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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -47.274126 0.0000000) to (33.425307 47.274126 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2186617 6.0462295 5.0973115 Created 692 atoms using lattice units in orthogonal box = (0.0000000 -47.274126 0.0000000) to (33.425307 47.274126 5.0973115) create_atoms CPU = 0.002 seconds 692 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2186617 6.0462295 5.0973115 Created 692 atoms using lattice units in orthogonal box = (0.0000000 -47.274126 0.0000000) to (33.425307 47.274126 5.0973115) create_atoms CPU = 0.001 seconds 692 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 31 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1360 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.052 | 5.052 | 5.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5736.5143 0 -5736.5143 -4923.7431 624 0 -5797.1381 0 -5797.1381 -28624.959 Loop time of 64.3062 on 1 procs for 624 steps with 1360 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 = -5736.51425395307 -5797.13302047966 -5797.13807754622 Force two-norm initial, final = 10.822954 0.20652562 Force max component initial, final = 2.0490204 0.046418483 Final line search alpha, max atom move = 1.0000000 0.046418483 Iterations, force evaluations = 624 1129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 63.969 | 63.969 | 63.969 | 0.0 | 99.48 Neigh | 0.1999 | 0.1999 | 0.1999 | 0.0 | 0.31 Comm | 0.068554 | 0.068554 | 0.068554 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06847 | | | 0.11 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5751.00 ave 5751 max 5751 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: 90050.0 ave 90050 max 90050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90050 Ave neighs/atom = 66.213235 Neighbor list builds = 26 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 624 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.673 | 4.673 | 4.673 Mbytes Step Temp E_pair E_mol TotEng Press Volume 624 0 -5797.1381 0 -5797.1381 -28624.959 16109.055 652 0 -5807.0002 0 -5807.0002 5280.6578 15758.468 Loop time of 4.10718 on 1 procs for 28 steps with 1360 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 = -5797.13807754622 -5807.00005064418 -5807.00015430873 Force two-norm initial, final = 734.07104 1.5195692 Force max component initial, final = 726.79444 0.96783861 Final line search alpha, max atom move = 0.00073257778 0.00070901705 Iterations, force evaluations = 28 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0908 | 4.0908 | 4.0908 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025093 | 0.0025093 | 0.0025093 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01388 | | | 0.34 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5750.00 ave 5750 max 5750 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: 90034.0 ave 90034 max 90034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90034 Ave neighs/atom = 66.201471 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5807.0002 0 -5807.0002 5280.6578 Loop time of 2.125e-06 on 1 procs for 0 steps with 1360 atoms 188.2% 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 | | 2.125e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5887.00 ave 5887 max 5887 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: 90630.0 ave 90630 max 90630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90630 Ave neighs/atom = 66.639706 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.813 | 4.813 | 4.813 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 -5807.0002 -5807.0002 33.601541 94.548252 4.9602242 5280.6578 5280.6578 -98.919767 15987.661 -46.767506 2.3025845 2344.1666 Loop time of 2.092e-06 on 1 procs for 0 steps with 1360 atoms 191.2% 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 | | 2.092e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5887.00 ave 5887 max 5887 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45315.0 ave 45315 max 45315 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90630.0 ave 90630 max 90630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90630 Ave neighs/atom = 66.639706 Neighbor list builds = 0 Dangerous builds = 0 1360 -5807.00015430873 eV 2.30258453067519 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:08