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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -35.262858 0.0000000) to (12.467303 35.262858 4.0449272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5932169 3.7118798 4.0449272 Created 152 atoms using lattice units in orthogonal box = (0.0000000 -35.262858 0.0000000) to (12.467303 35.262858 4.0449272) create_atoms CPU = 0.001 seconds 152 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5932169 3.7118798 4.0449272 Created 154 atoms using lattice units in orthogonal box = (0.0000000 -35.262858 0.0000000) to (12.467303 35.262858 4.0449272) create_atoms CPU = 0.001 seconds 154 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 306 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.797 | 4.797 | 4.797 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1169.6567 0 -1169.6567 76665.307 38 0 -1300.2234 0 -1300.2234 21817.321 Loop time of 2.62733 on 1 procs for 38 steps with 306 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1169.65665137963 -1300.22225351639 -1300.22339715295 Force two-norm initial, final = 352.31093 0.12455362 Force max component initial, final = 174.79560 0.029363108 Final line search alpha, max atom move = 1.0000000 0.029363108 Iterations, force evaluations = 38 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6228 | 2.6228 | 2.6228 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022413 | 0.0022413 | 0.0022413 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002274 | | | 0.09 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2001.00 ave 2001 max 2001 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: 17740.0 ave 17740 max 17740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17740 Ave neighs/atom = 57.973856 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.796 | 4.796 | 4.796 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -1300.2234 0 -1300.2234 21817.321 3556.5648 59 0 -1300.9061 0 -1300.9061 39.51461 3600.7672 Loop time of 1.00491 on 1 procs for 21 steps with 306 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 = -1300.22339715295 -1300.90601084436 -1300.9060887352 Force two-norm initial, final = 94.887133 0.84782033 Force max component initial, final = 84.635480 0.65169280 Final line search alpha, max atom move = 0.0065577755 0.0042736551 Iterations, force evaluations = 21 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98337 | 0.98337 | 0.98337 | 0.0 | 97.86 Neigh | 0.016599 | 0.016599 | 0.016599 | 0.0 | 1.65 Comm | 0.00099263 | 0.00099263 | 0.00099263 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003946 | | | 0.39 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2001.00 ave 2001 max 2001 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: 17580.0 ave 17580 max 17580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17580 Ave neighs/atom = 57.450980 Neighbor list builds = 1 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.934 | 4.934 | 4.934 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1300.9061 0 -1300.9061 39.51461 Loop time of 3.232e-06 on 1 procs for 0 steps with 306 atoms 123.8% 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 | | 3.232e-06 | | |100.00 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2001.00 ave 2001 max 2001 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: 17572.0 ave 17572 max 17572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17572 Ave neighs/atom = 57.424837 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.934 | 4.934 | 4.934 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 -1300.9061 -1300.9061 12.43439 71.829741 4.0314964 39.51461 39.51461 289.20793 5.4239994 -176.0881 2.2420853 217.28928 Loop time of 2.959e-06 on 1 procs for 0 steps with 306 atoms 169.0% 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 | | 2.959e-06 | | |100.00 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2001.00 ave 2001 max 2001 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8786.00 ave 8786 max 8786 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17572.0 ave 17572 max 17572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17572 Ave neighs/atom = 57.424837 Neighbor list builds = 0 Dangerous builds = 0 306 -1300.9060887352 eV 2.24208526856617 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04