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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -62.127688 0.0000000) to (31.063844 62.127688 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0373801 5.0373801 3.6110985 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -62.127688 0.0000000) to (31.063844 62.127688 3.6110985) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0373801 5.0373801 3.6110985 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.127688 0.0000000) to (31.063844 62.127688 3.6110985) create_atoms CPU = 0.001 seconds 594 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1184 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_924736622203_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.028 | 5.028 | 5.028 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4665.962 0 -4665.962 55199.785 73 0 -5010.9993 0 -5010.9993 4396.7402 Loop time of 9.09884 on 1 procs for 73 steps with 1184 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 = -4665.96201981506 -5010.99478815756 -5010.99928838885 Force two-norm initial, final = 559.31477 0.20937146 Force max component initial, final = 159.74787 0.029139307 Final line search alpha, max atom move = 1.0000000 0.029139307 Iterations, force evaluations = 73 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.0672 | 9.0672 | 9.0672 | 0.0 | 99.65 Neigh | 0.010872 | 0.010872 | 0.010872 | 0.0 | 0.12 Comm | 0.011069 | 0.011069 | 0.011069 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009724 | | | 0.11 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7287.00 ave 7287 max 7287 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: 102504.0 ave 102504 max 102504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102504 Ave neighs/atom = 86.574324 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -5010.9993 0 -5010.9993 4396.7402 13938.297 84 0 -5011.4005 0 -5011.4005 -405.99514 13976.841 Loop time of 0.78471 on 1 procs for 11 steps with 1184 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 = -5010.99928838885 -5011.39867364342 -5011.40054113763 Force two-norm initial, final = 88.348557 7.9196436 Force max component initial, final = 74.488905 5.6063542 Final line search alpha, max atom move = 0.00010765306 0.00060354119 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78044 | 0.78044 | 0.78044 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072318 | 0.00072318 | 0.00072318 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003542 | | | 0.45 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8066.00 ave 8066 max 8066 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: 102224.0 ave 102224 max 102224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102224 Ave neighs/atom = 86.337838 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.179 | 5.179 | 5.179 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5011.4005 0 -5011.4005 -405.99514 Loop time of 1.597e-06 on 1 procs for 0 steps with 1184 atoms 187.9% 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 | | 1.597e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8086.00 ave 8086 max 8086 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: 102200.0 ave 102200 max 102200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102200 Ave neighs/atom = 86.317568 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.179 | 5.179 | 5.179 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 -5011.4005 -5011.4005 30.881312 124.04116 3.6487783 -405.99514 -405.99514 -638.8846 -634.26744 55.166614 2.3005629 310.72126 Loop time of 2.01e-06 on 1 procs for 0 steps with 1184 atoms 149.3% 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 | | 2.01e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8086.00 ave 8086 max 8086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51100.0 ave 51100 max 51100 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102200.0 ave 102200 max 102200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102200 Ave neighs/atom = 86.317568 Neighbor list builds = 0 Dangerous builds = 0 1184 -5011.40054113763 eV 2.30056292668788 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10