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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -42.219711 0.0000000) to (21.108046 42.219711 3.6200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9665990 4.9665990 3.6200000 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -42.219711 0.0000000) to (21.108046 42.219711 3.6200000) create_atoms CPU = 0.003 seconds 273 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9665990 4.9665990 3.6200000 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -42.219711 0.0000000) to (21.108046 42.219711 3.6200000) create_atoms CPU = 0.002 seconds 273 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 539 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_313717476091_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1883.3515 0 -1883.3515 4516.1622 20 0 -1896.5768 0 -1896.5768 -1610.3543 Loop time of 1.01133 on 1 procs for 20 steps with 539 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 = -1883.35154795043 -1896.57576943017 -1896.57676624702 Force two-norm initial, final = 32.091138 0.28144040 Force max component initial, final = 9.6479035 0.090094242 Final line search alpha, max atom move = 0.19107794 0.017215022 Iterations, force evaluations = 20 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0031 | 1.0031 | 1.0031 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0042242 | 0.0042242 | 0.0042242 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003975 | | | 0.39 Nlocal: 539.000 ave 539 max 539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3815.00 ave 3815 max 3815 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: 41572.0 ave 41572 max 41572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41572 Ave neighs/atom = 77.128015 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -1896.5768 0 -1896.5768 -1610.3543 6452.1113 22 0 -1896.5911 0 -1896.5911 1273.1649 6438.4743 Loop time of 0.089823 on 1 procs for 2 steps with 539 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 = -1896.57676624703 -1896.59019505617 -1896.5911129214 Force two-norm initial, final = 18.717485 1.7818523 Force max component initial, final = 15.876750 1.7242512 Final line search alpha, max atom move = 0.00023458851 0.00040448953 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.088315 | 0.088315 | 0.088315 | 0.0 | 98.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003946 | 0.0003946 | 0.0003946 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001114 | | | 1.24 Nlocal: 539.000 ave 539 max 539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3815.00 ave 3815 max 3815 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: 41514.0 ave 41514 max 41514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41514 Ave neighs/atom = 77.020408 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.616 | 4.616 | 4.616 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1896.5911 0 -1896.5911 1273.1649 Loop time of 6.475e-06 on 1 procs for 0 steps with 539 atoms 185.3% 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 | | 6.475e-06 | | |100.00 Nlocal: 539.000 ave 539 max 539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3815.00 ave 3815 max 3815 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: 41520.0 ave 41520 max 41520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41520 Ave neighs/atom = 77.031540 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.616 | 4.616 | 4.616 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 -1896.5911 -1896.5911 21.078227 84.439423 3.6174591 1273.1649 1273.1649 -77.286321 3468.0125 428.76862 2.2964456 318.87207 Loop time of 6.986e-06 on 1 procs for 0 steps with 539 atoms 214.7% 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 | | 6.986e-06 | | |100.00 Nlocal: 539.000 ave 539 max 539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3815.00 ave 3815 max 3815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20760.0 ave 20760 max 20760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41520.0 ave 41520 max 41520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41520 Ave neighs/atom = 77.031540 Neighbor list builds = 0 Dangerous builds = 0 539 -1896.5911129214 eV 2.29644564369882 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01