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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -58.891004 0.0000000) to (29.445502 58.891004 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0001796 5.0001796 4.0446508 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -58.891004 0.0000000) to (29.445502 58.891004 4.0446508) create_atoms CPU = 0.002 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0001796 5.0001796 4.0446508 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -58.891004 0.0000000) to (29.445502 58.891004 4.0446508) create_atoms CPU = 0.001 seconds 426 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 848 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_616482358807_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2771.3302 0 -2771.3302 15574.737 79 0 -2840.3177 0 -2840.3177 3960.3828 Loop time of 10.488 on 1 procs for 79 steps with 848 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 = -2771.33018876581 -2840.3148831312 -2840.31766843794 Force two-norm initial, final = 132.93024 0.11219258 Force max component initial, final = 44.431016 0.012507690 Final line search alpha, max atom move = 1.0000000 0.012507690 Iterations, force evaluations = 79 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.445 | 10.445 | 10.445 | 0.0 | 99.59 Neigh | 0.0091317 | 0.0091317 | 0.0091317 | 0.0 | 0.09 Comm | 0.016958 | 0.016958 | 0.016958 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01709 | | | 0.16 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4556.00 ave 4556 max 4556 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: 65148.0 ave 65148 max 65148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65148 Ave neighs/atom = 76.825472 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -2840.3177 0 -2840.3177 3960.3828 14027.457 89 0 -2840.5969 0 -2840.5969 -28.349233 14097.246 Loop time of 0.833551 on 1 procs for 10 steps with 848 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 = -2840.31766843794 -2840.59690204155 -2840.59691187979 Force two-norm initial, final = 73.994611 0.51250865 Force max component initial, final = 69.742111 0.27094827 Final line search alpha, max atom move = 0.0055780817 0.0015113716 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8181 | 0.8181 | 0.8181 | 0.0 | 98.15 Neigh | 0.0091487 | 0.0091487 | 0.0091487 | 0.0 | 1.10 Comm | 0.0014783 | 0.0014783 | 0.0014783 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004819 | | | 0.58 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4556.00 ave 4556 max 4556 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: 65192.0 ave 65192 max 65192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65192 Ave neighs/atom = 76.877358 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.685 | 4.685 | 4.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2840.5969 0 -2840.5969 -28.349233 Loop time of 6.165e-06 on 1 procs for 0 steps with 848 atoms 178.4% 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 | | 6.165e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4556.00 ave 4556 max 4556 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: 65192.0 ave 65192 max 65192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65192 Ave neighs/atom = 76.877358 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.685 | 4.685 | 4.685 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 -2840.5969 -2840.5969 29.411989 118.84424 4.0330327 -28.349233 -28.349233 -26.652121 -27.690291 -30.705287 2.599559 451.40625 Loop time of 6.986e-06 on 1 procs for 0 steps with 848 atoms 272.0% 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 | | 6.986e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4556.00 ave 4556 max 4556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32596.0 ave 32596 max 32596 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 65192.0 ave 65192 max 65192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65192 Ave neighs/atom = 76.877358 Neighbor list builds = 0 Dangerous builds = 0 848 -2840.59691187979 eV 2.59955899088933 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11