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 = 4.0500004 4.0500004 4.0500004 Created orthogonal box = (0.0000000 -43.246221 0.0000000) to (24.965879 43.246221 7.0148065) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5699682 6.0690767 7.0148065 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.246221 0.0000000) to (24.965879 43.246221 7.0148065) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5699682 6.0690767 7.0148065 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.246221 0.0000000) to (24.965879 43.246221 7.0148065) create_atoms CPU = 0.001 seconds 458 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 23 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 898 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_820335782779_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.983 | 4.983 | 4.983 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2987.223 0 -2987.223 3444.879 80 0 -3006.3939 0 -3006.3939 -3529.5774 Loop time of 0.882099 on 1 procs for 80 steps with 898 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2987.22301947648 -3006.39116416459 -3006.39389726242 Force two-norm initial, final = 21.396477 0.16404628 Force max component initial, final = 4.7003076 0.051184733 Final line search alpha, max atom move = 1.0000000 0.051184733 Iterations, force evaluations = 80 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85587 | 0.85587 | 0.85587 | 0.0 | 97.03 Neigh | 0.014116 | 0.014116 | 0.014116 | 0.0 | 1.60 Comm | 0.0061592 | 0.0061592 | 0.0061592 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005953 | | | 0.67 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4818.00 ave 4818 max 4818 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: 117448.0 ave 117448 max 117448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117448 Ave neighs/atom = 130.78842 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.983 | 4.983 | 4.983 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -3006.3939 0 -3006.3939 -3529.5774 15147.492 84 0 -3006.4917 0 -3006.4917 38.941213 15081.139 Loop time of 0.0335912 on 1 procs for 4 steps with 898 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 = -3006.39389726242 -3006.49028037126 -3006.49174231845 Force two-norm initial, final = 56.622487 1.0807466 Force max component initial, final = 47.440387 0.86092091 Final line search alpha, max atom move = 0.00026911490 0.00023168664 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.032431 | 0.032431 | 0.032431 | 0.0 | 96.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021051 | 0.00021051 | 0.00021051 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009492 | | | 2.83 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4811.00 ave 4811 max 4811 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: 117456.0 ave 117456 max 117456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117456 Ave neighs/atom = 130.79733 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.121 | 5.121 | 5.121 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3006.4917 0 -3006.4917 38.941213 Loop time of 1.673e-06 on 1 procs for 0 steps with 898 atoms 119.5% 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 | | 1.673e-06 | | |100.00 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4815.00 ave 4815 max 4815 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: 117548.0 ave 117548 max 117548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117548 Ave neighs/atom = 130.89978 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.121 | 5.121 | 5.121 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 -3006.4917 -3006.4917 24.940482 86.492442 6.9911907 38.941213 38.941213 -64.811274 272.78874 -91.153828 2.6441088 862.66734 Loop time of 1.657e-06 on 1 procs for 0 steps with 898 atoms 120.7% 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 | | 1.657e-06 | | |100.00 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4815.00 ave 4815 max 4815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58774.0 ave 58774 max 58774 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117548.0 ave 117548 max 117548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117548 Ave neighs/atom = 130.89978 Neighbor list builds = 0 Dangerous builds = 0 898 -3006.49174231845 eV 2.6441088400363 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01