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 = 3.4919386 3.4919386 3.4919386 Created orthogonal box = (0.0000000 -43.192895 0.0000000) to (20.361326 43.192895 4.9383469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9886253 5.9284365 4.9383469 Created 407 atoms using lattice units in orthogonal box = (0.0000000 -43.192895 0.0000000) to (20.361326 43.192895 4.9383469) create_atoms CPU = 0.001 seconds 407 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9886253 5.9284365 4.9383469 Created 411 atoms using lattice units in orthogonal box = (0.0000000 -43.192895 0.0000000) to (20.361326 43.192895 4.9383469) create_atoms CPU = 0.001 seconds 411 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 6 26 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 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 816 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_108408461881_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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 6 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2684.1638 0 -2684.1638 165527.61 120 0 -3612.4576 0 -3612.4576 4833.8544 Loop time of 2.04678 on 1 procs for 120 steps with 816 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 = -2684.16379169915 -3612.45409081156 -3612.45760695257 Force two-norm initial, final = 1524.4291 0.23972286 Force max component initial, final = 354.89655 0.032617472 Final line search alpha, max atom move = 1.0000000 0.032617472 Iterations, force evaluations = 120 231 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0217 | 2.0217 | 2.0217 | 0.0 | 98.78 Neigh | 0.006564 | 0.006564 | 0.006564 | 0.0 | 0.32 Comm | 0.010226 | 0.010226 | 0.010226 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008263 | | | 0.40 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5112.00 ave 5112 max 5112 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: 108704.0 ave 108704 max 108704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108704 Ave neighs/atom = 133.21569 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 6 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 120 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press Volume 120 0 -3612.4576 0 -3612.4576 4833.8544 8686.2027 123 0 -3612.5327 0 -3612.5327 239.5986 8708.0082 Loop time of 0.0446946 on 1 procs for 3 steps with 816 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 = -3612.45760695257 -3612.53000740575 -3612.53271416077 Force two-norm initial, final = 57.976930 2.4664626 Force max component initial, final = 48.932559 1.9096779 Final line search alpha, max atom move = 0.00011173342 0.00021337484 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.043728 | 0.043728 | 0.043728 | 0.0 | 97.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019289 | 0.00019289 | 0.00019289 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007741 | | | 1.73 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5172.00 ave 5172 max 5172 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: 108648.0 ave 108648 max 108648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108648 Ave neighs/atom = 133.14706 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 6 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 5.101 | 5.101 | 5.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3612.5327 0 -3612.5327 239.5986 Loop time of 1.507e-06 on 1 procs for 0 steps with 816 atoms 132.7% 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 | | 1.507e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5156.00 ave 5156 max 5156 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: 108664.0 ave 108664 max 108664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108664 Ave neighs/atom = 133.16667 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 6 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 5.101 | 5.101 | 5.101 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 -3612.5327 -3612.5327 20.405933 86.309039 4.9443146 239.5986 239.5986 263.73812 103.27361 351.78406 2.3044241 748.9381 Loop time of 1.489e-06 on 1 procs for 0 steps with 816 atoms 134.3% 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 | | 1.489e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5156.00 ave 5156 max 5156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54332.0 ave 54332 max 54332 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108664.0 ave 108664 max 108664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108664 Ave neighs/atom = 133.16667 Neighbor list builds = 0 Dangerous builds = 0 816 -3612.53271416077 eV 2.30442413631152 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02