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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -63.956054 0.0000000) to (39.164924 63.956054 9.9479008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3169233 6.1892955 6.6319338 Created 1486 atoms using lattice units in orthogonal box = (0.0000000 -63.956054 0.0000000) to (39.164924 63.956054 9.9479008) create_atoms CPU = 0.002 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3169233 6.1892955 6.6319338 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -63.956054 0.0000000) to (39.164924 63.956054 9.9479008) create_atoms CPU = 0.002 seconds 1492 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2976 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_411898953661_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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 7.450 | 7.450 | 7.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7279.7014 0 -7279.7014 24013.149 72 0 -8005.8452 0 -8005.8452 2415.824 Loop time of 3.25883 on 1 procs for 72 steps with 2976 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 = -7279.70141650905 -8005.83800669012 -8005.84524518023 Force two-norm initial, final = 527.84287 0.24476043 Force max component initial, final = 85.038222 0.015495631 Final line search alpha, max atom move = 1.0000000 0.015495631 Iterations, force evaluations = 72 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1878 | 3.1878 | 3.1878 | 0.0 | 97.82 Neigh | 0.038383 | 0.038383 | 0.038383 | 0.0 | 1.18 Comm | 0.014249 | 0.014249 | 0.014249 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0184 | | | 0.56 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12411.0 ave 12411 max 12411 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: 669718.0 ave 669718 max 669718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 669718 Ave neighs/atom = 225.03965 Neighbor list builds = 1 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.447 | 7.447 | 7.447 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -8005.8452 0 -8005.8452 2415.824 49835.68 76 0 -8006.0504 0 -8006.0504 12.839833 49995.262 Loop time of 0.180502 on 1 procs for 4 steps with 2976 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 = -8005.84524518018 -8006.04986108176 -8006.05038819475 Force two-norm initial, final = 149.92225 1.8791463 Force max component initial, final = 132.73770 1.5045661 Final line search alpha, max atom move = 0.00014424175 0.00021702125 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17625 | 0.17625 | 0.17625 | 0.0 | 97.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066556 | 0.00066556 | 0.00066556 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00359 | | | 1.99 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12060.0 ave 12060 max 12060 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: 669256.0 ave 669256 max 669256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 669256 Ave neighs/atom = 224.88441 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 7.586 | 7.586 | 7.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8006.0504 0 -8006.0504 12.839833 Loop time of 1.992e-06 on 1 procs for 0 steps with 2976 atoms 200.8% 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 | | 1.992e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12042.0 ave 12042 max 12042 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: 668856.0 ave 668856 max 668856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 668856 Ave neighs/atom = 224.75000 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 7.586 | 7.586 | 7.586 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 -8006.0504 -8006.0504 39.277005 127.98736 9.9454266 12.839833 12.839833 19.455389 -29.140077 48.204186 2.617099 1182.2903 Loop time of 2.189e-06 on 1 procs for 0 steps with 2976 atoms 228.4% 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 | | 2.189e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12042.0 ave 12042 max 12042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 334428.0 ave 334428 max 334428 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 668856.0 ave 668856 max 668856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 668856 Ave neighs/atom = 224.75000 Neighbor list builds = 0 Dangerous builds = 0 2976 -8006.05038819475 eV 2.61709899459381 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04