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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -49.578464 0.0000000) to (13.493549 49.578464 8.8336012) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7829495 5.5087182 5.8890675 Created 504 atoms using lattice units in orthogonal box = (0.0000000 -49.578464 0.0000000) to (13.493549 49.578464 8.8336012) create_atoms CPU = 0.002 seconds 504 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7829495 5.5087182 5.8890675 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -49.578464 0.0000000) to (13.493549 49.578464 8.8336012) create_atoms CPU = 0.001 seconds 508 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 17 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1008 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.206 | 7.206 | 7.206 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4046.7819 0 -4046.7819 37778.736 65 0 -4214.2944 0 -4214.2944 6354.1906 Loop time of 3.47712 on 1 procs for 65 steps with 1008 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 = -4046.78194499722 -4214.29034550788 -4214.29439662302 Force two-norm initial, final = 216.86996 0.27408716 Force max component initial, final = 46.952124 0.036911986 Final line search alpha, max atom move = 1.0000000 0.036911986 Iterations, force evaluations = 65 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4192 | 3.4192 | 3.4192 | 0.0 | 98.34 Neigh | 0.032185 | 0.032185 | 0.032185 | 0.0 | 0.93 Comm | 0.017077 | 0.017077 | 0.017077 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008631 | | | 0.25 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11846.0 ave 11846 max 11846 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: 624544.0 ave 624544 max 624544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 624544 Ave neighs/atom = 619.58730 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.208 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -4214.2944 0 -4214.2944 6354.1906 11819.171 68 0 -4214.4158 0 -4214.4158 233.57275 11861.112 Loop time of 0.141251 on 1 procs for 3 steps with 1008 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 = -4214.29439662302 -4214.41185249202 -4214.4157521329 Force two-norm initial, final = 88.909371 3.3765249 Force max component initial, final = 66.155677 2.9141575 Final line search alpha, max atom move = 8.0486910e-05 0.00023455153 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13889 | 0.13889 | 0.13889 | 0.0 | 98.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048872 | 0.00048872 | 0.00048872 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001876 | | | 1.33 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12074.0 ave 12074 max 12074 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: 625656.0 ave 625656 max 625656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 625656 Ave neighs/atom = 620.69048 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.346 | 7.346 | 7.346 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4214.4158 0 -4214.4158 233.57275 Loop time of 2.595e-06 on 1 procs for 0 steps with 1008 atoms 0.0% 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 | | 2.595e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12074.0 ave 12074 max 12074 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: 621968.0 ave 621968 max 621968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621968 Ave neighs/atom = 617.03175 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.346 | 7.346 | 7.346 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 -4214.4158 -4214.4158 13.522374 99.332689 8.8303978 233.57275 233.57275 202.34355 394.33662 104.03809 2.3194137 372.01018 Loop time of 2.382e-06 on 1 procs for 0 steps with 1008 atoms 251.9% 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 | | 2.382e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12074.0 ave 12074 max 12074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 310984.0 ave 310984 max 310984 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 621968.0 ave 621968 max 621968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621968 Ave neighs/atom = 617.03175 Neighbor list builds = 0 Dangerous builds = 0 1008 -4214.4157521329 eV 2.31941369543716 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04