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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -41.590634 0.0000000) to (29.409019 41.590634 5.1194531) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2382768 5.6714501 5.1194531 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.590634 0.0000000) to (29.409019 41.590634 5.1194531) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2382768 5.6714501 5.1194531 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.590634 0.0000000) to (29.409019 41.590634 5.1194531) create_atoms CPU = 0.003 seconds 532 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 = 9 24 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1056 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 = 9 24 2 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) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3144.2344 0 -3144.2344 167436.64 57 0 -3728.3549 0 -3728.3549 3900.7196 Loop time of 6.9358 on 1 procs for 57 steps with 1056 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3144.23438782694 -3728.35238879073 -3728.35491041284 Force two-norm initial, final = 1473.0507 0.13218529 Force max component initial, final = 283.88171 0.014792274 Final line search alpha, max atom move = 1.0000000 0.014792274 Iterations, force evaluations = 57 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9083 | 6.9083 | 6.9083 | 0.0 | 99.60 Neigh | 0.0091681 | 0.0091681 | 0.0091681 | 0.0 | 0.13 Comm | 0.0097744 | 0.0097744 | 0.0097744 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008551 | | | 0.12 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5759.00 ave 5759 max 5759 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: 139696.0 ave 139696 max 139696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139696 Ave neighs/atom = 132.28788 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 = 9 24 2 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 : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -3728.3549 0 -3728.3549 3900.7196 12523.613 61 0 -3728.4381 0 -3728.4381 -27.200402 12559.022 Loop time of 0.497183 on 1 procs for 4 steps with 1056 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 = -3728.35491041284 -3728.43759621633 -3728.43805129569 Force two-norm initial, final = 59.841070 1.1418645 Force max component initial, final = 42.280792 1.0839521 Final line search alpha, max atom move = 0.00023361430 0.00025322671 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49494 | 0.49494 | 0.49494 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035901 | 0.00035901 | 0.00035901 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001886 | | | 0.38 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5356.00 ave 5356 max 5356 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: 139848.0 ave 139848 max 139848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139848 Ave neighs/atom = 132.43182 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 = 9 24 2 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) = 5.139 | 5.139 | 5.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3728.4381 0 -3728.4381 -27.200402 Loop time of 2.674e-06 on 1 procs for 0 steps with 1056 atoms 187.0% 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 | | 2.674e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5356.00 ave 5356 max 5356 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: 139568.0 ave 139568 max 139568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139568 Ave neighs/atom = 132.16667 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 = 9 24 2 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) = 5.139 | 5.139 | 5.139 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 -3728.4381 -3728.4381 29.462718 83.384078 5.1121065 -27.200402 -27.200402 -138.53416 24.63748 32.295478 2.3784763 643.24248 Loop time of 4.827e-06 on 1 procs for 0 steps with 1056 atoms 227.9% 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 | | 4.827e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5356.00 ave 5356 max 5356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69784.0 ave 69784 max 69784 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139568.0 ave 139568 max 139568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139568 Ave neighs/atom = 132.16667 Neighbor list builds = 0 Dangerous builds = 0 1056 -3728.43805129569 eV 2.37847632600378 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08