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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -61.664571 0.0000000) to (25.173002 61.664571 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0415205 5.3439543 5.8134559 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -61.664571 0.0000000) to (25.173002 61.664571 8.7201838) create_atoms CPU = 0.002 seconds 1205 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0415205 5.3439543 5.8134559 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -61.664571 0.0000000) to (25.173002 61.664571 8.7201838) create_atoms CPU = 0.002 seconds 1205 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 32 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2384 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.505 | 6.505 | 6.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10403.426 0 -10403.426 1942.3068 31 0 -10466.34 0 -10466.34 835.31085 Loop time of 1.07533 on 1 procs for 31 steps with 2384 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 = -10403.4255646542 -10466.3310567025 -10466.3400163702 Force two-norm initial, final = 55.482709 0.42213712 Force max component initial, final = 7.8224340 0.093097527 Final line search alpha, max atom move = 1.0000000 0.093097527 Iterations, force evaluations = 31 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0406 | 1.0406 | 1.0406 | 0.0 | 96.77 Neigh | 0.024646 | 0.024646 | 0.024646 | 0.0 | 2.29 Comm | 0.0045038 | 0.0045038 | 0.0045038 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005625 | | | 0.52 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9606.00 ave 9606 max 9606 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: 416818.0 ave 416818 max 416818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416818 Ave neighs/atom = 174.83977 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.504 | 6.504 | 6.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -10466.34 0 -10466.34 835.31085 27072.375 33 0 -10466.371 0 -10466.371 -220.45095 27087.683 Loop time of 0.0771563 on 1 procs for 2 steps with 2384 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 = -10466.3400163702 -10466.3640939527 -10466.3706323616 Force two-norm initial, final = 47.213320 1.3821591 Force max component initial, final = 47.088129 1.2577859 Final line search alpha, max atom move = 4.3610469e-05 5.4852634e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075586 | 0.075586 | 0.075586 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027618 | 0.00027618 | 0.00027618 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001294 | | | 1.68 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9520.00 ave 9520 max 9520 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: 416676.0 ave 416676 max 416676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416676 Ave neighs/atom = 174.78020 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.642 | 6.642 | 6.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10466.371 0 -10466.371 -220.45095 Loop time of 1.661e-06 on 1 procs for 0 steps with 2384 atoms 180.6% 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 | | 1.661e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9482.00 ave 9482 max 9482 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: 416600.0 ave 416600 max 416600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416600 Ave neighs/atom = 174.74832 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.642 | 6.642 | 6.642 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 -10466.371 -10466.371 25.203898 123.32914 8.7144189 -220.45095 -220.45095 74.486562 -757.07883 21.239431 2.400973 883.5023 Loop time of 2.068e-06 on 1 procs for 0 steps with 2384 atoms 241.8% 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 | | 2.068e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9482.00 ave 9482 max 9482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 208300.0 ave 208300 max 208300 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 416600.0 ave 416600 max 416600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416600 Ave neighs/atom = 174.74832 Neighbor list builds = 0 Dangerous builds = 0 2384 -10466.3706323616 eV 2.40097300613515 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01