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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -40.409265 0.0000000) to (4.0409265 40.409265 4.0409265) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0409265 4.0409265 4.0409265 Created 40 atoms using lattice units in orthogonal box = (0.0000000 -40.409265 0.0000000) to (4.0409265 40.409265 4.0409265) create_atoms CPU = 0.000 seconds 40 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0409265 4.0409265 4.0409265 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -40.409265 0.0000000) to (4.0409265 40.409265 4.0409265) create_atoms CPU = 0.000 seconds 42 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 1 17 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 80 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 1 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -312.4119 0 -312.4119 -0.0064884226 1 0 -312.4119 0 -312.4119 -0.0064884227 Loop time of 0.00394238 on 1 procs for 1 steps with 80 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -312.411904099012 -312.411904099012 -312.411904098997 Force two-norm initial, final = 3.8915115e-08 1.3282032e-08 Force max component initial, final = 1.9431107e-08 6.6053580e-09 Final line search alpha, max atom move = 1.0000000 6.6053580e-09 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0038134 | 0.0038134 | 0.0038134 | 0.0 | 96.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.6182e-05 | 7.6182e-05 | 7.6182e-05 | 0.0 | 1.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.285e-05 | | | 1.34 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3448.00 ave 3448 max 3448 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: 19840.0 ave 19840 max 19840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19840 Ave neighs/atom = 248.00000 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 1 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -312.4119 0 -312.4119 -0.0064884227 1319.6928 2 0 -312.4119 0 -312.4119 -7.812506e-08 1319.6928 Loop time of 0.00412967 on 1 procs for 1 steps with 80 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 = -312.411904098997 -312.411904098997 -312.41190409896 Force two-norm initial, final = 9.2569101e-06 3.1234217e-08 Force max component initial, final = 5.3741284e-06 2.3157971e-08 Final line search alpha, max atom move = 1.0000000 2.3157971e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0038568 | 0.0038568 | 0.0038568 | 0.0 | 93.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.3806e-05 | 7.3806e-05 | 7.3806e-05 | 0.0 | 1.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001991 | | | 4.82 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3448.00 ave 3448 max 3448 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: 19840.0 ave 19840 max 19840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19840 Ave neighs/atom = 248.00000 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 1 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -312.4119 0 -312.4119 -7.812506e-08 Loop time of 1.412e-06 on 1 procs for 0 steps with 80 atoms 141.6% 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 | | 1.412e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3448.00 ave 3448 max 3448 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: 19840.0 ave 19840 max 19840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19840 Ave neighs/atom = 248.00000 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 1 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 4.579 | 4.579 | 4.579 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 -312.4119 -312.4119 4.0409265 80.818529 4.0409265 -7.812506e-08 -7.812506e-08 1.3940336e-05 -2.8114997e-05 1.3940285e-05 2.8573665 1.0794661e-16 Loop time of 1.463e-06 on 1 procs for 0 steps with 80 atoms 136.7% 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 | | 1.463e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3448.00 ave 3448 max 3448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9920.00 ave 9920 max 9920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 19840.0 ave 19840 max 19840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19840 Ave neighs/atom = 248.00000 Neighbor list builds = 0 Dangerous builds = 0 80 -312.41190409896 eV 2.85736650253732 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00