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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -42.836038 0.0000000) to (52.458785 42.836038 8.8671530) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9952897 5.5070252 5.9114353 Created 1695 atoms using lattice units in orthogonal box = (0.0000000 -42.836038 0.0000000) to (52.458785 42.836038 8.8671530) create_atoms CPU = 0.002 seconds 1695 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9952897 5.5070252 5.9114353 Created 1695 atoms using lattice units in orthogonal box = (0.0000000 -42.836038 0.0000000) to (52.458785 42.836038 8.8671530) create_atoms CPU = 0.002 seconds 1695 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 78 atoms, new total = 3312 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.000 | 7.000 | 7.000 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11592.728 0 -11592.728 1202.8171 59 0 -11685.364 0 -11685.364 -11797.231 Loop time of 2.88019 on 1 procs for 59 steps with 3312 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 = -11592.7276046368 -11685.3525773282 -11685.3638724229 Force two-norm initial, final = 49.834821 0.29651566 Force max component initial, final = 5.1610934 0.040663210 Final line search alpha, max atom move = 1.0000000 0.040663210 Iterations, force evaluations = 59 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.821 | 2.821 | 2.821 | 0.0 | 97.95 Neigh | 0.032865 | 0.032865 | 0.032865 | 0.0 | 1.14 Comm | 0.010774 | 0.010774 | 0.010774 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01551 | | | 0.54 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10581.0 ave 10581 max 10581 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: 571932.0 ave 571932 max 571932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 571932 Ave neighs/atom = 172.68478 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.002 | 7.002 | 7.002 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -11685.364 0 -11685.364 -11797.231 39851.229 64 0 -11686.329 0 -11686.329 -2350.3364 39565.605 Loop time of 0.191845 on 1 procs for 5 steps with 3312 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 = -11685.3638724228 -11686.3267391881 -11686.3291885174 Force two-norm initial, final = 377.18157 2.7001660 Force max component initial, final = 286.58106 2.2252214 Final line search alpha, max atom move = 9.2474620e-05 0.00020577650 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18739 | 0.18739 | 0.18739 | 0.0 | 97.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059622 | 0.00059622 | 0.00059622 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003857 | | | 2.01 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10855.0 ave 10855 max 10855 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: 574272.0 ave 574272 max 574272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574272 Ave neighs/atom = 173.39130 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.141 | 7.141 | 7.141 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11686.329 0 -11686.329 -2350.3364 Loop time of 2.277e-06 on 1 procs for 0 steps with 3312 atoms 175.7% 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 | | 2.277e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10972.0 ave 10972 max 10972 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: 574512.0 ave 574512 max 574512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574512 Ave neighs/atom = 173.46377 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.141 | 7.141 | 7.141 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 -11686.329 -11686.329 52.308439 85.672077 8.8289031 -2350.3364 -2350.3364 89.850254 -7200.5517 59.692151 2.4296695 1472.0888 Loop time of 2.372e-06 on 1 procs for 0 steps with 3312 atoms 295.1% 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 | | 2.372e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10972.0 ave 10972 max 10972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 287256.0 ave 287256 max 287256 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 574512.0 ave 574512 max 574512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574512 Ave neighs/atom = 173.46377 Neighbor list builds = 0 Dangerous builds = 0 3312 -11686.3291885174 eV 2.42966951088927 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03