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 = 3.4524642 3.4524642 3.4524642 Created orthogonal box = (0.0000000 -36.862230 0.0000000) to (21.282419 36.862230 5.9798434) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6006365 5.1736464 5.9798434 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -36.862230 0.0000000) to (21.282419 36.862230 5.9798434) create_atoms CPU = 0.003 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6006365 5.1736464 5.9798434 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -36.862230 0.0000000) to (21.282419 36.862230 5.9798434) create_atoms CPU = 0.003 seconds 458 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 6 19 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.013 | 5.013 | 5.013 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3703.8129 0 -3703.8129 91669.168 88 0 -4087.6053 0 -4087.6053 30722.48 Loop time of 3.27293 on 1 procs for 88 steps with 912 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 = -3703.8128660323 -4087.60125720753 -4087.60526057702 Force two-norm initial, final = 547.27230 0.19727703 Force max component initial, final = 136.36976 0.034626746 Final line search alpha, max atom move = 0.90972316 0.031500753 Iterations, force evaluations = 88 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1814 | 3.1814 | 3.1814 | 0.0 | 97.20 Neigh | 0.047561 | 0.047561 | 0.047561 | 0.0 | 1.45 Comm | 0.02384 | 0.02384 | 0.02384 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02008 | | | 0.61 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5991.00 ave 5991 max 5991 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: 181824.0 ave 181824 max 181824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181824 Ave neighs/atom = 199.36842 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.017 | 5.017 | 5.017 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -4087.6053 0 -4087.6053 30722.48 9382.5826 98 0 -4088.7899 0 -4088.7899 -69.599439 9453.7696 Loop time of 0.240355 on 1 procs for 10 steps with 912 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4087.60526057694 -4088.78975497094 -4088.78989265987 Force two-norm initial, final = 337.21427 0.97389715 Force max component initial, final = 284.54239 0.53667775 Final line search alpha, max atom move = 0.00061333456 0.00032916301 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23316 | 0.23316 | 0.23316 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015926 | 0.0015926 | 0.0015926 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005607 | | | 2.33 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5984.00 ave 5984 max 5984 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: 181576.0 ave 181576 max 181576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181576 Ave neighs/atom = 199.09649 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.155 | 5.155 | 5.155 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4088.7899 0 -4088.7899 -69.599439 Loop time of 6.475e-06 on 1 procs for 0 steps with 912 atoms 169.9% 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 | | 6.475e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6005.00 ave 6005 max 6005 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: 181268.0 ave 181268 max 181268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181268 Ave neighs/atom = 198.75877 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.155 | 5.155 | 5.155 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 -4088.7899 -4088.7899 21.255425 74.396501 5.978369 -69.599439 -69.599439 -57.383884 -91.782492 -59.63194 2.2213536 499.25236 Loop time of 6.746e-06 on 1 procs for 0 steps with 912 atoms 281.6% 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 | | 6.746e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6005.00 ave 6005 max 6005 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90634.0 ave 90634 max 90634 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181268.0 ave 181268 max 181268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181268 Ave neighs/atom = 198.75877 Neighbor list builds = 0 Dangerous builds = 0 912 -4088.78989266213 eV 2.22135364431005 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04