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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -49.821678 0.0000000) to (61.018844 49.821678 10.314067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9735822 6.4056443 6.8760448 Created 1661 atoms using lattice units in orthogonal box = (0.0000000 -49.821678 0.0000000) to (61.018844 49.821678 10.314067) create_atoms CPU = 0.003 seconds 1661 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9735822 6.4056443 6.8760448 Created 1685 atoms using lattice units in orthogonal box = (0.0000000 -49.821678 0.0000000) to (61.018844 49.821678 10.314067) create_atoms CPU = 0.003 seconds 1685 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 ghost atom cutoff = 9 binsize = 4.5, bins = 14 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3346 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_878712978062_003#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 ghost atom cutoff = 9 binsize = 4.5, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.967 | 6.967 | 6.967 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11789.336 0 -11789.336 45347.076 109 0 -12454.007 0 -12454.007 593.0219 Loop time of 7.53109 on 1 procs for 109 steps with 3346 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 = -11789.3362290498 -12453.9955399832 -12454.0073684427 Force two-norm initial, final = 2487.1860 0.20762331 Force max component initial, final = 1238.3041 0.051103885 Final line search alpha, max atom move = 1.0000000 0.051103885 Iterations, force evaluations = 109 184 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2969 | 7.2969 | 7.2969 | 0.0 | 96.89 Neigh | 0.17198 | 0.17198 | 0.17198 | 0.0 | 2.28 Comm | 0.029102 | 0.029102 | 0.029102 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03314 | | | 0.44 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10701.0 ave 10701 max 10701 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: 577714.0 ave 577714 max 577714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577714 Ave neighs/atom = 172.65810 Neighbor list builds = 5 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 ghost atom cutoff = 9 binsize = 4.5, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.967 | 6.967 | 6.967 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -12454.007 0 -12454.007 593.0219 62710.791 111 0 -12454.032 0 -12454.032 0.3556814 62804.841 Loop time of 0.184022 on 1 procs for 2 steps with 3346 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 = -12454.0073684428 -12454.0273277537 -12454.0319728798 Force two-norm initial, final = 41.738431 0.38514345 Force max component initial, final = 30.958234 0.27511783 Final line search alpha, max atom move = 0.00014017506 3.8564657e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18147 | 0.18147 | 0.18147 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039414 | 0.00039414 | 0.00039414 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002155 | | | 1.17 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10707.0 ave 10707 max 10707 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: 577420.0 ave 577420 max 577420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577420 Ave neighs/atom = 172.57023 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 ghost atom cutoff = 9 binsize = 4.5, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 7.105 | 7.105 | 7.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12454.032 0 -12454.032 0.3556814 Loop time of 1.878e-06 on 1 procs for 0 steps with 3346 atoms 159.7% 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 | | 1.878e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10707.0 ave 10707 max 10707 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: 576966.0 ave 576966 max 576966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576966 Ave neighs/atom = 172.43455 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 ghost atom cutoff = 9 binsize = 4.5, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 7.105 | 7.105 | 7.105 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 -12454.032 -12454.032 61.052546 99.781662 10.309524 0.3556814 0.3556814 7.0222416 -3.5220994 -2.433098 2.7172329 3075.6586 Loop time of 3.025e-06 on 1 procs for 0 steps with 3346 atoms 264.5% 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 | | 3.025e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10707.0 ave 10707 max 10707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288483.0 ave 288483 max 288483 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 576966.0 ave 576966 max 576966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576966 Ave neighs/atom = 172.43455 Neighbor list builds = 0 Dangerous builds = 0 3346 -12454.0319728798 eV 2.71723294994571 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09