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 = 3.5240105 3.5240105 3.5240105 Created orthogonal box = (0.0000000 -49.587223 0.0000000) to (11.687821 49.587223 4.9837035) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3126457 6.0105725 4.9837035 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -49.587223 0.0000000) to (11.687821 49.587223 4.9837035) create_atoms CPU = 0.003 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3126457 6.0105725 4.9837035 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -49.587223 0.0000000) to (11.687821 49.587223 4.9837035) create_atoms CPU = 0.003 seconds 266 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 524 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_535504325462_003#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2347.8546 0 -2347.8546 3257.7779 73 0 -2365.3697 0 -2365.3697 -3389.9678 Loop time of 1.58344 on 1 procs for 73 steps with 524 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2347.8546335125 -2365.36768659983 -2365.36972556005 Force two-norm initial, final = 28.766552 0.14770064 Force max component initial, final = 10.129470 0.018712292 Final line search alpha, max atom move = 1.0000000 0.018712292 Iterations, force evaluations = 73 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5402 | 1.5402 | 1.5402 | 0.0 | 97.27 Neigh | 0.012789 | 0.012789 | 0.012789 | 0.0 | 0.81 Comm | 0.017966 | 0.017966 | 0.017966 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01249 | | | 0.79 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5464.00 ave 5464 max 5464 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: 91328.0 ave 91328 max 91328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91328 Ave neighs/atom = 174.29008 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -2365.3697 0 -2365.3697 -3389.9678 5776.7758 75 0 -2365.3852 0 -2365.3852 -3.2801281 5765.8438 Loop time of 0.0554426 on 1 procs for 2 steps with 524 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 = -2365.36972556006 -2365.38363809583 -2365.3852033008 Force two-norm initial, final = 22.412747 0.90225709 Force max component initial, final = 16.251745 0.69392359 Final line search alpha, max atom move = 0.00023532790 0.00016329958 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053327 | 0.053327 | 0.053327 | 0.0 | 96.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054569 | 0.00054569 | 0.00054569 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00157 | | | 2.83 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5480.00 ave 5480 max 5480 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: 91208.0 ave 91208 max 91208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91208 Ave neighs/atom = 174.06107 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 4.687 | 4.687 | 4.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2365.3852 0 -2365.3852 -3.2801281 Loop time of 6.335e-06 on 1 procs for 0 steps with 524 atoms 157.9% 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 | | 6.335e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5498.00 ave 5498 max 5498 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: 91216.0 ave 91216 max 91216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91216 Ave neighs/atom = 174.07634 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 4.687 | 4.687 | 4.687 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 -2365.3852 -2365.3852 11.67339 99.08868 4.9847324 -3.2801281 -3.2801281 -141.55154 192.65638 -60.945222 2.2857647 249.62357 Loop time of 7.026e-06 on 1 procs for 0 steps with 524 atoms 256.2% 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 | | 7.026e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5498.00 ave 5498 max 5498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45608.0 ave 45608 max 45608 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91216.0 ave 91216 max 91216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91216 Ave neighs/atom = 174.07634 Neighbor list builds = 0 Dangerous builds = 0 524 -2365.3852033008 eV 2.285764729244 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01