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 = 3.5226425 3.5226425 3.5226425 Created orthogonal box = (0.0000000 -37.611530 0.0000000) to (21.715027 37.611530 6.1013958) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7144807 5.2788112 6.1013958 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.611530 0.0000000) to (21.715027 37.611530 6.1013958) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7144807 5.2788112 6.1013958 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.611530 0.0000000) to (21.715027 37.611530 6.1013958) create_atoms CPU = 0.001 seconds 458 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 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 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_381861218831_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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 6.670 | 6.670 | 6.670 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3495.1768 0 -3495.1768 71101.938 75 0 -3838.6027 0 -3838.6027 8870.3126 Loop time of 3.31163 on 1 procs for 75 steps with 912 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 = -3495.17676144711 -3838.59938586482 -3838.60266717449 Force two-norm initial, final = 514.66577 0.25357242 Force max component initial, final = 147.64452 0.033829808 Final line search alpha, max atom move = 1.0000000 0.033829808 Iterations, force evaluations = 75 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2264 | 3.2264 | 3.2264 | 0.0 | 97.43 Neigh | 0.060032 | 0.060032 | 0.060032 | 0.0 | 1.81 Comm | 0.015523 | 0.015523 | 0.015523 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009695 | | | 0.29 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10772.0 ave 10772 max 10772 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: 567888.0 ave 567888 max 567888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 567888 Ave neighs/atom = 622.68421 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.685 | 6.685 | 6.685 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -3838.6027 0 -3838.6027 8870.3126 9966.4515 80 0 -3838.7966 0 -3838.7966 37.005097 10013.687 Loop time of 0.212632 on 1 procs for 5 steps with 912 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 = -3838.60266717448 -3838.79642464066 -3838.79661373299 Force two-norm initial, final = 105.38206 0.84579000 Force max component initial, final = 91.379405 0.74793555 Final line search alpha, max atom move = 0.00031704277 0.00023712756 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20865 | 0.20865 | 0.20865 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073009 | 0.00073009 | 0.00073009 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003253 | | | 1.53 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11507.0 ave 11507 max 11507 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: 568712.0 ave 568712 max 568712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 568712 Ave neighs/atom = 623.58772 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 6.822 | 6.822 | 6.822 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3838.7966 0 -3838.7966 37.005097 Loop time of 2.506e-06 on 1 procs for 0 steps with 912 atoms 159.6% 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 | | 2.506e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11379.0 ave 11379 max 11379 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: 568100.0 ave 568100 max 568100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 568100 Ave neighs/atom = 622.91667 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 6.822 | 6.822 | 6.822 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 -3838.7966 -3838.7966 21.799862 75.230635 6.1058415 37.005097 37.005097 10.835953 -19.576545 119.75588 2.2715781 629.79677 Loop time of 2.772e-06 on 1 procs for 0 steps with 912 atoms 324.7% 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 | | 2.772e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11379.0 ave 11379 max 11379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 284050.0 ave 284050 max 284050 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 568100.0 ave 568100 max 568100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 568100 Ave neighs/atom = 622.91667 Neighbor list builds = 0 Dangerous builds = 0 912 -3838.79661373299 eV 2.27157814212218 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04