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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -42.112284 0.0000000) to (14.888941 42.112284 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1307403 6.1929830 5.1068646 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.112284 0.0000000) to (14.888941 42.112284 5.1068646) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1307403 6.1929830 5.1068646 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.112284 0.0000000) to (14.888941 42.112284 5.1068646) create_atoms CPU = 0.001 seconds 274 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_150993986463_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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2202.0691 0 -2202.0691 43535.029 462 0 -2314.6787 0 -2314.6787 3704.0993 Loop time of 19.8336 on 1 procs for 462 steps with 544 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 = -2202.06912617754 -2314.67666451501 -2314.67869096947 Force two-norm initial, final = 217.69574 0.14160464 Force max component initial, final = 75.389096 0.021857765 Final line search alpha, max atom move = 1.0000000 0.021857765 Iterations, force evaluations = 462 909 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.736 | 19.736 | 19.736 | 0.0 | 99.51 Neigh | 0.035535 | 0.035535 | 0.035535 | 0.0 | 0.18 Comm | 0.033661 | 0.033661 | 0.033661 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02862 | | | 0.14 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3193.00 ave 3193 max 3193 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: 36238.0 ave 36238 max 36238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36238 Ave neighs/atom = 66.613971 Neighbor list builds = 10 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 462 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 462 0 -2314.6787 0 -2314.6787 3704.0993 6404.0828 486 0 -2318.2472 0 -2318.2472 45.578115 6412.7993 Loop time of 0.526824 on 1 procs for 24 steps with 544 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 = -2314.67869096947 -2318.2469810186 -2318.2471676272 Force two-norm initial, final = 232.13430 1.3717344 Force max component initial, final = 165.59387 1.0268974 Final line search alpha, max atom move = 0.0016932256 0.0017387690 Iterations, force evaluations = 24 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52182 | 0.52182 | 0.52182 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079016 | 0.00079016 | 0.00079016 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004219 | | | 0.80 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3238.00 ave 3238 max 3238 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: 36172.0 ave 36172 max 36172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36172 Ave neighs/atom = 66.492647 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 ghost atom cutoff = 6 binsize = 3, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2318.2472 0 -2318.2472 45.578115 Loop time of 1.809e-06 on 1 procs for 0 steps with 544 atoms 165.8% 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 | | 1.809e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3251.00 ave 3251 max 3251 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: 36168.0 ave 36168 max 36168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36168 Ave neighs/atom = 66.485294 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 ghost atom cutoff = 6 binsize = 3, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.633 | 4.633 | 4.633 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 -2318.2472 -2318.2472 15.181278 84.609433 4.9925284 45.578115 45.578115 -53.828399 257.73284 -67.170093 2.3485174 990.96135 Loop time of 1.987e-06 on 1 procs for 0 steps with 544 atoms 151.0% 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 | | 1.987e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3251.00 ave 3251 max 3251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18084.0 ave 18084 max 18084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36168.0 ave 36168 max 36168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36168 Ave neighs/atom = 66.485294 Neighbor list builds = 0 Dangerous builds = 0 544 -2318.2471676272 eV 2.34851735099618 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20