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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -52.094774 0.0000000) to (42.532331 52.094774 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2437120 4.9950518 5.7481372 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -52.094774 0.0000000) to (42.532331 52.094774 8.6222058) create_atoms CPU = 0.002 seconds 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2437120 4.9950518 5.7481372 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -52.094774 0.0000000) to (42.532331 52.094774 8.6222058) create_atoms CPU = 0.002 seconds 1757 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 = 11 27 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 42 atoms, new total = 3472 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_657255834688_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 = 11 27 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) = 7.405 | 7.405 | 7.405 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15311.74 0 -15311.74 52.014385 61 0 -15379.455 0 -15379.455 -7158.6455 Loop time of 3.04867 on 1 procs for 61 steps with 3472 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 = -15311.7400638066 -15379.4402483206 -15379.4550318198 Force two-norm initial, final = 44.994300 0.52373582 Force max component initial, final = 5.6304608 0.096653893 Final line search alpha, max atom move = 0.45145419 0.043634806 Iterations, force evaluations = 61 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.949 | 2.949 | 2.949 | 0.0 | 96.73 Neigh | 0.073582 | 0.073582 | 0.073582 | 0.0 | 2.41 Comm | 0.011105 | 0.011105 | 0.011105 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01501 | | | 0.49 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11702.0 ave 11702 max 11702 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: 609662.0 ave 609662 max 609662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609662 Ave neighs/atom = 175.59389 Neighbor list builds = 2 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 = 11 27 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.406 | 7.406 | 7.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -15379.455 0 -15379.455 -7158.6455 38208.653 64 0 -15379.684 0 -15379.684 -1594.3136 38095.474 Loop time of 0.161749 on 1 procs for 3 steps with 3472 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 = -15379.4550318198 -15379.6841769432 -15379.684478193 Force two-norm initial, final = 219.00203 0.58294764 Force max component initial, final = 157.20055 0.079718464 Final line search alpha, max atom move = 0.00025971087 2.0703751e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15854 | 0.15854 | 0.15854 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050139 | 0.00050139 | 0.00050139 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002704 | | | 1.67 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11705.0 ave 11705 max 11705 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: 609600.0 ave 609600 max 609600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609600 Ave neighs/atom = 175.57604 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 = 11 27 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) = 7.545 | 7.545 | 7.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15379.684 0 -15379.684 -1594.3136 Loop time of 1.721e-06 on 1 procs for 0 steps with 3472 atoms 174.3% 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 | | 1.721e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11752.0 ave 11752 max 11752 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: 609918.0 ave 609918 max 609918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609918 Ave neighs/atom = 175.66763 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 = 11 27 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) = 7.545 | 7.545 | 7.545 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 -15379.684 -15379.684 42.46546 104.18955 8.6102029 -1594.3136 -1594.3136 0.73155009 -4780.7642 -2.9079782 2.2676148 1625.5401 Loop time of 1.989e-06 on 1 procs for 0 steps with 3472 atoms 201.1% 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 | | 1.989e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11752.0 ave 11752 max 11752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 304959.0 ave 304959 max 304959 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 609918.0 ave 609918 max 609918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609918 Ave neighs/atom = 175.66763 Neighbor list builds = 0 Dangerous builds = 0 3472 -15379.684478193 eV 2.26761483362593 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03