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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -43.286357 0.0000000) to (53.014743 43.286357 8.9611272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0588278 5.5653887 5.9740848 Created 1664 atoms using lattice units in orthogonal box = (0.0000000 -43.286357 0.0000000) to (53.014743 43.286357 8.9611272) create_atoms CPU = 0.003 seconds 1664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0588278 5.5653887 5.9740848 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -43.286357 0.0000000) to (53.014743 43.286357 8.9611272) create_atoms CPU = 0.003 seconds 1688 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 3351 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_469343973171_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.582 | 6.582 | 6.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12509.934 0 -12509.934 76479.703 1058 0 -13592.505 0 -13592.505 -74262.374 Loop time of 54.7067 on 1 procs for 1058 steps with 3351 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12509.9342422295 -13592.4915745995 -13592.5046217549 Force two-norm initial, final = 872.01991 0.34682378 Force max component initial, final = 80.223784 0.048946171 Final line search alpha, max atom move = 0.76837438 0.037608984 Iterations, force evaluations = 1058 2034 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 53.171 | 53.171 | 53.171 | 0.0 | 97.19 Neigh | 0.88797 | 0.88797 | 0.88797 | 0.0 | 1.62 Comm | 0.26679 | 0.26679 | 0.26679 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3805 | | | 0.70 Nlocal: 3351.00 ave 3351 max 3351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10358.0 ave 10358 max 10358 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: 497090.0 ave 497090 max 497090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 497090 Ave neighs/atom = 148.34079 Neighbor list builds = 23 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1058 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.961 | 6.961 | 6.961 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1058 0 -13592.505 0 -13592.505 -74262.374 41128.26 1118 0 -13723.458 0 -13723.458 -16.812705 39270.395 Loop time of 1.73128 on 1 procs for 60 steps with 3351 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 = -13592.5046217549 -13723.4541530163 -13723.458109307 Force two-norm initial, final = 4066.2842 9.1958613 Force max component initial, final = 2913.4006 4.2998587 Final line search alpha, max atom move = 0.00010300135 0.00044289123 Iterations, force evaluations = 60 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5364 | 1.5364 | 1.5364 | 0.0 | 88.74 Neigh | 0.14648 | 0.14648 | 0.14648 | 0.0 | 8.46 Comm | 0.0066782 | 0.0066782 | 0.0066782 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04176 | | | 2.41 Nlocal: 3351.00 ave 3351 max 3351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10258.0 ave 10258 max 10258 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: 551038.0 ave 551038 max 551038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551038 Ave neighs/atom = 164.43987 Neighbor list builds = 4 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.098 | 7.098 | 7.098 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13723.458 0 -13723.458 -16.812705 Loop time of 2.339e-06 on 1 procs for 0 steps with 3351 atoms 171.0% 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 | | 2.339e-06 | | |100.00 Nlocal: 3351.00 ave 3351 max 3351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10222.0 ave 10222 max 10222 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: 551456.0 ave 551456 max 551456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551456 Ave neighs/atom = 164.56461 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.098 | 7.098 | 7.098 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 -13723.458 -13723.458 50.9667 82.57329 9.3312359 -16.812705 -16.812705 104.65984 27.575653 -182.6736 2.2281171 4488.3877 Loop time of 2.84e-06 on 1 procs for 0 steps with 3351 atoms 246.5% 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 | | 2.84e-06 | | |100.00 Nlocal: 3351.00 ave 3351 max 3351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10222.0 ave 10222 max 10222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 275728.0 ave 275728 max 275728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 551456.0 ave 551456 max 551456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551456 Ave neighs/atom = 164.56461 Neighbor list builds = 0 Dangerous builds = 0 3351 -13723.458109307 eV 2.2281171134602 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:57