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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -54.984157 0.0000000) to (27.492079 54.984157 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9575880 4.9575880 3.5200000 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -54.984157 0.0000000) to (27.492079 54.984157 3.5200000) create_atoms CPU = 0.002 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9575880 4.9575880 3.5200000 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -54.984157 0.0000000) to (27.492079 54.984157 3.5200000) create_atoms CPU = 0.002 seconds 490 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4285.3282 0 -4285.3282 9881.0033 69 0 -4342.1901 0 -4342.1901 7604.1235 Loop time of 4.57133 on 1 procs for 69 steps with 978 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 = -4285.32816607001 -4342.18662476951 -4342.19013043689 Force two-norm initial, final = 31.773919 0.19229691 Force max component initial, final = 4.5993065 0.011868323 Final line search alpha, max atom move = 1.0000000 0.011868323 Iterations, force evaluations = 69 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4921 | 4.4921 | 4.4921 | 0.0 | 98.27 Neigh | 0.030367 | 0.030367 | 0.030367 | 0.0 | 0.66 Comm | 0.030731 | 0.030731 | 0.030731 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01809 | | | 0.40 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10140.0 ave 10140 max 10140 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: 242024.0 ave 242024 max 242024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242024 Ave neighs/atom = 247.46830 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -4342.1901 0 -4342.1901 7604.1235 10641.867 74 0 -4342.4412 0 -4342.4412 260.48833 10685.053 Loop time of 0.253601 on 1 procs for 5 steps with 978 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 = -4342.19013043689 -4342.438851614 -4342.44118497673 Force two-norm initial, final = 111.74386 3.2496181 Force max component initial, final = 98.993813 2.2411052 Final line search alpha, max atom move = 0.00011899838 0.00026668789 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24743 | 0.24743 | 0.24743 | 0.0 | 97.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014682 | 0.0014682 | 0.0014682 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004707 | | | 1.86 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10134.0 ave 10134 max 10134 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: 242240.0 ave 242240 max 242240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242240 Ave neighs/atom = 247.68916 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.579 | 5.579 | 5.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4342.4412 0 -4342.4412 260.48833 Loop time of 6.264e-06 on 1 procs for 0 steps with 978 atoms 207.5% 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 | | 6.264e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10140.0 ave 10140 max 10140 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: 241784.0 ave 241784 max 241784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241784 Ave neighs/atom = 247.22290 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.579 | 5.579 | 5.579 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 -4342.4412 -4342.4412 27.446915 110.43125 3.5252599 260.48833 260.48833 110.00889 334.91012 336.54598 2.2323481 147.68734 Loop time of 7.177e-06 on 1 procs for 0 steps with 978 atoms 264.7% 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 | | 7.177e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10140.0 ave 10140 max 10140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120892.0 ave 120892 max 120892 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 241784.0 ave 241784 max 241784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241784 Ave neighs/atom = 247.22290 Neighbor list builds = 0 Dangerous builds = 0 978 -4342.44118497673 eV 2.2323480972691 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05