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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -40.902450 0.0000000) to (20.036234 40.902450 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3429958 4.9078550 5.9736509 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -40.902450 0.0000000) to (20.036234 40.902450 8.9604763) create_atoms CPU = 0.001 seconds 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3429958 4.9078550 5.9736509 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -40.902450 0.0000000) to (20.036234 40.902450 8.9604763) create_atoms CPU = 0.001 seconds 612 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 23 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 1188 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.019 | 5.019 | 5.019 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4576.8226 0 -4576.8226 3451.3025 76 0 -4611.3743 0 -4611.3743 -3406.8334 Loop time of 1.00163 on 1 procs for 76 steps with 1188 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 = -4576.82255957023 -4611.37175733874 -4611.3743159955 Force two-norm initial, final = 18.688125 0.14738361 Force max component initial, final = 3.6148712 0.016333408 Final line search alpha, max atom move = 1.0000000 0.016333408 Iterations, force evaluations = 76 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98988 | 0.98988 | 0.98988 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0054645 | 0.0054645 | 0.0054645 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006291 | | | 0.63 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4988.00 ave 4988 max 4988 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: 157608.0 ave 157608 max 157608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157608 Ave neighs/atom = 132.66667 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.020 | 5.020 | 5.020 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -4611.3743 0 -4611.3743 -3406.8334 14686.777 84 0 -4611.574 0 -4611.574 -5323.1637 14732.457 Loop time of 0.0751884 on 1 procs for 8 steps with 1188 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 = -4611.37431599554 -4611.57043396408 -4611.57402578407 Force two-norm initial, final = 45.779238 0.47717787 Force max component initial, final = 45.255381 0.076988361 Final line search alpha, max atom move = 0.00024607043 1.8944559e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072611 | 0.072611 | 0.072611 | 0.0 | 96.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040456 | 0.00040456 | 0.00040456 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002173 | | | 2.89 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5074.00 ave 5074 max 5074 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: 159648.0 ave 159648 max 159648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159648 Ave neighs/atom = 134.38384 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.157 | 5.157 | 5.157 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4611.574 0 -4611.574 -5323.1637 Loop time of 3.051e-06 on 1 procs for 0 steps with 1188 atoms 131.1% 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 | | 3.051e-06 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5064.00 ave 5064 max 5064 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: 159888.0 ave 159888 max 159888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159888 Ave neighs/atom = 134.58586 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.157 | 5.157 | 5.157 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 -4611.574 -4611.574 20.195117 81.8049 8.9176312 -5323.1637 -5323.1637 -8.4389907 -15957.125 -3.9271082 2.3216204 645.49443 Loop time of 2.415e-06 on 1 procs for 0 steps with 1188 atoms 248.4% 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 | | 2.415e-06 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5064.00 ave 5064 max 5064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79944.0 ave 79944 max 79944 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159888.0 ave 159888 max 159888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159888 Ave neighs/atom = 134.58586 Neighbor list builds = 0 Dangerous builds = 0 1188 -4443.56513657514 eV 2.32162035764342 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01