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 = 3.6149390 3.6149390 3.6149390 Created orthogonal box = (0.0000000 -40.416247 0.0000000) to (8.0832494 40.416247 3.6149390) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8499496 4.8499496 3.6149390 Created 100 atoms using lattice units in orthogonal box = (0.0000000 -40.416247 0.0000000) to (8.0832494 40.416247 3.6149390) create_atoms CPU = 0.001 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8499496 4.8499496 3.6149390 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -40.416247 0.0000000) to (8.0832494 40.416247 3.6149390) 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, 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 8.395337104797363 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_547744193826_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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -687.42204 0 -687.42204 27689.482 16 0 -704.72339 0 -704.72339 12088.803 Loop time of 0.161593 on 1 procs for 16 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 = -687.422041663629 -704.722837583336 -704.723388429682 Force two-norm initial, final = 55.431718 0.073800463 Force max component initial, final = 19.593815 0.012247711 Final line search alpha, max atom move = 1.0000000 0.012247711 Iterations, force evaluations = 16 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15726 | 0.15726 | 0.15726 | 0.0 | 97.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026948 | 0.0026948 | 0.0026948 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001639 | | | 1.01 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3931.00 ave 3931 max 3931 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: 40224.0 ave 40224 max 40224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40224 Ave neighs/atom = 201.12000 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 16 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 16 0 -704.72339 0 -704.72339 12088.803 2361.9622 31 0 -704.90812 0 -704.90812 88.459868 2382.0203 Loop time of 0.0987625 on 1 procs for 15 steps with 200 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -704.723388429683 -704.908068876969 -704.908124876979 Force two-norm initial, final = 36.216176 0.37808023 Force max component initial, final = 33.073927 0.16788380 Final line search alpha, max atom move = 0.0015504680 0.00026029846 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087456 | 0.087456 | 0.087456 | 0.0 | 88.55 Neigh | 0.0055779 | 0.0055779 | 0.0055779 | 0.0 | 5.65 Comm | 0.0015381 | 0.0015381 | 0.0015381 | 0.0 | 1.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00419 | | | 4.24 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3931.00 ave 3931 max 3931 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: 39896.0 ave 39896 max 39896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39896 Ave neighs/atom = 199.48000 Neighbor list builds = 1 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -704.90812 0 -704.90812 88.459868 Loop time of 6.655e-06 on 1 procs for 0 steps with 200 atoms 165.3% 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 | | 6.655e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3931.00 ave 3931 max 3931 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: 39896.0 ave 39896 max 39896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39896 Ave neighs/atom = 199.48000 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.595 | 4.595 | 4.595 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 -704.90812 -704.90812 8.0783661 81.909097 3.5998946 88.459868 88.459868 71.267979 114.42472 79.686904 2.3143978 126.58035 Loop time of 6.646e-06 on 1 procs for 0 steps with 200 atoms 180.6% 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 | | 6.646e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3931.00 ave 3931 max 3931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19948.0 ave 19948 max 19948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39896.0 ave 39896 max 39896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39896 Ave neighs/atom = 199.48000 Neighbor list builds = 0 Dangerous builds = 0 200 -704.908124876979 eV 2.31439781641757 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00