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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -47.722671 0.0000000) to (58.448097 47.722671 9.8795315) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6797825 6.1357720 6.5863543 Created 1661 atoms using lattice units in orthogonal box = (0.0000000 -47.722671 0.0000000) to (58.448097 47.722671 9.8795315) create_atoms CPU = 0.003 seconds 1661 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6797825 6.1357720 6.5863543 Created 1685 atoms using lattice units in orthogonal box = (0.0000000 -47.722671 0.0000000) to (58.448097 47.722671 9.8795315) create_atoms CPU = 0.003 seconds 1685 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 3341 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.609 | 6.609 | 6.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10922.913 0 -10922.913 16538.826 79 0 -11223.589 0 -11223.589 -62.933141 Loop time of 3.61048 on 1 procs for 79 steps with 3341 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 = -10922.9125645283 -11223.5784683521 -11223.5885784041 Force two-norm initial, final = 173.01955 0.25146052 Force max component initial, final = 16.674342 0.054331020 Final line search alpha, max atom move = 1.0000000 0.054331020 Iterations, force evaluations = 79 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3855 | 3.3855 | 3.3855 | 0.0 | 93.77 Neigh | 0.18246 | 0.18246 | 0.18246 | 0.0 | 5.05 Comm | 0.016705 | 0.016705 | 0.016705 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02577 | | | 0.71 Nlocal: 3341.00 ave 3341 max 3341 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10519.0 ave 10519 max 10519 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: 476152.0 ave 476152 max 476152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 476152 Ave neighs/atom = 142.51781 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.608 | 6.608 | 6.608 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -11223.589 0 -11223.589 -62.933141 55113.94 81 0 -11223.633 0 -11223.633 -159.80739 55119.73 Loop time of 0.112816 on 1 procs for 2 steps with 3341 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 = -11223.588578404 -11223.6294579928 -11223.633017085 Force two-norm initial, final = 44.596046 10.232262 Force max component initial, final = 31.465380 7.9481953 Final line search alpha, max atom move = 7.4636455e-05 0.00059322512 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11034 | 0.11034 | 0.11034 | 0.0 | 97.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036489 | 0.00036489 | 0.00036489 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002112 | | | 1.87 Nlocal: 3341.00 ave 3341 max 3341 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10510.0 ave 10510 max 10510 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: 475860.0 ave 475860 max 475860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475860 Ave neighs/atom = 142.43041 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.746 | 6.746 | 6.746 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11223.633 0 -11223.633 -159.80739 Loop time of 2.107e-06 on 1 procs for 0 steps with 3341 atoms 142.4% 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 | | 2.107e-06 | | |100.00 Nlocal: 3341.00 ave 3341 max 3341 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10520.0 ave 10520 max 10520 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: 475764.0 ave 475764 max 475764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475764 Ave neighs/atom = 142.40168 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.746 | 6.746 | 6.746 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 -11223.633 -11223.633 58.438039 95.583399 9.8679964 -159.80739 -159.80739 -169.71267 -78.947422 -230.76207 2.5381262 2138.6816 Loop time of 2.562e-06 on 1 procs for 0 steps with 3341 atoms 234.2% 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 | | 2.562e-06 | | |100.00 Nlocal: 3341.00 ave 3341 max 3341 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10520.0 ave 10520 max 10520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 237882.0 ave 237882 max 237882 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 475764.0 ave 475764 max 475764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475764 Ave neighs/atom = 142.40168 Neighbor list builds = 0 Dangerous builds = 0 3341 -11223.633017085 eV 2.53812618331614 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04