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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -35.730574 0.0000000) to (11.910191 35.730574 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5029974 3.5029974 2.8886457 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -35.730574 0.0000000) to (11.910191 35.730574 2.8886457) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5029974 3.5029974 2.8886457 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -35.730574 0.0000000) to (11.910191 35.730574 2.8886457) create_atoms CPU = 0.001 seconds 103 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 27 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 205 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.384 | 4.384 | 4.384 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -805.56388 0 -805.56388 64038.827 52 0 -851.20369 0 -851.20369 16225.628 Loop time of 3.5694 on 1 procs for 52 steps with 205 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 = -805.563882168606 -851.202921127436 -851.203685714182 Force two-norm initial, final = 89.023975 0.12384313 Force max component initial, final = 36.220694 0.045014570 Final line search alpha, max atom move = 1.0000000 0.045014570 Iterations, force evaluations = 52 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5616 | 3.5616 | 3.5616 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043169 | 0.0043169 | 0.0043169 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00352 | | | 0.10 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1821.00 ave 1821 max 1821 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: 11852.0 ave 11852 max 11852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11852 Ave neighs/atom = 57.814634 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.384 | 4.384 | 4.384 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -851.20369 0 -851.20369 16225.628 2458.5724 67 0 -851.49616 0 -851.49616 -122.65347 2479.5672 Loop time of 0.630158 on 1 procs for 15 steps with 205 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 = -851.203685714182 -851.495432783277 -851.496155178601 Force two-norm initial, final = 50.960793 0.88729575 Force max component initial, final = 47.064627 0.42375235 Final line search alpha, max atom move = 0.0013128362 0.00055631740 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61319 | 0.61319 | 0.61319 | 0.0 | 97.31 Neigh | 0.013649 | 0.013649 | 0.013649 | 0.0 | 2.17 Comm | 0.00075645 | 0.00075645 | 0.00075645 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002561 | | | 0.41 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1813.00 ave 1813 max 1813 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: 11756.0 ave 11756 max 11756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11756 Ave neighs/atom = 57.346341 Neighbor list builds = 1 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -851.49616 0 -851.49616 -122.65347 Loop time of 6.014e-06 on 1 procs for 0 steps with 205 atoms 166.3% 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 | | 6.014e-06 | | |100.00 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1813.00 ave 1813 max 1813 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: 11756.0 ave 11756 max 11756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11756 Ave neighs/atom = 57.346341 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.522 | 4.522 | 4.522 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 -851.49616 -851.49616 11.901704 72.48692 2.8741345 -122.65347 -122.65347 -273.61317 -222.00313 127.6559 2.356064 131.60038 Loop time of 8.139e-06 on 1 procs for 0 steps with 205 atoms 417.7% 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 | | 8.139e-06 | | |100.00 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1813.00 ave 1813 max 1813 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5878.00 ave 5878 max 5878 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11756.0 ave 11756 max 11756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11756 Ave neighs/atom = 57.346341 Neighbor list builds = 0 Dangerous builds = 0 205 -851.496155178601 eV 2.35606395766586 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04