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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -53.667675 0.0000000) to (32.864605 53.667675 9.9090513) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9753827 6.0985995 6.6060342 Created 1047 atoms using lattice units in orthogonal box = (0.0000000 -53.667675 0.0000000) to (32.864605 53.667675 9.9090513) create_atoms CPU = 0.002 seconds 1047 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9753827 6.0985995 6.6060342 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -53.667675 0.0000000) to (32.864605 53.667675 9.9090513) create_atoms CPU = 0.001 seconds 1071 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 35 4 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 2111 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 35 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7068.3017 0 -7068.3017 2340.9749 41 0 -7081.3775 0 -7081.3775 1579.2605 Loop time of 4.55346 on 1 procs for 41 steps with 2111 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 = -7068.30174156576 -7081.37231354861 -7081.37751441074 Force two-norm initial, final = 12.817042 0.13301281 Force max component initial, final = 1.4189270 0.0079723900 Final line search alpha, max atom move = 1.0000000 0.0079723900 Iterations, force evaluations = 41 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5402 | 4.5402 | 4.5402 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0047149 | 0.0047149 | 0.0047149 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008553 | | | 0.19 Nlocal: 2111.00 ave 2111 max 2111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5249.00 ave 5249 max 5249 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: 114882.0 ave 114882 max 114882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114882 Ave neighs/atom = 54.420654 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 35 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -7081.3775 0 -7081.3775 1579.2605 34954.514 47 0 -7081.6122 0 -7081.6122 90.238322 35023.208 Loop time of 0.452258 on 1 procs for 6 steps with 2111 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 = -7081.37751441073 -7081.61061871488 -7081.61220910341 Force two-norm initial, final = 90.830997 3.4832319 Force max component initial, final = 89.726643 2.5183065 Final line search alpha, max atom move = 0.00023029946 0.00057996463 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44926 | 0.44926 | 0.44926 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037106 | 0.00037106 | 0.00037106 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002631 | | | 0.58 Nlocal: 2111.00 ave 2111 max 2111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5518.00 ave 5518 max 5518 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: 114036.0 ave 114036 max 114036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114036 Ave neighs/atom = 54.019896 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 35 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.181 | 5.181 | 5.181 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7081.6122 0 -7081.6122 90.238322 Loop time of 1.959e-06 on 1 procs for 0 steps with 2111 atoms 153.1% 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 | | 1.959e-06 | | |100.00 Nlocal: 2111.00 ave 2111 max 2111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5518.00 ave 5518 max 5518 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: 114036.0 ave 114036 max 114036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114036 Ave neighs/atom = 54.019896 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 11 35 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.181 | 5.181 | 5.181 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 -7081.6122 -7081.6122 32.788347 107.90823 9.8987839 90.238322 90.238322 74.588432 115.81766 80.308871 2.6840799 882.92222 Loop time of 2.181e-06 on 1 procs for 0 steps with 2111 atoms 229.3% 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 | | 2.181e-06 | | |100.00 Nlocal: 2111.00 ave 2111 max 2111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5518.00 ave 5518 max 5518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57018.0 ave 57018 max 57018 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114036.0 ave 114036 max 114036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114036 Ave neighs/atom = 54.019896 Neighbor list builds = 0 Dangerous builds = 0 2111 -7081.61220910341 eV 2.68407994787506 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05