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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -44.545995 0.0000000) to (11.135618 44.545995 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4542474 4.4542474 3.5213917 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -44.545995 0.0000000) to (11.135618 44.545995 3.5213917) create_atoms CPU = 0.002 seconds 162 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4542474 4.4542474 3.5213917 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -44.545995 0.0000000) to (11.135618 44.545995 3.5213917) 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 28 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_008996216289_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 28 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) = 4.443 | 4.443 | 4.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1383.6228 0 -1383.6228 12929.715 55 0 -1399.1775 0 -1399.1775 -10560.014 Loop time of 4.11691 on 1 procs for 55 steps with 316 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 = -1383.62280176148 -1399.17621478018 -1399.17752923222 Force two-norm initial, final = 36.670605 0.11081196 Force max component initial, final = 13.667061 0.016075179 Final line search alpha, max atom move = 1.0000000 0.016075179 Iterations, force evaluations = 55 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0974 | 4.0974 | 4.0974 | 0.0 | 99.53 Neigh | 0.0046813 | 0.0046813 | 0.0046813 | 0.0 | 0.11 Comm | 0.0082389 | 0.0082389 | 0.0082389 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006594 | | | 0.16 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3189.00 ave 3189 max 3189 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: 27548.0 ave 27548 max 27548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27548 Ave neighs/atom = 87.177215 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 28 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.443 | 4.443 | 4.443 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -1399.1775 0 -1399.1775 -10560.014 3493.5531 59 0 -1399.23 0 -1399.23 -1837.3353 3476.8417 Loop time of 0.316154 on 1 procs for 4 steps with 316 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 = -1399.17752923222 -1399.22949027384 -1399.22999417483 Force two-norm initial, final = 30.373429 0.13587827 Force max component initial, final = 22.673045 0.034446029 Final line search alpha, max atom move = 0.00077167089 2.6580998e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31353 | 0.31353 | 0.31353 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056242 | 0.00056242 | 0.00056242 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002058 | | | 0.65 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3189.00 ave 3189 max 3189 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: 27380.0 ave 27380 max 27380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27380 Ave neighs/atom = 86.645570 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 28 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) = 4.581 | 4.581 | 4.581 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1399.23 0 -1399.23 -1837.3353 Loop time of 7.789e-06 on 1 procs for 0 steps with 316 atoms 166.9% 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 | | 7.789e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3189.00 ave 3189 max 3189 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: 27432.0 ave 27432 max 27432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27432 Ave neighs/atom = 86.810127 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 28 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) = 4.581 | 4.581 | 4.581 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 -1399.23 -1399.23 11.117289 89.09199 3.5103252 -1837.3353 -1837.3353 -6.6865762 -5507.17 1.8505579 2.2952989 158.84908 Loop time of 7.277e-06 on 1 procs for 0 steps with 316 atoms 247.4% 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 | | 7.277e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3189.00 ave 3189 max 3189 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13716.0 ave 13716 max 13716 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27432.0 ave 27432 max 27432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27432 Ave neighs/atom = 86.810127 Neighbor list builds = 0 Dangerous builds = 0 316 -1399.22999417483 eV 2.29529889966488 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04