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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -51.128678 0.0000000) to (18.075605 51.128678 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9297105 3.8731463 4.4499063 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -51.128678 0.0000000) to (18.075605 51.128678 4.4499063) create_atoms CPU = 0.002 seconds 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9297105 3.8731463 4.4499063 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -51.128678 0.0000000) to (18.075605 51.128678 4.4499063) create_atoms CPU = 0.001 seconds 266 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 528 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3541.6373 0 -3541.6373 21872.878 58 0 -3578.3056 0 -3578.3056 8287.7296 Loop time of 3.50146 on 1 procs for 58 steps with 528 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 = -3541.63732421241 -3578.30277832109 -3578.3056149721 Force two-norm initial, final = 27.377635 0.14711115 Force max component initial, final = 5.6364662 0.017052909 Final line search alpha, max atom move = 1.0000000 0.017052909 Iterations, force evaluations = 58 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4791 | 3.4791 | 3.4791 | 0.0 | 99.36 Neigh | 0.0048618 | 0.0048618 | 0.0048618 | 0.0 | 0.14 Comm | 0.0083831 | 0.0083831 | 0.0083831 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009123 | | | 0.26 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2876.00 ave 2876 max 2876 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: 30428.0 ave 30428 max 30428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30428 Ave neighs/atom = 57.628788 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.471 | 4.471 | 4.471 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -3578.3056 0 -3578.3056 8287.7296 8225.0449 60 0 -3578.3459 0 -3578.3459 2282.4764 8243.5786 Loop time of 0.122339 on 1 procs for 2 steps with 528 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 = -3578.3056149721 -3578.34448043654 -3578.34589697084 Force two-norm initial, final = 50.667972 1.9493008 Force max component initial, final = 38.819494 1.7516572 Final line search alpha, max atom move = 0.00012118458 0.00021227383 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12099 | 0.12099 | 0.12099 | 0.0 | 98.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001058 | | | 0.87 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2888.00 ave 2888 max 2888 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: 30444.0 ave 30444 max 30444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30444 Ave neighs/atom = 57.659091 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3578.3459 0 -3578.3459 2282.4764 Loop time of 6.355e-06 on 1 procs for 0 steps with 528 atoms 173.1% 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 | | 6.355e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2882.00 ave 2882 max 2882 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: 30440.0 ave 30440 max 30440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30440 Ave neighs/atom = 57.651515 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.608 | 4.608 | 4.608 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 -3578.3459 -3578.3459 18.093233 102.25736 4.4555883 2282.4764 2282.4764 -340.77444 7025.5095 162.69418 2.2232615 327.8005 Loop time of 6.375e-06 on 1 procs for 0 steps with 528 atoms 251.0% 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 | | 6.375e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2882.00 ave 2882 max 2882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15220.0 ave 15220 max 15220 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30440.0 ave 30440 max 30440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30440 Ave neighs/atom = 57.651515 Neighbor list builds = 0 Dangerous builds = 0 528 -3578.34589697084 eV 2.22326152076722 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04