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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -57.546193 0.0000000) to (33.222653 57.546193 4.9709860) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4627444 4.5805630 4.9709860 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -57.546193 0.0000000) to (33.222653 57.546193 4.9709860) create_atoms CPU = 0.004 seconds 806 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4627444 4.5805630 4.9709860 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -57.546193 0.0000000) to (33.222653 57.546193 4.9709860) create_atoms CPU = 0.003 seconds 806 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 38 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1608 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.119 | 5.119 | 5.119 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6770.5662 0 -6770.5662 17099.189 39 0 -6856.1945 0 -6856.1945 6181.2879 Loop time of 0.775567 on 1 procs for 39 steps with 1608 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6770.56620697934 -6856.18808837076 -6856.19445764688 Force two-norm initial, final = 92.522117 0.30463589 Force max component initial, final = 16.317165 0.071390148 Final line search alpha, max atom move = 0.57165951 0.040810857 Iterations, force evaluations = 39 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73762 | 0.73762 | 0.73762 | 0.0 | 95.11 Neigh | 0.018368 | 0.018368 | 0.018368 | 0.0 | 2.37 Comm | 0.0095805 | 0.0095805 | 0.0095805 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01 | | | 1.29 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6937.00 ave 6937 max 6937 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: 105420.0 ave 105420 max 105420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105420 Ave neighs/atom = 65.559701 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.119 | 5.119 | 5.119 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -6856.1945 0 -6856.1945 6181.2879 19007.432 42 0 -6856.3172 0 -6856.3172 815.23983 19068.287 Loop time of 0.0644285 on 1 procs for 3 steps with 1608 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 = -6856.19445764688 -6856.31722301725 -6856.31723369709 Force two-norm initial, final = 108.61687 0.67456517 Force max component initial, final = 81.462060 0.44517815 Final line search alpha, max atom move = 0.0083077692 0.0036984373 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.06085 | 0.06085 | 0.06085 | 0.0 | 94.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064961 | 0.00064961 | 0.00064961 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002929 | | | 4.55 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6934.00 ave 6934 max 6934 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: 105504.0 ave 105504 max 105504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105504 Ave neighs/atom = 65.611940 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.257 | 5.257 | 5.257 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6856.3172 0 -6856.3172 815.23983 Loop time of 3.24e-06 on 1 procs for 0 steps with 1608 atoms 154.3% 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 | | 3.24e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6932.00 ave 6932 max 6932 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: 105376.0 ave 105376 max 105376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105376 Ave neighs/atom = 65.532338 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.257 | 5.257 | 5.257 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 -6856.3172 -6856.3172 33.271739 115.09239 4.9795442 815.23983 815.23983 33.831322 2449.3578 -37.469644 2.2899169 737.07054 Loop time of 3.655e-06 on 1 procs for 0 steps with 1608 atoms 164.2% 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 | | 3.655e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6932.00 ave 6932 max 6932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52688.0 ave 52688 max 52688 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105376.0 ave 105376 max 105376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105376 Ave neighs/atom = 65.532338 Neighbor list builds = 0 Dangerous builds = 0 1608 -6856.31707289709 eV 2.28991694488897 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01