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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -37.484352 0.0000000) to (17.670293 37.484352 4.0538432) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7200617 4.6033415 4.0538432 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -37.484352 0.0000000) to (17.670293 37.484352 4.0538432) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7200617 4.6033415 4.0538432 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -37.484352 0.0000000) to (17.670293 37.484352 4.0538432) create_atoms CPU = 0.001 seconds 230 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 20 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 452 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 10880.288 0 10880.288 15926649 65 0 -1922.7438 0 -1922.7438 -4157.9006 Loop time of 0.490269 on 1 procs for 65 steps with 452 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 = 10880.2880635701 -1922.74249564993 -1922.74376428555 Force two-norm initial, final = 84226.403 0.19126736 Force max component initial, final = 29188.853 0.061119676 Final line search alpha, max atom move = 1.0000000 0.061119676 Iterations, force evaluations = 65 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47739 | 0.47739 | 0.47739 | 0.0 | 97.37 Neigh | 0.0049758 | 0.0049758 | 0.0049758 | 0.0 | 1.01 Comm | 0.0046677 | 0.0046677 | 0.0046677 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003233 | | | 0.66 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4608.00 ave 4608 max 4608 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: 74764.0 ave 74764 max 74764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74764 Ave neighs/atom = 165.40708 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -1922.7438 0 -1922.7438 -4157.9006 5370.203 68 0 -1922.765 0 -1922.765 -78.786399 5357.9522 Loop time of 0.0236258 on 1 procs for 3 steps with 452 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 = -1922.74376428555 -1922.76431311938 -1922.76498382178 Force two-norm initial, final = 25.298010 1.3860188 Force max component initial, final = 19.999281 1.3078979 Final line search alpha, max atom move = 0.00023909286 0.00031270907 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022504 | 0.022504 | 0.022504 | 0.0 | 95.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002086 | 0.0002086 | 0.0002086 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009132 | | | 3.87 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4608.00 ave 4608 max 4608 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: 75012.0 ave 75012 max 75012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75012 Ave neighs/atom = 165.95575 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1922.765 0 -1922.765 -78.786399 Loop time of 1.969e-06 on 1 procs for 0 steps with 452 atoms 203.1% 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 | | 1.969e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4608.00 ave 4608 max 4608 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: 75056.0 ave 75056 max 75056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75056 Ave neighs/atom = 166.05310 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.631 | 4.631 | 4.631 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 -1922.765 -1922.765 17.672607 74.834569 4.0513144 -78.786399 -78.786399 76.588498 77.906141 -390.85384 2.3125777 359.28535 Loop time of 2.218e-06 on 1 procs for 0 steps with 452 atoms 225.4% 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 | | 2.218e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4608.00 ave 4608 max 4608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37528.0 ave 37528 max 37528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75056.0 ave 75056 max 75056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75056 Ave neighs/atom = 166.05310 Neighbor list builds = 0 Dangerous builds = 0 452 -1922.76498382178 eV 2.3125777294419 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00