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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -30.611336 0.0000000) to (21.643456 30.611336 4.0541907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9362268 4.8329161 4.0541907 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -30.611336 0.0000000) to (21.643456 30.611336 4.0541907) create_atoms CPU = 0.001 seconds 229 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9362268 4.8329161 4.0541907 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -30.611336 0.0000000) to (21.643456 30.611336 4.0541907) create_atoms CPU = 0.001 seconds 229 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 455 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1787.0946 0 -1787.0946 90390.995 159 0 -1932.961 0 -1932.961 2929.8983 Loop time of 1.0538 on 1 procs for 159 steps with 455 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 = -1787.09464201304 -1932.95923842393 -1932.96102142229 Force two-norm initial, final = 232.20844 0.19465936 Force max component initial, final = 43.236521 0.064705429 Final line search alpha, max atom move = 1.0000000 0.064705429 Iterations, force evaluations = 159 298 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0211 | 1.0211 | 1.0211 | 0.0 | 96.90 Neigh | 0.0171 | 0.0171 | 0.0171 | 0.0 | 1.62 Comm | 0.009148 | 0.009148 | 0.009148 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006407 | | | 0.61 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3925.00 ave 3925 max 3925 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: 75596.0 ave 75596 max 75596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75596 Ave neighs/atom = 166.14505 Neighbor list builds = 4 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 159 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 159 0 -1932.961 0 -1932.961 2929.8983 5372.0872 162 0 -1932.9966 0 -1932.9966 3091.4192 5371.6457 Loop time of 0.0213911 on 1 procs for 3 steps with 455 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 = -1932.9610214223 -1932.99653631581 -1932.99658020039 Force two-norm initial, final = 27.207003 1.2136783 Force max component initial, final = 20.116934 0.86253476 Final line search alpha, max atom move = 0.022075189 0.019040618 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020575 | 0.020575 | 0.020575 | 0.0 | 96.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001673 | 0.0001673 | 0.0001673 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006492 | | | 3.03 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3925.00 ave 3925 max 3925 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: 75610.0 ave 75610 max 75610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75610 Ave neighs/atom = 166.17582 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1932.9966 0 -1932.9966 3091.4192 Loop time of 1.578e-06 on 1 procs for 0 steps with 455 atoms 190.1% 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 | | 1.578e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3925.00 ave 3925 max 3925 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: 75610.0 ave 75610 max 75610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75610 Ave neighs/atom = 166.17582 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.611 | 4.611 | 4.611 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 -1932.9966 -1932.9966 21.682665 61.222671 4.0465267 3091.4192 3091.4192 257.73041 8775.444 241.08315 2.3040904 388.37457 Loop time of 1.508e-06 on 1 procs for 0 steps with 455 atoms 132.6% 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 | | 1.508e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3925.00 ave 3925 max 3925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37805.0 ave 37805 max 37805 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75610.0 ave 75610 max 75610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75610 Ave neighs/atom = 166.17582 Neighbor list builds = 0 Dangerous builds = 0 455 -1932.99658020039 eV 2.30409036865931 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01