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 = 3.6406460 3.6406460 3.6406460 Created orthogonal box = (0.0000000 -43.990093 0.0000000) to (53.876641 43.990093 8.9177251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1662532 5.4234361 5.9451500 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -43.990093 0.0000000) to (53.876641 43.990093 8.9177251) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1662532 5.4234361 5.9451500 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.990093 0.0000000) to (53.876641 43.990093 8.9177251) create_atoms CPU = 0.002 seconds 1756 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 12 19 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 3480 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_945018740343_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 13.36 | 13.36 | 13.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8369.2699 0 -8369.2699 166185.95 80 0 -11359.224 0 -11359.224 -2611.332 Loop time of 15.1794 on 1 procs for 80 steps with 3480 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8369.26991351198 -11359.213047574 -11359.2236721598 Force two-norm initial, final = 3933.9121 0.25689250 Force max component initial, final = 748.32342 0.0080311055 Final line search alpha, max atom move = 1.0000000 0.0080311055 Iterations, force evaluations = 80 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.892 | 14.892 | 14.892 | 0.0 | 98.10 Neigh | 0.23127 | 0.23127 | 0.23127 | 0.0 | 1.52 Comm | 0.028178 | 0.028178 | 0.028178 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02834 | | | 0.19 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14703.0 ave 14703 max 14703 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: 1.10185e+06 ave 1.10185e+06 max 1.10185e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1101850 Ave neighs/atom = 316.62356 Neighbor list builds = 4 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.37 | 13.37 | 13.37 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -11359.224 0 -11359.224 -2611.332 42270.703 83 0 -11359.324 0 -11359.324 49.515873 42192.493 Loop time of 0.729641 on 1 procs for 3 steps with 3480 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 = -11359.2236721599 -11359.3237247665 -11359.3243956546 Force two-norm initial, final = 127.98659 2.3218784 Force max component initial, final = 104.15023 1.5659936 Final line search alpha, max atom move = 0.00020316339 0.00031815257 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72559 | 0.72559 | 0.72559 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066184 | 0.00066184 | 0.00066184 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003384 | | | 0.46 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14694.0 ave 14694 max 14694 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: 1.10278e+06 ave 1.10278e+06 max 1.10278e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1102776 Ave neighs/atom = 316.88966 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.88 | 12.88 | 12.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11359.324 0 -11359.324 49.515873 Loop time of 2.29e-06 on 1 procs for 0 steps with 3480 atoms 174.7% 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 | | 2.29e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14719.0 ave 14719 max 14719 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: 1.10310e+06 ave 1.1031e+06 max 1.1031e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1103100 Ave neighs/atom = 316.98276 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.88 | 12.88 | 12.88 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 -11359.324 -11359.324 53.867139 87.808306 8.9202224 49.515873 49.515873 59.455022 53.237861 35.854736 2.3706137 1506.9391 Loop time of 2.804e-06 on 1 procs for 0 steps with 3480 atoms 249.6% 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 | | 2.804e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14719.0 ave 14719 max 14719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 551550.0 ave 551550 max 551550 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.10310e+06 ave 1.1031e+06 max 1.1031e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1103100 Ave neighs/atom = 316.98276 Neighbor list builds = 0 Dangerous builds = 0 3480 -11359.3243956546 eV 2.37061366479549 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17