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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -30.832357 0.0000000) to (3.0829274 30.832357 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.0829274 3.0829274 3.0829274 Created 21 atoms using lattice units in orthogonal box = (0.0000000 -30.832357 0.0000000) to (3.0829274 30.832357 3.0829274) create_atoms CPU = 0.000 seconds 21 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.0829274 3.0829274 3.0829274 Created 21 atoms using lattice units in orthogonal box = (0.0000000 -30.832357 0.0000000) to (3.0829274 30.832357 3.0829274) create_atoms CPU = 0.000 seconds 21 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 1 19 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 42 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 1 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.378 | 4.378 | 4.378 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -124.36757 0 -124.36757 965227.57 20 0 -271.49249 0 -271.49249 119291.38 Loop time of 0.401083 on 1 procs for 20 steps with 42 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 = -124.367565392451 -271.492437489707 -271.492490396227 Force two-norm initial, final = 418.05643 0.022408388 Force max component initial, final = 152.49416 0.0071967696 Final line search alpha, max atom move = 1.0000000 0.0071967696 Iterations, force evaluations = 20 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40055 | 0.40055 | 0.40055 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031524 | 0.00031524 | 0.00031524 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002189 | | | 0.05 Nlocal: 42.0000 ave 42 max 42 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1258.00 ave 1258 max 1258 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: 3040.00 ave 3040 max 3040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3040 Ave neighs/atom = 72.380952 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 1 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.378 | 4.378 | 4.378 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -271.49249 0 -271.49249 119291.38 586.08864 46 0 -272.52596 0 -272.52596 1476.2275 615.28524 Loop time of 0.376392 on 1 procs for 26 steps with 42 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 = -271.492490396227 -272.52594096591 -272.525957088609 Force two-norm initial, final = 61.540395 0.019582387 Force max component initial, final = 43.515628 0.0058672148 Final line search alpha, max atom move = 1.0000000 0.0058672148 Iterations, force evaluations = 26 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37482 | 0.37482 | 0.37482 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029651 | 0.00029651 | 0.00029651 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001277 | | | 0.34 Nlocal: 42.0000 ave 42 max 42 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1258.00 ave 1258 max 1258 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: 3696.00 ave 3696 max 3696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3696 Ave neighs/atom = 88.000000 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 1 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -272.52596 0 -272.52596 1476.2275 Loop time of 1.927e-06 on 1 procs for 0 steps with 42 atoms 155.7% 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 | | 1.927e-06 | | |100.00 Nlocal: 42.0000 ave 42 max 42 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1258.00 ave 1258 max 1258 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: 3696.00 ave 3696 max 3696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3696 Ave neighs/atom = 88.000000 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 1 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.516 | 4.516 | 4.516 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 -272.52596 -272.52596 3.1587837 61.664713 3.1587837 1476.2275 1476.2275 -5.3121582 4439.3068 -5.3121582 2.6723559 2.0750298e-05 Loop time of 1.845e-06 on 1 procs for 0 steps with 42 atoms 162.6% 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 | | 1.845e-06 | | |100.00 Nlocal: 42.0000 ave 42 max 42 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1258.00 ave 1258 max 1258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1848.00 ave 1848 max 1848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3696.00 ave 3696 max 3696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3696 Ave neighs/atom = 88.000000 Neighbor list builds = 0 Dangerous builds = 0 42 -272.525957088609 eV 2.67235588657494 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00