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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -71.453534 0.0000000) to (41.253717 71.453534 7.0065955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3467257 6.4124966 7.0065955 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -71.453534 0.0000000) to (41.253717 71.453534 7.0065955) create_atoms CPU = 0.009 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3467257 6.4124966 7.0065955 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -71.453534 0.0000000) to (41.253717 71.453534 7.0065955) create_atoms CPU = 0.009 seconds 1250 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 34 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2494 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_106969701023_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.129 | 6.129 | 6.129 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8220.2468 0 -8220.2468 18964.123 107 0 -8486.1563 0 -8486.1563 3500.2763 Loop time of 8.00165 on 1 procs for 107 steps with 2494 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 = -8220.24684301511 -8486.14788398007 -8486.15633780785 Force two-norm initial, final = 293.78845 0.19626936 Force max component initial, final = 66.387324 0.018358916 Final line search alpha, max atom move = 1.0000000 0.018358916 Iterations, force evaluations = 107 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6292 | 7.6292 | 7.6292 | 0.0 | 95.35 Neigh | 0.27516 | 0.27516 | 0.27516 | 0.0 | 3.44 Comm | 0.049232 | 0.049232 | 0.049232 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04807 | | | 0.60 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11317.0 ave 11317 max 11317 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: 353308.0 ave 353308 max 353308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 353308 Ave neighs/atom = 141.66319 Neighbor list builds = 5 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.143 | 6.143 | 6.143 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -8486.1563 0 -8486.1563 3500.2763 41307.018 113 0 -8486.5487 0 -8486.5487 -117.33247 41492.073 Loop time of 0.366876 on 1 procs for 6 steps with 2494 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 = -8486.15633780784 -8486.54719827826 -8486.54869298105 Force two-norm initial, final = 176.82987 6.6365743 Force max component initial, final = 157.40619 4.9307557 Final line search alpha, max atom move = 0.00010135139 0.00049973894 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35696 | 0.35696 | 0.35696 | 0.0 | 97.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021411 | 0.0021411 | 0.0021411 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007772 | | | 2.12 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11941.0 ave 11941 max 11941 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: 351370.0 ave 351370 max 351370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 351370 Ave neighs/atom = 140.88613 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.281 | 6.281 | 6.281 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8486.5487 0 -8486.5487 -117.33247 Loop time of 6.826e-06 on 1 procs for 0 steps with 2494 atoms 161.1% 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 | | 6.826e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11941.0 ave 11941 max 11941 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: 350804.0 ave 350804 max 350804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350804 Ave neighs/atom = 140.65918 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.281 | 6.281 | 6.281 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 -8486.5487 -8486.5487 41.24733 143.66496 7.0019411 -117.33247 -117.33247 -190.36691 9.2377219 -170.86821 2.5098613 1213.1988 Loop time of 6.776e-06 on 1 procs for 0 steps with 2494 atoms 280.4% 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 | | 6.776e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11941.0 ave 11941 max 11941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 175402.0 ave 175402 max 175402 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 350804.0 ave 350804 max 350804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350804 Ave neighs/atom = 140.65918 Neighbor list builds = 0 Dangerous builds = 0 2494 -8486.54869298105 eV 2.50986125166193 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09