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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -33.446406 0.0000000) to (23.650180 33.446406 4.6834336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1735613 5.2464950 4.6834336 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -33.446406 0.0000000) to (23.650180 33.446406 4.6834336) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1735613 5.2464950 4.6834336 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -33.446406 0.0000000) to (23.650180 33.446406 4.6834336) create_atoms CPU = 0.001 seconds 410 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 18 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 818 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_255315407910_000#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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.974 | 4.974 | 4.974 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2735.8656 0 -2735.8656 214888.25 126 0 -3170.5616 0 -3170.5616 230320.06 Loop time of 2.19648 on 1 procs for 126 steps with 818 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 = -2735.8655553063 -3170.55888853708 -3170.56155174319 Force two-norm initial, final = 544.71161 0.31798784 Force max component initial, final = 120.44804 0.051260843 Final line search alpha, max atom move = 0.61068594 0.031304276 Iterations, force evaluations = 126 245 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1582 | 2.1582 | 2.1582 | 0.0 | 98.26 Neigh | 0.0101 | 0.0101 | 0.0101 | 0.0 | 0.46 Comm | 0.015889 | 0.015889 | 0.015889 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01232 | | | 0.56 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6111.00 ave 6111 max 6111 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: 158496.0 ave 158496 max 158496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158496 Ave neighs/atom = 193.76039 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 126 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.975 | 4.975 | 4.975 Mbytes Step Temp E_pair E_mol TotEng Press Volume 126 0 -3170.5616 0 -3170.5616 230320.06 7409.3187 1126 0 -3294.5009 0 -3294.5009 -1110.0316 9193.5034 Loop time of 9.19398 on 1 procs for 1000 steps with 818 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3170.56155174318 -3294.40657089608 -3294.50089088686 Force two-norm initial, final = 1882.8355 13.985410 Force max component initial, final = 1245.4655 9.3902586 Final line search alpha, max atom move = 0.00020800699 0.0019532394 Iterations, force evaluations = 1000 1155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.722 | 8.722 | 8.722 | 0.0 | 94.87 Neigh | 0.1365 | 0.1365 | 0.1365 | 0.0 | 1.48 Comm | 0.055673 | 0.055673 | 0.055673 | 0.0 | 0.61 Output | 7.723e-05 | 7.723e-05 | 7.723e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2797 | | | 3.04 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5361.00 ave 5361 max 5361 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: 128424.0 ave 128424 max 128424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128424 Ave neighs/atom = 156.99756 Neighbor list builds = 15 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.108 | 5.108 | 5.108 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3294.5009 0 -3294.5009 -1110.0316 Loop time of 2.498e-06 on 1 procs for 0 steps with 818 atoms 200.2% 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 | | 2.498e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5368.00 ave 5368 max 5368 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: 128364.0 ave 128364 max 128364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128364 Ave neighs/atom = 156.92421 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.108 | 5.108 | 5.108 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 -3294.5009 -3294.5009 21.277017 77.15697 5.6000916 -1110.0316 -1110.0316 -1472.2554 -1098.8447 -758.99483 2.2871556 1280.8674 Loop time of 2.364e-06 on 1 procs for 0 steps with 818 atoms 253.8% 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 | | 2.364e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5368.00 ave 5368 max 5368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64182.0 ave 64182 max 64182 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128364.0 ave 128364 max 128364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128364 Ave neighs/atom = 156.92421 Neighbor list builds = 0 Dangerous builds = 0 818 -3294.50089088686 eV 2.28715562035963 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12