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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -38.427995 0.0000000) to (38.427995 38.427995 3.6150017) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1010613 5.1010613 3.6150017 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -38.427995 0.0000000) to (38.427995 38.427995 3.6150017) create_atoms CPU = 0.002 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1010613 5.1010613 3.6150017 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.427995 0.0000000) to (38.427995 38.427995 3.6150017) create_atoms CPU = 0.002 seconds 454 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 19 1 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3037.8692 0 -3037.8692 47968.691 75 0 -3199.489 0 -3199.489 7426.0016 Loop time of 3.00311 on 1 procs for 75 steps with 906 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 = -3037.86916864965 -3199.48616793271 -3199.48895245992 Force two-norm initial, final = 156.27892 0.15952168 Force max component initial, final = 24.900590 0.025540264 Final line search alpha, max atom move = 1.0000000 0.025540264 Iterations, force evaluations = 75 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9073 | 2.9073 | 2.9073 | 0.0 | 96.81 Neigh | 0.051588 | 0.051588 | 0.051588 | 0.0 | 1.72 Comm | 0.026328 | 0.026328 | 0.026328 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01791 | | | 0.60 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8652.00 ave 8652 max 8652 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: 188576.0 ave 188576 max 188576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188576 Ave neighs/atom = 208.14128 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.013 | 5.013 | 5.013 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -3199.489 0 -3199.489 7426.0016 10676.624 81 0 -3199.7005 0 -3199.7005 -6.3877866 10732.412 Loop time of 0.207446 on 1 procs for 6 steps with 906 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 = -3199.48895245993 -3199.70005777571 -3199.70053759959 Force two-norm initial, final = 95.519131 0.54000270 Force max component initial, final = 79.123526 0.36472623 Final line search alpha, max atom move = 0.00023458992 8.5561097e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20089 | 0.20089 | 0.20089 | 0.0 | 96.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016279 | 0.0016279 | 0.0016279 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004933 | | | 2.38 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8670.00 ave 8670 max 8670 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: 188432.0 ave 188432 max 188432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188432 Ave neighs/atom = 207.98234 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.150 | 5.150 | 5.150 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3199.7005 0 -3199.7005 -6.3877866 Loop time of 6.505e-06 on 1 procs for 0 steps with 906 atoms 184.5% 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 | | 6.505e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8664.00 ave 8664 max 8664 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: 186848.0 ave 186848 max 186848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186848 Ave neighs/atom = 206.23400 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.150 | 5.150 | 5.150 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 -3199.7005 -3199.7005 38.38507 77.199501 3.6217672 -6.3877866 -6.3877866 -30.6785 -43.034516 54.549656 2.3056967 142.85107 Loop time of 7.177e-06 on 1 procs for 0 steps with 906 atoms 292.6% 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 | | 7.177e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8664.00 ave 8664 max 8664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93424.0 ave 93424 max 93424 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186848.0 ave 186848 max 186848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186848 Ave neighs/atom = 206.23400 Neighbor list builds = 0 Dangerous builds = 0 906 -3199.70053759959 eV 2.30569665327593 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03