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 = 3.9946083 3.9946083 3.9946083 Created orthogonal box = (0.0000000 -62.397777 0.0000000) to (31.198889 62.397777 3.9946083) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6260291 5.6260291 3.9946083 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -62.397777 0.0000000) to (31.198889 62.397777 3.9946083) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6260291 5.6260291 3.9946083 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -62.397777 0.0000000) to (31.198889 62.397777 3.9946083) create_atoms CPU = 0.001 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 33 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 7.600097095572612 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_623376124862_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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 4.999 | 4.999 | 4.999 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3138.2476 0 -3138.2476 10603.241 98 0 -3208.4622 0 -3208.4622 1289.0831 Loop time of 2.08213 on 1 procs for 98 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 = -3138.24759145958 -3208.45941924172 -3208.46219014939 Force two-norm initial, final = 77.007768 0.12517820 Force max component initial, final = 14.805530 0.026325110 Final line search alpha, max atom move = 1.0000000 0.026325110 Iterations, force evaluations = 98 174 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0358 | 2.0358 | 2.0358 | 0.0 | 97.77 Neigh | 0.023705 | 0.023705 | 0.023705 | 0.0 | 1.14 Comm | 0.012321 | 0.012321 | 0.012321 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01033 | | | 0.50 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7147.00 ave 7147 max 7147 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: 128700.0 ave 128700 max 128700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128700 Ave neighs/atom = 131.59509 Neighbor list builds = 3 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.999 | 4.999 | 4.999 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -3208.4622 0 -3208.4622 1289.0831 15552.938 102 0 -3208.514 0 -3208.514 140.48917 15597.457 Loop time of 0.0712522 on 1 procs for 4 steps with 978 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 = -3208.46219014939 -3208.5121415616 -3208.51397370612 Force two-norm initial, final = 29.063845 2.5868901 Force max component initial, final = 23.258950 1.8991934 Final line search alpha, max atom move = 0.00040775719 0.00077440976 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.069311 | 0.069311 | 0.069311 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032699 | 0.00032699 | 0.00032699 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001614 | | | 2.27 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7162.00 ave 7162 max 7162 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: 128936.0 ave 128936 max 128936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128936 Ave neighs/atom = 131.83640 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 5.137 | 5.137 | 5.137 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3208.514 0 -3208.514 140.48917 Loop time of 2.125e-06 on 1 procs for 0 steps with 978 atoms 141.2% 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 | | 2.125e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7167.00 ave 7167 max 7167 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: 128760.0 ave 128760 max 128760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128760 Ave neighs/atom = 131.65644 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 5.137 | 5.137 | 5.137 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 -3208.514 -3208.514 31.135309 125.03426 4.0065594 140.48917 140.48917 171.05824 54.739766 195.6695 2.526186 187.40553 Loop time of 2.097e-06 on 1 procs for 0 steps with 978 atoms 238.4% 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 | | 2.097e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7167.00 ave 7167 max 7167 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64380.0 ave 64380 max 64380 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128760.0 ave 128760 max 128760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128760 Ave neighs/atom = 131.65644 Neighbor list builds = 0 Dangerous builds = 0 978 -3208.51397370612 eV 2.52618598122132 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02