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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -43.781665 0.0000000) to (35.747580 43.781665 8.8452321) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1067972 5.0631858 5.8968214 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -43.781665 0.0000000) to (35.747580 43.781665 8.8452321) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1067972 5.0631858 5.8968214 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.781665 0.0000000) to (35.747580 43.781665 8.8452321) create_atoms CPU = 0.002 seconds 1184 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 17 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2336 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_984358344196_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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 8.516 | 8.516 | 8.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9274.6764 0 -9274.6764 26997.04 67 0 -9633.1697 0 -9633.1697 -1792.5492 Loop time of 4.35592 on 1 procs for 67 steps with 2336 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9274.67637357818 -9633.16146758492 -9633.16967521767 Force two-norm initial, final = 350.76941 0.39181556 Force max component initial, final = 52.759940 0.032958252 Final line search alpha, max atom move = 1.0000000 0.032958252 Iterations, force evaluations = 67 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2079 | 4.2079 | 4.2079 | 0.0 | 96.60 Neigh | 0.10656 | 0.10656 | 0.10656 | 0.0 | 2.45 Comm | 0.023612 | 0.023612 | 0.023612 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01781 | | | 0.41 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12807.0 ave 12807 max 12807 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: 884192.0 ave 884192 max 884192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 884192 Ave neighs/atom = 378.50685 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.516 | 8.516 | 8.516 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -9633.1697 0 -9633.1697 -1792.5492 27687.144 70 0 -9633.2577 0 -9633.2577 -55.689269 27658.801 Loop time of 0.192459 on 1 procs for 3 steps with 2336 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 = -9633.16967521769 -9633.25755455675 -9633.25773248375 Force two-norm initial, final = 93.296212 2.4286345 Force max component initial, final = 92.321391 2.3168762 Final line search alpha, max atom move = 0.00024306774 0.00056315787 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18916 | 0.18916 | 0.18916 | 0.0 | 98.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059696 | 0.00059696 | 0.00059696 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002698 | | | 1.40 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12794.0 ave 12794 max 12794 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: 884848.0 ave 884848 max 884848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 884848 Ave neighs/atom = 378.78767 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 8.654 | 8.654 | 8.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9633.2577 0 -9633.2577 -55.689269 Loop time of 2.38e-06 on 1 procs for 0 steps with 2336 atoms 126.1% 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 | | 2.38e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12794.0 ave 12794 max 12794 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: 884816.0 ave 884816 max 884816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 884816 Ave neighs/atom = 378.77397 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 8.654 | 8.654 | 8.654 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 -9633.2577 -9633.2577 35.751283 87.625462 8.8289977 -55.689269 -55.689269 -134.22234 0.82643404 -33.671896 2.2755319 1315.8224 Loop time of 2.52e-06 on 1 procs for 0 steps with 2336 atoms 317.5% 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 | | 2.52e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12794.0 ave 12794 max 12794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 442408.0 ave 442408 max 442408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 884816.0 ave 884816 max 884816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 884816 Ave neighs/atom = 378.77397 Neighbor list builds = 0 Dangerous builds = 0 2336 -9633.25773248375 eV 2.27553191588296 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05