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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -38.882951 0.0000000) to (18.329599 38.882951 4.4455807) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3910585 5.3368756 4.4455807 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -38.882951 0.0000000) to (18.329599 38.882951 4.4455807) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3910585 5.3368756 4.4455807 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -38.882951 0.0000000) to (18.329599 38.882951 4.4455807) create_atoms CPU = 0.001 seconds 206 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 16 1 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 406 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_534363225491_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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.896 | 4.896 | 4.896 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2262.9238 0 -2262.9238 165419.14 124 0 -2697.5342 0 -2697.5342 92.344897 Loop time of 1.11292 on 1 procs for 124 steps with 406 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 = -2262.92381279598 -2697.5315746222 -2697.53415591431 Force two-norm initial, final = 891.21531 0.30914906 Force max component initial, final = 269.26203 0.047518685 Final line search alpha, max atom move = 1.0000000 0.047518685 Iterations, force evaluations = 124 223 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0705 | 1.0705 | 1.0705 | 0.0 | 96.19 Neigh | 0.026193 | 0.026193 | 0.026193 | 0.0 | 2.35 Comm | 0.010138 | 0.010138 | 0.010138 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006059 | | | 0.54 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5484.00 ave 5484 max 5484 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: 111968.0 ave 111968 max 111968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111968 Ave neighs/atom = 275.78325 Neighbor list builds = 4 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 124 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.896 | 4.896 | 4.896 Mbytes Step Temp E_pair E_mol TotEng Press Volume 124 0 -2697.5342 0 -2697.5342 92.344897 6336.8099 130 0 -2697.8735 0 -2697.8735 -19.68781 6336.7171 Loop time of 0.045666 on 1 procs for 6 steps with 406 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 = -2697.5341559143 -2697.87340421828 -2697.87347317119 Force two-norm initial, final = 108.89997 1.0601602 Force max component initial, final = 81.386665 0.56918814 Final line search alpha, max atom move = 0.0010742657 0.00061145929 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.043599 | 0.043599 | 0.043599 | 0.0 | 95.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003927 | 0.0003927 | 0.0003927 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001675 | | | 3.67 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5476.00 ave 5476 max 5476 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: 112740.0 ave 112740 max 112740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112740 Ave neighs/atom = 277.68473 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2697.8735 0 -2697.8735 -19.68781 Loop time of 1.895e-06 on 1 procs for 0 steps with 406 atoms 158.3% 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 | | 1.895e-06 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5454.00 ave 5454 max 5454 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: 112596.0 ave 112596 max 112596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112596 Ave neighs/atom = 277.33005 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.034 | 5.034 | 5.034 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 -2697.8735 -2697.8735 18.397967 77.859529 4.4236699 -19.68781 -19.68781 76.97404 -144.08688 8.0494106 2.5513235 391.65112 Loop time of 2.106e-06 on 1 procs for 0 steps with 406 atoms 189.9% 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 | | 2.106e-06 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5454.00 ave 5454 max 5454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56298.0 ave 56298 max 56298 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 112596.0 ave 112596 max 112596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112596 Ave neighs/atom = 277.33005 Neighbor list builds = 0 Dangerous builds = 0 406 -2697.87347317119 eV 2.55132347674183 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01