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 = 4.1768978 4.1768978 4.1768978 Created orthogonal box = (0.0000000 -52.838219 0.0000000) to (13.208511 52.838219 4.1768978) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2834043 5.2834043 4.1768978 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -52.838219 0.0000000) to (13.208511 52.838219 4.1768978) create_atoms CPU = 0.002 seconds 162 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2834043 5.2834043 4.1768978 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -52.838219 0.0000000) to (13.208511 52.838219 4.1768978) create_atoms CPU = 0.001 seconds 162 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 5 33 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 320 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_072689718616_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 5 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.427 | 4.427 | 4.427 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2329.6911 0 -2329.6911 16606.193 60 0 -2352.6524 0 -2352.6524 7640.8993 Loop time of 2.74906 on 1 procs for 60 steps with 320 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 = -2329.6911223303 -2352.6502285616 -2352.65237818946 Force two-norm initial, final = 41.789523 0.13262724 Force max component initial, final = 10.110216 0.038428095 Final line search alpha, max atom move = 1.0000000 0.038428095 Iterations, force evaluations = 60 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7356 | 2.7356 | 2.7356 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0068106 | 0.0068106 | 0.0068106 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006607 | | | 0.24 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2472.00 ave 2472 max 2472 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: 17540.0 ave 17540 max 17540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17540 Ave neighs/atom = 54.812500 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 5 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.428 | 4.428 | 4.428 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -2352.6524 0 -2352.6524 7640.8993 5830.2324 66 0 -2352.7247 0 -2352.7247 338.80443 5852.6189 Loop time of 0.203816 on 1 procs for 6 steps with 320 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2352.65237818946 -2352.72331932557 -2352.72471252714 Force two-norm initial, final = 39.712431 0.70945821 Force max component initial, final = 33.365768 0.61144292 Final line search alpha, max atom move = 0.00016841057 0.00010297345 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20174 | 0.20174 | 0.20174 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043775 | 0.00043775 | 0.00043775 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001636 | | | 0.80 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2544.00 ave 2544 max 2544 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: 20052.0 ave 20052 max 20052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20052 Ave neighs/atom = 62.662500 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 4 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.565 | 4.565 | 4.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2352.7247 0 -2352.7247 338.80443 Loop time of 6.415e-06 on 1 procs for 0 steps with 320 atoms 187.1% 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 | | 6.415e-06 | | |100.00 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2544.00 ave 2544 max 2544 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: 20748.0 ave 20748 max 20748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20748 Ave neighs/atom = 64.837500 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 4 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.565 | 4.565 | 4.565 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 -2352.7247 -2352.7247 13.193351 105.67644 4.1977537 338.80443 338.80443 78.224644 769.96806 168.22058 2.6187432 216.27501 Loop time of 7.016e-06 on 1 procs for 0 steps with 320 atoms 242.3% 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 | | 7.016e-06 | | |100.00 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2544.00 ave 2544 max 2544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10374.0 ave 10374 max 10374 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20748.0 ave 20748 max 20748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20748 Ave neighs/atom = 64.837500 Neighbor list builds = 0 Dangerous builds = 0 320 -2352.72471252714 eV 2.61874317022961 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03