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 = 2.8436425 2.8436425 2.8436425 Created orthogonal box = (0.0000000 -29.554844 0.0000000) to (20.896420 29.554844 4.0215178) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6436488 3.8308148 4.0215178 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -29.554844 0.0000000) to (20.896420 29.554844 4.0215178) create_atoms CPU = 0.002 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6436488 3.8308148 4.0215178 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -29.554844 0.0000000) to (20.896420 29.554844 4.0215178) create_atoms CPU = 0.001 seconds 218 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 15 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 428 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_044341472608_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1663.1797 0 -1663.1797 46170.349 30 0 -1716.069 0 -1716.069 -5299.6274 Loop time of 0.446243 on 1 procs for 30 steps with 428 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 = -1663.17973817747 -1716.06766385763 -1716.06897434195 Force two-norm initial, final = 160.83008 0.10369480 Force max component initial, final = 58.942720 0.014528704 Final line search alpha, max atom move = 1.0000000 0.014528704 Iterations, force evaluations = 30 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42742 | 0.42742 | 0.42742 | 0.0 | 95.78 Neigh | 0.0098097 | 0.0098097 | 0.0098097 | 0.0 | 2.20 Comm | 0.0048938 | 0.0048938 | 0.0048938 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004118 | | | 0.92 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3919.00 ave 3919 max 3919 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: 72672.0 ave 72672 max 72672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72672 Ave neighs/atom = 169.79439 Neighbor list builds = 1 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -1716.069 0 -1716.069 -5299.6274 4967.3018 32 0 -1716.0749 0 -1716.0749 -3020.5159 4961.0092 Loop time of 0.0430899 on 1 procs for 2 steps with 428 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1716.06897434195 -1716.07477391714 -1716.07489415118 Force two-norm initial, final = 11.860201 0.12249884 Force max component initial, final = 10.509909 0.024550150 Final line search alpha, max atom move = 0.00094526870 2.3206488e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041376 | 0.041376 | 0.041376 | 0.0 | 96.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043866 | 0.00043866 | 0.00043866 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001275 | | | 2.96 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3919.00 ave 3919 max 3919 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: 72604.0 ave 72604 max 72604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72604 Ave neighs/atom = 169.63551 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1716.0749 0 -1716.0749 -3020.5159 Loop time of 6.776e-06 on 1 procs for 0 steps with 428 atoms 132.8% 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 | | 6.776e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3919.00 ave 3919 max 3919 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: 72608.0 ave 72608 max 72608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72608 Ave neighs/atom = 169.64486 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.611 | 4.611 | 4.611 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 -1716.0749 -1716.0749 20.876112 59.109687 4.0203305 -3020.5159 -3020.5159 3.6294582 -9062.7618 -2.4153813 2.2807231 431.17677 Loop time of 6.766e-06 on 1 procs for 0 steps with 428 atoms 236.5% 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 | | 6.766e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3919.00 ave 3919 max 3919 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36304.0 ave 36304 max 36304 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72608.0 ave 72608 max 72608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72608 Ave neighs/atom = 169.64486 Neighbor list builds = 0 Dangerous builds = 0 428 -1716.07489415118 eV 2.2807230741858 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00