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 = 2.8509989 2.8509989 2.8509989 Created orthogonal box = (0.0000000 -45.970976 0.0000000) to (22.985488 45.970976 2.8509989) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.1826060 3.1826060 2.8509989 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -45.970976 0.0000000) to (22.985488 45.970976 2.8509989) create_atoms CPU = 0.001 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.1826060 3.1826060 2.8509989 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -45.970976 0.0000000) to (22.985488 45.970976 2.8509989) create_atoms CPU = 0.001 seconds 261 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 521 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_262519520678_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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2031.2475 0 -2031.2475 157576.31 50 0 -2224.487 0 -2224.487 8084.9024 Loop time of 6.58954 on 1 procs for 50 steps with 521 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 = -2031.2474685793 -2224.48511685213 -2224.48695814646 Force two-norm initial, final = 328.64614 0.14770482 Force max component initial, final = 138.63028 0.044921235 Final line search alpha, max atom move = 1.0000000 0.044921235 Iterations, force evaluations = 50 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5611 | 6.5611 | 6.5611 | 0.0 | 99.57 Neigh | 0.0095263 | 0.0095263 | 0.0095263 | 0.0 | 0.14 Comm | 0.011116 | 0.011116 | 0.011116 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00775 | | | 0.12 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4770.00 ave 4770 max 4770 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: 68456.0 ave 68456 max 68456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68456 Ave neighs/atom = 131.39347 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2224.487 0 -2224.487 8084.9024 6025.1033 62 0 -2224.8282 0 -2224.8282 -0.0068733469 6053.213 Loop time of 1.05481 on 1 procs for 12 steps with 521 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 = -2224.48695814646 -2224.82706211751 -2224.828165687 Force two-norm initial, final = 67.924324 0.42706994 Force max component initial, final = 64.512398 0.13626627 Final line search alpha, max atom move = 0.00049750638 6.7793341e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0387 | 1.0387 | 1.0387 | 0.0 | 98.48 Neigh | 0.0093292 | 0.0093292 | 0.0093292 | 0.0 | 0.88 Comm | 0.0017374 | 0.0017374 | 0.0017374 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005008 | | | 0.47 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4786.00 ave 4786 max 4786 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: 67968.0 ave 67968 max 67968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67968 Ave neighs/atom = 130.45681 Neighbor list builds = 1 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2224.8282 0 -2224.8282 -0.0068733469 Loop time of 6.054e-06 on 1 procs for 0 steps with 521 atoms 181.7% 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 | | 6.054e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4786.00 ave 4786 max 4786 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: 67750.0 ave 67750 max 67750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67750 Ave neighs/atom = 130.03839 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.631 | 4.631 | 4.631 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 -2224.8282 -2224.8282 22.961419 93.011207 2.83434 -0.0068733469 -0.0068733469 19.816452 -19.408642 -0.42843045 2.3669642 236.33495 Loop time of 6.826e-06 on 1 procs for 0 steps with 521 atoms 307.6% 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 | | 6.826e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4786.00 ave 4786 max 4786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33875.0 ave 33875 max 33875 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67750.0 ave 67750 max 67750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67750 Ave neighs/atom = 130.03839 Neighbor list builds = 0 Dangerous builds = 0 521 -2224.828165687 eV 2.36696424473423 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08