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 = 4.0500004 4.0500004 4.0500004 Created orthogonal box = (0.0000000 -65.304294 0.0000000) to (32.652147 65.304294 4.0500004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5257480 5.5257480 4.0500004 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -65.304294 0.0000000) to (32.652147 65.304294 4.0500004) create_atoms CPU = 0.002 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5257480 5.5257480 4.0500004 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -65.304294 0.0000000) to (32.652147 65.304294 4.0500004) create_atoms CPU = 0.002 seconds 522 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 = 9 34 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1040 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_820335782779_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 = 9 34 2 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) = 5.017 | 5.017 | 5.017 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3433.665 0 -3433.665 7039.5721 32 0 -3486.2844 0 -3486.2844 4922.5522 Loop time of 0.998918 on 1 procs for 32 steps with 1040 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 = -3433.66503187146 -3486.28121088207 -3486.28443144419 Force two-norm initial, final = 32.021428 0.17220517 Force max component initial, final = 6.2650125 0.033649707 Final line search alpha, max atom move = 1.0000000 0.033649707 Iterations, force evaluations = 32 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98026 | 0.98026 | 0.98026 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010388 | 0.010388 | 0.010388 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008268 | | | 0.83 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7570.00 ave 7570 max 7570 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: 138416.0 ave 138416 max 138416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138416 Ave neighs/atom = 133.09231 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 34 2 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.016 | 5.016 | 5.016 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -3486.2844 0 -3486.2844 4922.5522 17271.838 44 0 -3486.8984 0 -3486.8984 8.2593456 17376.901 Loop time of 0.245011 on 1 procs for 12 steps with 1040 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 = -3486.28443144419 -3486.89750929403 -3486.89837515012 Force two-norm initial, final = 122.41844 0.83815150 Force max component initial, final = 118.56332 0.39414135 Final line search alpha, max atom move = 0.00041191502 0.00016235274 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21722 | 0.21722 | 0.21722 | 0.0 | 88.66 Neigh | 0.0173 | 0.0173 | 0.0173 | 0.0 | 7.06 Comm | 0.0025402 | 0.0025402 | 0.0025402 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007956 | | | 3.25 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7495.00 ave 7495 max 7495 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: 137272.0 ave 137272 max 137272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137272 Ave neighs/atom = 131.99231 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 34 2 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) = 5.154 | 5.154 | 5.154 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3486.8984 0 -3486.8984 8.2593456 Loop time of 6.235e-06 on 1 procs for 0 steps with 1040 atoms 192.5% 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 | | 6.235e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7495.00 ave 7495 max 7495 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: 137248.0 ave 137248 max 137248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137248 Ave neighs/atom = 131.96923 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 = 9 34 2 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) = 5.154 | 5.154 | 5.154 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 -3486.8984 -3486.8984 32.555464 132.09793 4.0406613 8.2593456 8.2593456 36.232823 -11.618959 0.16417317 2.6276033 629.72479 Loop time of 6.856e-06 on 1 procs for 0 steps with 1040 atoms 248.0% 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 | | 6.856e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7495.00 ave 7495 max 7495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68624.0 ave 68624 max 68624 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137248.0 ave 137248 max 137248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137248 Ave neighs/atom = 131.96923 Neighbor list builds = 0 Dangerous builds = 0 1040 -3486.89837515012 eV 2.62760326058911 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01