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 -41.665669 0.0000000) to (51.029815 41.665669 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8319788 5.3570146 5.7504086 Created 1662 atoms using lattice units in orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029815 41.665669 8.6256130) create_atoms CPU = 0.003 seconds 1662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8319788 5.3570146 5.7504086 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029815 41.665669 8.6256130) create_atoms CPU = 0.003 seconds 1686 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 27 3 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3342 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.693 | 5.693 | 5.693 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13661.295 0 -13661.295 124159.83 160 0 -14799.573 0 -14799.573 2580.4455 Loop time of 36.8876 on 1 procs for 160 steps with 3342 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13661.2952792537 -14799.5599270975 -14799.573421844 Force two-norm initial, final = 1264.6228 0.40441595 Force max component initial, final = 111.44453 0.11810281 Final line search alpha, max atom move = 1.0000000 0.11810281 Iterations, force evaluations = 160 303 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 36.754 | 36.754 | 36.754 | 0.0 | 99.64 Neigh | 0.053331 | 0.053331 | 0.053331 | 0.0 | 0.14 Comm | 0.030879 | 0.030879 | 0.030879 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04969 | | | 0.13 Nlocal: 3342.00 ave 3342 max 3342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8244.00 ave 8244 max 8244 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: 286438.0 ave 286438 max 286438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286438 Ave neighs/atom = 85.708558 Neighbor list builds = 2 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 160 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.690 | 5.690 | 5.690 Mbytes Step Temp E_pair E_mol TotEng Press Volume 160 0 -14799.573 0 -14799.573 2580.4455 36679.408 164 0 -14799.824 0 -14799.824 -2.9462146 36730.859 Loop time of 0.823684 on 1 procs for 4 steps with 3342 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 = -14799.573421844 -14799.8236312479 -14799.8243974416 Force two-norm initial, final = 172.77505 0.83684333 Force max component initial, final = 172.13248 0.46213805 Final line search alpha, max atom move = 8.5726629e-05 3.9617538e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81962 | 0.81962 | 0.81962 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051094 | 0.00051094 | 0.00051094 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003558 | | | 0.43 Nlocal: 3342.00 ave 3342 max 3342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8242.00 ave 8242 max 8242 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: 286384.0 ave 286384 max 286384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286384 Ave neighs/atom = 85.692400 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.828 | 5.828 | 5.828 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14799.824 0 -14799.824 -2.9462146 Loop time of 2.461e-06 on 1 procs for 0 steps with 3342 atoms 162.5% 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 | | 2.461e-06 | | |100.00 Nlocal: 3342.00 ave 3342 max 3342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8243.00 ave 8243 max 8243 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: 286294.0 ave 286294 max 286294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286294 Ave neighs/atom = 85.665470 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.828 | 5.828 | 5.828 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 -14799.824 -14799.824 51.004269 83.574853 8.616858 -2.9462146 -2.9462146 17.740591 -6.4415294 -20.137705 2.2526437 1730.5437 Loop time of 2.422e-06 on 1 procs for 0 steps with 3342 atoms 206.4% 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 | | 2.422e-06 | | |100.00 Nlocal: 3342.00 ave 3342 max 3342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8243.00 ave 8243 max 8243 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143147.0 ave 143147 max 143147 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 286294.0 ave 286294 max 286294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286294 Ave neighs/atom = 85.665470 Neighbor list builds = 0 Dangerous builds = 0 3342 -14799.8243974416 eV 2.25264368156001 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:38