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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -49.555184 0.0000000) to (12.387817 49.555184 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9551266 4.9551266 3.9173716 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -49.555184 0.0000000) to (12.387817 49.555184 3.9173716) create_atoms CPU = 0.002 seconds 162 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9551266 4.9551266 3.9173716 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -49.555184 0.0000000) to (12.387817 49.555184 3.9173716) create_atoms CPU = 0.001 seconds 162 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 316 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1791.6542 0 -1791.6542 12765.163 69 0 -1813.3452 0 -1813.3452 -7797.0316 Loop time of 1.75621 on 1 procs for 69 steps with 316 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 = -1791.65419298198 -1813.34375050303 -1813.34522538217 Force two-norm initial, final = 42.909367 0.15529100 Force max component initial, final = 15.196710 0.039804847 Final line search alpha, max atom move = 1.0000000 0.039804847 Iterations, force evaluations = 69 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.735 | 1.735 | 1.735 | 0.0 | 98.79 Neigh | 0.0042094 | 0.0042094 | 0.0042094 | 0.0 | 0.24 Comm | 0.0093509 | 0.0093509 | 0.0093509 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007689 | | | 0.44 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 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: 24392.0 ave 24392 max 24392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24392 Ave neighs/atom = 77.189873 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -1813.3452 0 -1813.3452 -7797.0316 4809.5963 72 0 -1813.3953 0 -1813.3953 -506.41359 4789.208 Loop time of 0.078266 on 1 procs for 3 steps with 316 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 = -1813.34522538217 -1813.39351469473 -1813.39527444417 Force two-norm initial, final = 33.615404 2.6246615 Force max component initial, final = 25.997199 2.5780665 Final line search alpha, max atom move = 0.00018422691 0.00047494923 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07629 | 0.07629 | 0.07629 | 0.0 | 97.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038964 | 0.00038964 | 0.00038964 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001587 | | | 2.03 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2968.00 ave 2968 max 2968 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: 24392.0 ave 24392 max 24392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24392 Ave neighs/atom = 77.189873 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.574 | 4.574 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1813.3953 0 -1813.3953 -506.41359 Loop time of 6.866e-06 on 1 procs for 0 steps with 316 atoms 189.3% 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 | | 6.866e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2973.00 ave 2973 max 2973 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: 24392.0 ave 24392 max 24392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24392 Ave neighs/atom = 77.189873 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.574 | 4.574 | 4.574 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 -1813.3953 -1813.3953 12.367803 99.110368 3.9070777 -506.41359 -506.41359 861.07021 -2232.2543 -148.05668 2.5525507 216.91095 Loop time of 6.805e-06 on 1 procs for 0 steps with 316 atoms 264.5% 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 | | 6.805e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2973.00 ave 2973 max 2973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12196.0 ave 12196 max 12196 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24392.0 ave 24392 max 24392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24392 Ave neighs/atom = 77.189873 Neighbor list builds = 0 Dangerous builds = 0 316 -1813.39527444417 eV 2.55255071769679 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02