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 = 3.5483741 3.5483741 3.5483741 Created orthogonal box = (0.0000000 -39.672028 0.0000000) to (7.9344056 39.672028 3.5483741) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7606434 4.7606434 3.5483741 Created 100 atoms using lattice units in orthogonal box = (0.0000000 -39.672028 0.0000000) to (7.9344056 39.672028 3.5483741) create_atoms CPU = 0.002 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7606434 4.7606434 3.5483741 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -39.672028 0.0000000) to (7.9344056 39.672028 3.5483741) create_atoms CPU = 0.001 seconds 102 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 20 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 200 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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -774.78695 0 -774.78695 62702.156 41 0 -806.3289 0 -806.3289 25607.466 Loop time of 0.415334 on 1 procs for 41 steps with 200 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 = -774.786945451344 -806.328159122125 -806.328898665681 Force two-norm initial, final = 101.51772 0.097188454 Force max component initial, final = 34.657844 0.022341796 Final line search alpha, max atom move = 1.0000000 0.022341796 Iterations, force evaluations = 41 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40395 | 0.40395 | 0.40395 | 0.0 | 97.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0069355 | 0.0069355 | 0.0069355 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004446 | | | 1.07 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3793.00 ave 3793 max 3793 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: 39828.0 ave 39828 max 39828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39828 Ave neighs/atom = 199.14000 Neighbor list builds = 0 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -806.3289 0 -806.3289 25607.466 2233.8715 51 0 -806.58441 0 -806.58441 33.58982 2254.8485 Loop time of 0.0645835 on 1 procs for 10 steps with 200 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 = -806.328898665681 -806.583814769598 -806.584408837687 Force two-norm initial, final = 66.662854 0.46122635 Force max component initial, final = 55.946265 0.19897182 Final line search alpha, max atom move = 0.00083902443 0.00016694221 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060812 | 0.060812 | 0.060812 | 0.0 | 94.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097077 | 0.00097077 | 0.00097077 | 0.0 | 1.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002801 | | | 4.34 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3727.00 ave 3727 max 3727 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: 39308.0 ave 39308 max 39308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39308 Ave neighs/atom = 196.54000 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -806.58441 0 -806.58441 33.58982 Loop time of 6.154e-06 on 1 procs for 0 steps with 200 atoms 178.7% 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 | | 6.154e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3727.00 ave 3727 max 3727 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: 39196.0 ave 39196 max 39196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39196 Ave neighs/atom = 195.98000 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.590 | 4.590 | 4.590 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 -806.58441 -806.58441 7.9393445 80.089964 3.5461297 33.58982 33.58982 141.46689 -102.15634 61.458908 2.3480036 123.38805 Loop time of 6.546e-06 on 1 procs for 0 steps with 200 atoms 259.7% 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 | | 6.546e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3727.00 ave 3727 max 3727 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19598.0 ave 19598 max 19598 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39196.0 ave 39196 max 39196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39196 Ave neighs/atom = 195.98000 Neighbor list builds = 0 Dangerous builds = 0 200 -806.584408837687 eV 2.34800357875001 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01