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 = 3.6239511 3.6239511 3.6239511 Created orthogonal box = (0.0000000 -42.262169 0.0000000) to (14.941933 42.262169 5.1250408) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1525607 6.2150248 5.1250408 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.262169 0.0000000) to (14.941933 42.262169 5.1250408) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1525607 6.2150248 5.1250408 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.262169 0.0000000) to (14.941933 42.262169 5.1250408) 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_427873955970_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2240.0939 0 -2240.0939 31126.282 201 0 -2297.625 0 -2297.625 6164.083 Loop time of 16.1263 on 1 procs for 201 steps with 546 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 = -2240.09394860568 -2297.62292485418 -2297.62502378887 Force two-norm initial, final = 69.262113 0.13276844 Force max component initial, final = 18.773087 0.022463218 Final line search alpha, max atom move = 1.0000000 0.022463218 Iterations, force evaluations = 201 385 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.059 | 16.059 | 16.059 | 0.0 | 99.58 Neigh | 0.033384 | 0.033384 | 0.033384 | 0.0 | 0.21 Comm | 0.019258 | 0.019258 | 0.019258 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01465 | | | 0.09 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4000.00 ave 4000 max 4000 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: 68444.0 ave 68444 max 68444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68444 Ave neighs/atom = 125.35531 Neighbor list builds = 7 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 201 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press Volume 201 0 -2297.625 0 -2297.625 6164.083 6472.7062 282 0 -2308.7848 0 -2308.7848 -31.951049 6483.3515 Loop time of 4.06277 on 1 procs for 81 steps with 546 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 = -2297.62502378887 -2308.7833473486 -2308.7848091858 Force two-norm initial, final = 319.64763 2.3793076 Force max component initial, final = 280.92221 0.99375087 Final line search alpha, max atom move = 0.00041895508 0.00041633698 Iterations, force evaluations = 81 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0362 | 4.0362 | 4.0362 | 0.0 | 99.35 Neigh | 0.0087759 | 0.0087759 | 0.0087759 | 0.0 | 0.22 Comm | 0.0032825 | 0.0032825 | 0.0032825 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01452 | | | 0.36 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3919.00 ave 3919 max 3919 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: 66848.0 ave 66848 max 66848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66848 Ave neighs/atom = 122.43223 Neighbor list builds = 2 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.651 | 4.651 | 4.651 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2308.7848 0 -2308.7848 -31.951049 Loop time of 1.777e-06 on 1 procs for 0 steps with 546 atoms 112.5% 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 | | 1.777e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3824.00 ave 3824 max 3824 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: 65456.0 ave 65456 max 65456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65456 Ave neighs/atom = 119.88278 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.651 | 4.651 | 4.651 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 -2308.7848 -2308.7848 14.589906 81.659269 5.4417875 -31.951049 -31.951049 -64.160867 229.06267 -260.75495 2.3271504 1649.0123 Loop time of 2.11e-06 on 1 procs for 0 steps with 546 atoms 189.6% 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 | | 2.11e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3824.00 ave 3824 max 3824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32728.0 ave 32728 max 32728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 65456.0 ave 65456 max 65456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65456 Ave neighs/atom = 119.88278 Neighbor list builds = 0 Dangerous builds = 0 546 -2308.7848091858 eV 2.32715037369909 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20