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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -41.069653 0.0000000) to (14.519070 41.069653 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9784406 6.0391370 4.9800000 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.069653 0.0000000) to (14.519070 41.069653 4.9800000) create_atoms CPU = 0.001 seconds 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9784406 6.0391370 4.9800000 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.069653 0.0000000) to (14.519070 41.069653 4.9800000) create_atoms CPU = 0.001 seconds 274 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 27 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 540 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2375.5121 0 -2375.5121 9905.047 59 0 -2394.5746 0 -2394.5746 -5572.637 Loop time of 1.94928 on 1 procs for 59 steps with 540 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 = -2375.51211354694 -2394.57227046575 -2394.57458812733 Force two-norm initial, final = 34.772628 0.15606841 Force max component initial, final = 13.328297 0.029065104 Final line search alpha, max atom move = 1.0000000 0.029065104 Iterations, force evaluations = 59 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9386 | 1.9386 | 1.9386 | 0.0 | 99.45 Neigh | 0.0038963 | 0.0038963 | 0.0038963 | 0.0 | 0.20 Comm | 0.0036655 | 0.0036655 | 0.0036655 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003146 | | | 0.16 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3780.00 ave 3780 max 3780 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: 46380.0 ave 46380 max 46380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46380 Ave neighs/atom = 85.888889 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -2394.5746 0 -2394.5746 -5572.637 5939.08 61 0 -2394.5807 0 -2394.5807 -3487.8457 5932.3795 Loop time of 0.0940203 on 1 procs for 2 steps with 540 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 = -2394.57458812732 -2394.58049602124 -2394.58070917638 Force two-norm initial, final = 13.849770 0.15813374 Force max component initial, final = 11.940603 0.027090582 Final line search alpha, max atom move = 0.00065932643 1.7861537e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.093317 | 0.093317 | 0.093317 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014515 | 0.00014515 | 0.00014515 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005585 | | | 0.59 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3829.00 ave 3829 max 3829 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: 46408.0 ave 46408 max 46408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46408 Ave neighs/atom = 85.940741 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.643 | 4.643 | 4.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2394.5807 0 -2394.5807 -3487.8457 Loop time of 1.571e-06 on 1 procs for 0 steps with 540 atoms 127.3% 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 | | 1.571e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3829.00 ave 3829 max 3829 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: 46416.0 ave 46416 max 46416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46416 Ave neighs/atom = 85.955556 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.643 | 4.643 | 4.643 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 -2394.5807 -2394.5807 14.515346 82.139306 4.9756579 -3487.8457 -3487.8457 -4.226644 -10458.229 -1.0809369 2.3528681 259.05752 Loop time of 1.554e-06 on 1 procs for 0 steps with 540 atoms 193.1% 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 | | 1.554e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3829.00 ave 3829 max 3829 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23208.0 ave 23208 max 23208 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46416.0 ave 46416 max 46416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46416 Ave neighs/atom = 85.955556 Neighbor list builds = 0 Dangerous builds = 0 540 -2394.58070917638 eV 2.3528681312873 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02