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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -55.604755 0.0000000) to (15.133697 55.604755 9.9073306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4858703 6.1783061 6.6048870 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -55.604755 0.0000000) to (15.133697 55.604755 9.9073306) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4858703 6.1783061 6.6048870 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -55.604755 0.0000000) to (15.133697 55.604755 9.9073306) create_atoms CPU = 0.001 seconds 507 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 = 5 35 4 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 2 atoms, new total = 1008 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_099716416216_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 = 5 35 4 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) = 4.524 | 4.524 | 4.524 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2976.6313 0 -2976.6313 44636.147 85 0 -3376.3584 0 -3376.3584 3756.4401 Loop time of 5.09693 on 1 procs for 85 steps with 1008 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 = -2976.63126306613 -3376.35590973258 -3376.35841205001 Force two-norm initial, final = 460.42373 0.12247287 Force max component initial, final = 99.137221 0.026649562 Final line search alpha, max atom move = 1.0000000 0.026649562 Iterations, force evaluations = 85 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0656 | 5.0656 | 5.0656 | 0.0 | 99.39 Neigh | 0.016989 | 0.016989 | 0.016989 | 0.0 | 0.33 Comm | 0.0060933 | 0.0060933 | 0.0060933 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008253 | | | 0.16 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3726.00 ave 3726 max 3726 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: 77186.0 ave 77186 max 77186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77186 Ave neighs/atom = 76.573413 Neighbor list builds = 3 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 = 5 35 4 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.525 | 4.525 | 4.525 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -3376.3584 0 -3376.3584 3756.4401 16674.147 93 0 -3376.6319 0 -3376.6319 -3.5764402 16752.532 Loop time of 0.346653 on 1 procs for 8 steps with 1008 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 = -3376.35841205001 -3376.62872944745 -3376.63191396764 Force two-norm initial, final = 82.894643 0.25663452 Force max component initial, final = 77.818227 0.057673105 Final line search alpha, max atom move = 0.00019844326 1.1444839e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34445 | 0.34445 | 0.34445 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030625 | 0.00030625 | 0.00030625 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001894 | | | 0.55 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3761.00 ave 3761 max 3761 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: 77336.0 ave 77336 max 77336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77336 Ave neighs/atom = 76.722222 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 = 5 35 4 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) = 4.663 | 4.663 | 4.663 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3376.6319 0 -3376.6319 -3.5764402 Loop time of 1.91e-06 on 1 procs for 0 steps with 1008 atoms 209.4% 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 | | 1.91e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3763.00 ave 3763 max 3763 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: 77160.0 ave 77160 max 77160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77160 Ave neighs/atom = 76.547619 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 = 5 35 4 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) = 4.663 | 4.663 | 4.663 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 -3376.6319 -3376.6319 15.120604 112.08169 9.8849989 -3.5764402 -3.5764402 -2.4272625 -4.6045569 -3.6975012 2.5684362 499.56795 Loop time of 1.815e-06 on 1 procs for 0 steps with 1008 atoms 220.4% 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 | | 1.815e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3763.00 ave 3763 max 3763 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38580.0 ave 38580 max 38580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77160.0 ave 77160 max 77160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77160 Ave neighs/atom = 76.547619 Neighbor list builds = 0 Dangerous builds = 0 1008 -3376.63191396764 eV 2.56843624561165 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06