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 -38.871462 0.0000000) to (27.486275 38.871462 5.1486510) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3043688 6.1375993 5.1486510 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.871462 0.0000000) to (27.486275 38.871462 5.1486510) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3043688 6.1375993 5.1486510 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.871462 0.0000000) to (27.486275 38.871462 5.1486510) create_atoms CPU = 0.001 seconds 458 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 = 6 17 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 6 atoms, new total = 908 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 = 6 17 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) = 5.419 | 5.419 | 5.419 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2559.543 0 -2559.543 105900.95 76 0 -2958.6155 0 -2958.6155 2978.3006 Loop time of 4.73207 on 1 procs for 76 steps with 908 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2559.54300876975 -2958.6135269805 -2958.61545610803 Force two-norm initial, final = 965.32410 0.10776841 Force max component initial, final = 296.67461 0.010838721 Final line search alpha, max atom move = 1.0000000 0.010838721 Iterations, force evaluations = 76 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6866 | 4.6866 | 4.6866 | 0.0 | 99.04 Neigh | 0.029301 | 0.029301 | 0.029301 | 0.0 | 0.62 Comm | 0.009379 | 0.009379 | 0.009379 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006768 | | | 0.14 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8191.00 ave 8191 max 8191 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: 287520.0 ave 287520 max 287520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287520 Ave neighs/atom = 316.65198 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 17 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.422 | 5.422 | 5.422 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -2958.6155 0 -2958.6155 2978.3006 11001.964 80 0 -2958.7005 0 -2958.7005 139.89347 11023.713 Loop time of 0.21356 on 1 procs for 4 steps with 908 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 = -2958.61545610801 -2958.69809616024 -2958.7004919804 Force two-norm initial, final = 51.446700 2.3249391 Force max component initial, final = 50.650105 2.1616734 Final line search alpha, max atom move = 0.00019973024 0.00043175155 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21178 | 0.21178 | 0.21178 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035654 | 0.00035654 | 0.00035654 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00142 | | | 0.66 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8209.00 ave 8209 max 8209 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: 287320.0 ave 287320 max 287320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287320 Ave neighs/atom = 316.43172 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 = 6 17 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) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2958.7005 0 -2958.7005 139.89347 Loop time of 1.652e-06 on 1 procs for 0 steps with 908 atoms 181.6% 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 | | 1.652e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8191.00 ave 8191 max 8191 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: 287048.0 ave 287048 max 287048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287048 Ave neighs/atom = 316.13216 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 = 6 17 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) = 5.560 | 5.560 | 5.560 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 -2958.7005 -2958.7005 27.467183 78.015408 5.144384 139.89347 139.89347 -14.668115 120.43324 313.91529 2.2639486 665.0461 Loop time of 1.817e-06 on 1 procs for 0 steps with 908 atoms 385.3% 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 | | 1.817e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8191.00 ave 8191 max 8191 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143524.0 ave 143524 max 143524 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 287048.0 ave 287048 max 287048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287048 Ave neighs/atom = 316.13216 Neighbor list builds = 0 Dangerous builds = 0 908 -2958.7004919804 eV 2.26394858108291 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05