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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -38.167071 0.0000000) to (46.744924 38.167071 8.9139073) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9493540 5.5515739 5.9426049 Created 1318 atoms using lattice units in orthogonal box = (0.0000000 -38.167071 0.0000000) to (46.744924 38.167071 8.9139073) create_atoms CPU = 0.002 seconds 1318 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9493540 5.5515739 5.9426049 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -38.167071 0.0000000) to (46.744924 38.167071 8.9139073) create_atoms CPU = 0.002 seconds 1324 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2628 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_609260676108_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 8.144 | 8.144 | 8.144 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6327.6346 0 -6327.6346 179568.58 66 0 -8581.8321 0 -8581.8321 586.95544 Loop time of 4.4013 on 1 procs for 66 steps with 2628 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6327.63460536778 -8581.82456621524 -8581.8321049412 Force two-norm initial, final = 2829.2330 0.22866527 Force max component initial, final = 375.57765 0.0099081431 Final line search alpha, max atom move = 1.0000000 0.0099081431 Iterations, force evaluations = 66 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2286 | 4.2286 | 4.2286 | 0.0 | 96.08 Neigh | 0.13943 | 0.13943 | 0.13943 | 0.0 | 3.17 Comm | 0.016897 | 0.016897 | 0.016897 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01641 | | | 0.37 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12049.0 ave 12049 max 12049 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: 832792.0 ave 832792 max 832792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 832792 Ave neighs/atom = 316.89193 Neighbor list builds = 3 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.144 | 8.144 | 8.144 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -8581.8321 0 -8581.8321 586.95544 31806.904 69 0 -8581.9353 0 -8581.9353 -264.99212 31825.682 Loop time of 0.201385 on 1 procs for 3 steps with 2628 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 = -8581.83210494119 -8581.93221080377 -8581.93526848284 Force two-norm initial, final = 73.201299 10.522903 Force max component initial, final = 69.101823 7.7828472 Final line search alpha, max atom move = 6.5007474e-05 0.00050594324 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19859 | 0.19859 | 0.19859 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047451 | 0.00047451 | 0.00047451 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002322 | | | 1.15 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12028.0 ave 12028 max 12028 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: 832576.0 ave 832576 max 832576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 832576 Ave neighs/atom = 316.80974 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 8.282 | 8.282 | 8.282 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8581.9353 0 -8581.9353 -264.99212 Loop time of 2.002e-06 on 1 procs for 0 steps with 2628 atoms 149.9% 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 | | 2.002e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12034.0 ave 12034 max 12034 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: 832122.0 ave 832122 max 832122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 832122 Ave neighs/atom = 316.63699 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 8.282 | 8.282 | 8.282 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 -8581.9353 -8581.9353 46.703834 76.51689 8.9056962 -264.99212 -264.99212 -352.27047 -51.26076 -391.44514 2.2699246 1425.2884 Loop time of 2.669e-06 on 1 procs for 0 steps with 2628 atoms 299.7% 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 | | 2.669e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12034.0 ave 12034 max 12034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 416061.0 ave 416061 max 416061 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 832122.0 ave 832122 max 832122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 832122 Ave neighs/atom = 316.63699 Neighbor list builds = 0 Dangerous builds = 0 2628 -8581.93526848284 eV 2.26992459591288 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05