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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -73.163862 0.0000000) to (25.867331 73.163862 5.7131378) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9400157 6.2456955 5.7131378 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -73.163862 0.0000000) to (25.867331 73.163862 5.7131378) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9400157 6.2456955 5.7131378 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -73.163862 0.0000000) to (25.867331 73.163862 5.7131378) create_atoms CPU = 0.002 seconds 658 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 25 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.780 | 6.780 | 6.780 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3679.9623 0 -3679.9623 10335.547 82 0 -3781.096 0 -3781.096 1012.086 Loop time of 4.12264 on 1 procs for 82 steps with 1312 atoms 96.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3679.9623096159 -3781.09285925671 -3781.09600315854 Force two-norm initial, final = 136.56463 0.17568423 Force max component initial, final = 44.543417 0.018802719 Final line search alpha, max atom move = 1.0000000 0.018802719 Iterations, force evaluations = 82 156 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.045 | 4.045 | 4.045 | 0.0 | 98.12 Neigh | 0.030266 | 0.030266 | 0.030266 | 0.0 | 0.73 Comm | 0.031181 | 0.031181 | 0.031181 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01618 | | | 0.39 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13978.0 ave 13978 max 13978 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: 536104.0 ave 536104 max 536104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536104 Ave neighs/atom = 408.61585 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.775 | 6.775 | 6.775 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -3781.096 0 -3781.096 1012.086 21624.842 85 0 -3781.1821 0 -3781.1821 119.7748 21649.928 Loop time of 0.127021 on 1 procs for 3 steps with 1312 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 = -3781.09600315855 -3781.17870153011 -3781.18205512348 Force two-norm initial, final = 55.855712 3.6102112 Force max component initial, final = 45.625106 3.3661467 Final line search alpha, max atom move = 0.00010770343 0.00036254555 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12405 | 0.12405 | 0.12405 | 0.0 | 97.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055381 | 0.00055381 | 0.00055381 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002413 | | | 1.90 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13328.0 ave 13328 max 13328 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: 533760.0 ave 533760 max 533760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533760 Ave neighs/atom = 406.82927 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.912 | 6.912 | 6.912 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3781.1821 0 -3781.1821 119.7748 Loop time of 2.497e-06 on 1 procs for 0 steps with 1312 atoms 160.2% 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 | | 2.497e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13296.0 ave 13296 max 13296 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: 532800.0 ave 532800 max 532800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 532800 Ave neighs/atom = 406.09756 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.912 | 6.912 | 6.912 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 -3781.1821 -3781.1821 25.921138 146.49693 5.7012995 119.7748 119.7748 15.899245 249.39564 94.029519 2.6923946 575.92043 Loop time of 2.964e-06 on 1 procs for 0 steps with 1312 atoms 337.4% 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 | | 2.964e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13296.0 ave 13296 max 13296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 266400.0 ave 266400 max 266400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 532800.0 ave 532800 max 532800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 532800 Ave neighs/atom = 406.09756 Neighbor list builds = 0 Dangerous builds = 0 1312 -3781.18205512348 eV 2.69239455536998 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04