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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -41.258716 0.0000000) to (35.727592 41.258716 7.0067573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4126448 6.3468723 7.0067573 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.258716 0.0000000) to (35.727592 41.258716 7.0067573) create_atoms CPU = 0.004 seconds 629 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4126448 6.3468723 7.0067573 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -41.258716 0.0000000) to (35.727592 41.258716 7.0067573) create_atoms CPU = 0.003 seconds 628 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 1234 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4106.5345 0 -4106.5345 1804.5073 74 0 -4126.7773 0 -4126.7773 -2829.0116 Loop time of 13.1759 on 1 procs for 74 steps with 1234 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 = -4106.53445579601 -4126.7736468749 -4126.77727724321 Force two-norm initial, final = 22.912535 0.14678253 Force max component initial, final = 4.6260296 0.027764721 Final line search alpha, max atom move = 1.0000000 0.027764721 Iterations, force evaluations = 74 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.117 | 13.117 | 13.117 | 0.0 | 99.56 Neigh | 0.025437 | 0.025437 | 0.025437 | 0.0 | 0.19 Comm | 0.013367 | 0.013367 | 0.013367 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01977 | | | 0.15 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3844.00 ave 3844 max 3844 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: 67116.0 ave 67116 max 67116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67116 Ave neighs/atom = 54.388979 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -4126.7773 0 -4126.7773 -2829.0116 20656.966 77 0 -4126.8429 0 -4126.8429 -284.65323 20584.262 Loop time of 0.456782 on 1 procs for 3 steps with 1234 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4126.77727724321 -4126.84208123106 -4126.84294153885 Force two-norm initial, final = 51.718765 1.3610914 Force max component initial, final = 41.253941 1.1287308 Final line search alpha, max atom move = 0.00031976527 0.00036092892 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45446 | 0.45446 | 0.45446 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044355 | 0.00044355 | 0.00044355 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001874 | | | 0.41 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3869.00 ave 3869 max 3869 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: 67116.0 ave 67116 max 67116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67116 Ave neighs/atom = 54.388979 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.717 | 4.717 | 4.717 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4126.8429 0 -4126.8429 -284.65323 Loop time of 8.941e-06 on 1 procs for 0 steps with 1234 atoms 156.6% 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 | | 8.941e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3869.00 ave 3869 max 3869 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: 67174.0 ave 67174 max 67174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67174 Ave neighs/atom = 54.435981 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.717 | 4.717 | 4.717 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 -4126.8429 -4126.8429 35.687008 82.517431 6.9900369 -284.65323 -284.65323 87.754991 -999.17196 57.457285 2.4933514 1045.9682 Loop time of 6.956e-06 on 1 procs for 0 steps with 1234 atoms 258.8% 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 | | 6.956e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3869.00 ave 3869 max 3869 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33587.0 ave 33587 max 33587 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67174.0 ave 67174 max 67174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67174 Ave neighs/atom = 54.435981 Neighbor list builds = 0 Dangerous builds = 0 1234 -4126.84294153885 eV 2.49335144501238 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14