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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -46.929195 0.0000000) to (27.092493 46.929195 6.2706937) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8055343 5.5863780 6.2706937 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.929195 0.0000000) to (27.092493 46.929195 6.2706937) create_atoms CPU = 0.002 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8055343 5.5863780 6.2706937 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.929195 0.0000000) to (27.092493 46.929195 6.2706937) create_atoms CPU = 0.001 seconds 676 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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1332 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_390178379548_001#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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4666.3897 0 -4666.3897 4969.8911 29 0 -4697.0173 0 -4697.0173 -5364.2025 Loop time of 1.07244 on 1 procs for 29 steps with 1332 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4666.38971914134 -4697.01290413906 -4697.01725673798 Force two-norm initial, final = 50.859923 0.19875460 Force max component initial, final = 10.368938 0.036120576 Final line search alpha, max atom move = 1.0000000 0.036120576 Iterations, force evaluations = 29 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0664 | 1.0664 | 1.0664 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024165 | 0.0024165 | 0.0024165 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003671 | | | 0.34 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4448.00 ave 4448 max 4448 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: 102600.0 ave 102600 max 102600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102600 Ave neighs/atom = 77.027027 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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -4697.0173 0 -4697.0173 -5364.2025 15945.482 32 0 -4697.1007 0 -4697.1007 -957.30008 15895.722 Loop time of 0.118923 on 1 procs for 3 steps with 1332 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 = -4697.01725673799 -4697.10045318376 -4697.10070812282 Force two-norm initial, final = 73.342279 0.22209426 Force max component initial, final = 58.937911 0.039040385 Final line search alpha, max atom move = 0.00045337009 1.7699743e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11763 | 0.11763 | 0.11763 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020258 | 0.00020258 | 0.00020258 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001086 | | | 0.91 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4452.00 ave 4452 max 4452 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: 102856.0 ave 102856 max 102856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102856 Ave neighs/atom = 77.219219 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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.134 | 5.134 | 5.134 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4697.1007 0 -4697.1007 -957.30008 Loop time of 1.729e-06 on 1 procs for 0 steps with 1332 atoms 115.7% 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 | | 1.729e-06 | | |100.00 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4452.00 ave 4452 max 4452 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: 102856.0 ave 102856 max 102856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102856 Ave neighs/atom = 77.219219 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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.134 | 5.134 | 5.134 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 -4697.1007 -4697.1007 27.061284 93.85839 6.2583344 -957.30008 -957.30008 -3.2953 -2869.0366 0.43164065 2.3588423 764.81805 Loop time of 1.594e-06 on 1 procs for 0 steps with 1332 atoms 188.2% 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 | | 1.594e-06 | | |100.00 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4452.00 ave 4452 max 4452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51428.0 ave 51428 max 51428 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102856.0 ave 102856 max 102856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102856 Ave neighs/atom = 77.219219 Neighbor list builds = 0 Dangerous builds = 0 1332 -4697.10070812282 eV 2.35884230518504 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01