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 = 4.0496966 4.0496966 4.0496966 Created orthogonal box = (0.0000000 -80.179901 0.0000000) to (49.099961 80.179901 9.9196902) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6782268 5.7271358 6.6131268 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -80.179901 0.0000000) to (49.099961 80.179901 9.9196902) create_atoms CPU = 0.011 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6782268 5.7271358 6.6131268 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -80.179901 0.0000000) to (49.099961 80.179901 9.9196902) create_atoms CPU = 0.010 seconds 2357 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 3 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 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 4692 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_284963179498_005#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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 11.34 | 11.34 | 11.34 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14441.997 0 -14441.997 35313.056 51 0 -15782.452 0 -15782.452 1516.2934 Loop time of 4.53047 on 1 procs for 51 steps with 4692 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 = -14441.9972920831 -15782.4377479752 -15782.4516601081 Force two-norm initial, final = 1142.6151 0.28424049 Force max component initial, final = 159.16908 0.029991522 Final line search alpha, max atom move = 1.0000000 0.029991522 Iterations, force evaluations = 51 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2947 | 4.2947 | 4.2947 | 0.0 | 94.80 Neigh | 0.16971 | 0.16971 | 0.16971 | 0.0 | 3.75 Comm | 0.025898 | 0.025898 | 0.025898 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04011 | | | 0.89 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12120.0 ave 12120 max 12120 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: 603054.0 ave 603054 max 603054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603054 Ave neighs/atom = 128.52813 Neighbor list builds = 2 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.34 | 11.34 | 11.34 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -15782.452 0 -15782.452 1516.2934 78104.269 55 0 -15782.703 0 -15782.703 -0.66004768 78271.664 Loop time of 0.313271 on 1 procs for 4 steps with 4692 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 = -15782.4516601081 -15782.6887442151 -15782.7031602101 Force two-norm initial, final = 157.30709 4.3904087 Force max component initial, final = 148.51798 3.4105195 Final line search alpha, max atom move = 1.6322099e-05 5.5666838e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30397 | 0.30397 | 0.30397 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016112 | 0.0016112 | 0.0016112 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007692 | | | 2.46 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12130.0 ave 12130 max 12130 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: 610444.0 ave 610444 max 610444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610444 Ave neighs/atom = 130.10315 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 10.85 | 10.85 | 10.85 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15782.703 0 -15782.703 -0.66004768 Loop time of 6.455e-06 on 1 procs for 0 steps with 4692 atoms 216.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12135.0 ave 12135 max 12135 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: 608528.0 ave 608528 max 608528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 608528 Ave neighs/atom = 129.69480 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 10.85 | 10.85 | 10.85 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 -15782.703 -15782.703 49.058492 160.96129 9.9121741 -0.66004768 -0.66004768 -69.752435 13.21455 54.557743 2.6413342 2354.5041 Loop time of 8.119e-06 on 1 procs for 0 steps with 4692 atoms 221.7% 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 | | 8.119e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12135.0 ave 12135 max 12135 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 304264.0 ave 304264 max 304264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 608528.0 ave 608528 max 608528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 608528 Ave neighs/atom = 129.69480 Neighbor list builds = 0 Dangerous builds = 0 4692 -15782.7031602101 eV 2.64133419633507 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06