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 -59.518141 0.0000000) to (21.042841 59.518141 5.7271358) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4555513 6.6131268 5.7271358 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.518141 0.0000000) to (21.042841 59.518141 5.7271358) create_atoms CPU = 0.004 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4555513 6.6131268 5.7271358 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.518141 0.0000000) to (21.042841 59.518141 5.7271358) create_atoms CPU = 0.004 seconds 434 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 = 6 32 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 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 860 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 = 6 32 2 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) = 4.976 | 4.976 | 4.976 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2731.4268 0 -2731.4268 30333.145 87 0 -2892.2299 0 -2892.2299 755.53483 Loop time of 1.81243 on 1 procs for 87 steps with 860 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 = -2731.42675108091 -2892.22745184896 -2892.2299403097 Force two-norm initial, final = 308.61452 0.11410802 Force max component initial, final = 85.531311 0.014838228 Final line search alpha, max atom move = 1.0000000 0.014838228 Iterations, force evaluations = 87 161 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.739 | 1.739 | 1.739 | 0.0 | 95.95 Neigh | 0.031168 | 0.031168 | 0.031168 | 0.0 | 1.72 Comm | 0.022769 | 0.022769 | 0.022769 | 0.0 | 1.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01948 | | | 1.07 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5370.00 ave 5370 max 5370 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: 109148.0 ave 109148 max 109148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109148 Ave neighs/atom = 126.91628 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 = 6 32 2 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 : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.977 | 4.977 | 4.977 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -2892.2299 0 -2892.2299 755.53483 14345.682 90 0 -2892.2517 0 -2892.2517 -59.01734 14360.638 Loop time of 0.0558699 on 1 procs for 3 steps with 860 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 = -2892.2299403097 -2892.25112023968 -2892.25173594293 Force two-norm initial, final = 18.370423 2.0606060 Force max component initial, final = 18.162374 1.2871252 Final line search alpha, max atom move = 0.00024173753 0.00031114646 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053186 | 0.053186 | 0.053186 | 0.0 | 95.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068633 | 0.00068633 | 0.00068633 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001997 | | | 3.57 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5444.00 ave 5444 max 5444 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: 111468.0 ave 111468 max 111468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111468 Ave neighs/atom = 129.61395 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 = 6 32 2 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) = 5.115 | 5.115 | 5.115 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2892.2517 0 -2892.2517 -59.01734 Loop time of 6.515e-06 on 1 procs for 0 steps with 860 atoms 199.5% 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 | | 6.515e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5444.00 ave 5444 max 5444 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: 111208.0 ave 111208 max 111208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111208 Ave neighs/atom = 129.31163 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 = 6 32 2 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) = 5.115 | 5.115 | 5.115 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 -2892.2517 -2892.2517 21.035053 119.30361 5.7223779 -59.01734 -59.01734 -142.31036 108.74003 -143.48169 2.6611697 597.79295 Loop time of 7.057e-06 on 1 procs for 0 steps with 860 atoms 269.2% 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 | | 7.057e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5444.00 ave 5444 max 5444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55604.0 ave 55604 max 55604 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111208.0 ave 111208 max 111208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111208 Ave neighs/atom = 129.31163 Neighbor list builds = 0 Dangerous builds = 0 860 -2892.25173594293 eV 2.66116968998579 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02