610 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: 63472.0 ave 63472 max 63472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63472 Ave neighs/atom = 132.23333 Neighbor list builds = 2 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 3 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -1605.1038 0 -1605.1038 10839.97 7980.631 106 0 -1605.6679 0 -1605.6679 -63.330408 8068.9431 Loop time of 0.06498 on 1 procs for 13 steps with 480 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 = -1605.10382149975 -1605.66781212695 -1605.66788214567 Force two-norm initial, final = 108.55626 0.86789973 Force max component initial, final = 98.505805 0.64048883 Final line search alpha, max atom move = 0.0023742684 0.0015206924 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057481 | 0.057481 | 0.057481 | 0.0 | 88.46 Neigh | 0.0046401 | 0.0046401 | 0.0046401 | 0.0 | 7.14 Comm | 0.00055964 | 0.00055964 | 0.00055964 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002299 | | | 3.54 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3446.00 ave 3446 max 3446 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: 63292.0 ave 63292 max 63292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63292 Ave neighs/atom = 131.85833 Neighbor list builds = 1 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 3 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 4.642 | 4.642 | 4.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1605.6679 0 -1605.6679 -63.330408 Loop time of 3.095e-06 on 1 procs for 0 steps with 480 atoms 129.2% 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 | | 3.095e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3446.00 ave 3446 max 3446 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: 63292.0 ave 63292 max 63292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63292 Ave neighs/atom = 131.85833 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 3 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 4.642 | 4.642 | 4.642 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 -1605.6679 -1605.6679 9.0552873 89.828017 9.919793 -63.330408 -63.330408 -8.78624 -54.085071 -127.11991 2.6081505 373.81271 Loop time of 3.282e-06 on 1 procs for 0 steps with 480 atoms 182.8% 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 | | 3.282e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3446.00 ave 3446 max 3446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31646.0 ave 31646 max 31646 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63292.0 ave 63292 max 63292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63292 Ave neighs/atom = 131.85833 Neighbor list builds = 0 Dangerous builds = 0 480 -1605.66788214124 eV 2.60815046437716 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01