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 -31.646417 0.0000000) to (6.4592081 31.646417 7.0757080) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8755249 4.2191371 4.7171386 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -31.646417 0.0000000) to (6.4592081 31.646417 7.0757080) create_atoms CPU = 0.001 seconds 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8755249 4.2191371 4.7171386 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -31.646417 0.0000000) to (6.4592081 31.646417 7.0757080) create_atoms CPU = 0.000 seconds 122 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 = 3 24 3 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 8 atoms, new total = 236 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 = 3 24 3 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) = 4.403 | 4.403 | 4.403 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -973.05095 0 -973.05095 -6712.6994 45 0 -978.95573 0 -978.95573 -19292.733 Loop time of 1.28076 on 1 procs for 45 steps with 236 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 = -973.050953262641 -978.954928140088 -978.955726172425 Force two-norm initial, final = 11.076323 0.10873332 Force max component initial, final = 3.2320025 0.017737525 Final line search alpha, max atom move = 1.0000000 0.017737525 Iterations, force evaluations = 45 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2784 | 1.2784 | 1.2784 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001154 | 0.001154 | 0.001154 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001182 | | | 0.09 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1757.00 ave 1757 max 1757 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: 13392.0 ave 13392 max 13392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13392 Ave neighs/atom = 56.745763 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 = 3 24 3 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 : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -978.95573 0 -978.95573 -19292.733 2892.7021 54 0 -979.1932 0 -979.1932 -190.12421 2861.4729 Loop time of 0.175686 on 1 procs for 9 steps with 236 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 = -978.955726172425 -979.192963254827 -979.193200883008 Force two-norm initial, final = 57.754789 1.2558614 Force max component initial, final = 47.639758 0.93012928 Final line search alpha, max atom move = 0.0011147148 0.0010368289 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17486 | 0.17486 | 0.17486 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014947 | 0.00014947 | 0.00014947 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006725 | | | 0.38 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1675.00 ave 1675 max 1675 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: 13520.0 ave 13520 max 13520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13520 Ave neighs/atom = 57.288136 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 = 3 24 3 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) = 4.540 | 4.540 | 4.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -979.1932 0 -979.1932 -190.12421 Loop time of 1.529e-06 on 1 procs for 0 steps with 236 atoms 130.8% 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 | | 1.529e-06 | | |100.00 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1675.00 ave 1675 max 1675 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: 13532.0 ave 13532 max 13532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13532 Ave neighs/atom = 57.338983 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 = 3 24 3 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) = 4.540 | 4.540 | 4.540 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 -979.1932 -979.1932 6.4101466 63.292833 7.0528906 -190.12421 -190.12421 -74.83964 23.579268 -519.11225 2.3115004 230.53275 Loop time of 1.362e-06 on 1 procs for 0 steps with 236 atoms 146.8% 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 | | 1.362e-06 | | |100.00 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1675.00 ave 1675 max 1675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6766.00 ave 6766 max 6766 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13532.0 ave 13532 max 13532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13532 Ave neighs/atom = 57.338983 Neighbor list builds = 0 Dangerous builds = 0 236 -979.193200883008 eV 2.31150039021813 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01