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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -58.290151 0.0000000) to (29.145075 58.290151 3.6150017) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0354720 4.0354720 3.6150017 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.290151 0.0000000) to (29.145075 58.290151 3.6150017) create_atoms CPU = 0.002 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0354720 4.0354720 3.6150017 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.290151 0.0000000) to (29.145075 58.290151 3.6150017) create_atoms CPU = 0.001 seconds 522 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 28 1 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1036 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.442 | 5.442 | 5.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3447.2367 0 -3447.2367 22927.062 59 0 -3657.5859 0 -3657.5859 -611.7374 Loop time of 2.83178 on 1 procs for 59 steps with 1036 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 = -3447.23671481968 -3657.58261029542 -3657.58585313044 Force two-norm initial, final = 280.06076 0.17728310 Force max component initial, final = 88.721799 0.034344854 Final line search alpha, max atom move = 1.0000000 0.034344854 Iterations, force evaluations = 59 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7593 | 2.7593 | 2.7593 | 0.0 | 97.44 Neigh | 0.031645 | 0.031645 | 0.031645 | 0.0 | 1.12 Comm | 0.024893 | 0.024893 | 0.024893 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0159 | | | 0.56 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9291.00 ave 9291 max 9291 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: 215216.0 ave 215216 max 215216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215216 Ave neighs/atom = 207.73745 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.442 | 5.442 | 5.442 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -3657.5859 0 -3657.5859 -611.7374 12282.842 60 0 -3657.5879 0 -3657.5879 232.28846 12275.372 Loop time of 0.076864 on 1 procs for 1 steps with 1036 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 = -3657.58585313043 -3657.58585313043 -3657.58792186425 Force two-norm initial, final = 9.7767509 5.5498783 Force max component initial, final = 6.9168430 5.5450918 Final line search alpha, max atom move = 0.00014457463 0.00080167958 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07482 | 0.07482 | 0.07482 | 0.0 | 97.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061084 | 0.00061084 | 0.00061084 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001434 | | | 1.87 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9285.00 ave 9285 max 9285 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: 210032.0 ave 210032 max 210032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210032 Ave neighs/atom = 202.73359 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.580 | 5.580 | 5.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3657.5879 0 -3657.5879 232.28846 Loop time of 6.886e-06 on 1 procs for 0 steps with 1036 atoms 188.8% 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 | | 6.886e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9285.00 ave 9285 max 9285 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: 210144.0 ave 210144 max 210144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210144 Ave neighs/atom = 202.84170 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.580 | 5.580 | 5.580 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 -3657.5879 -3657.5879 29.13636 116.54551 3.6149626 232.28846 232.28846 -11.67946 -15.190421 723.73527 2.3455341 211.51911 Loop time of 6.676e-06 on 1 procs for 0 steps with 1036 atoms 239.7% 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 | | 6.676e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9285.00 ave 9285 max 9285 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105072.0 ave 105072 max 105072 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 210144.0 ave 210144 max 210144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210144 Ave neighs/atom = 202.84170 Neighbor list builds = 0 Dangerous builds = 0 1036 -3657.58792186425 eV 2.3455341171535 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03