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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -43.286809 0.0000000) to (53.015297 43.286809 8.9612207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0588911 5.5654468 5.9741471 Created 1664 atoms using lattice units in orthogonal box = (0.0000000 -43.286809 0.0000000) to (53.015297 43.286809 8.9612207) create_atoms CPU = 0.004 seconds 1664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0588911 5.5654468 5.9741471 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -43.286809 0.0000000) to (53.015297 43.286809 8.9612207) create_atoms CPU = 0.003 seconds 1688 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 3344 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.439 | 7.439 | 7.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12843.359 0 -12843.359 9802.3663 1347 0 -13197.195 0 -13197.195 -79336.164 Loop time of 99.8874 on 1 procs for 1347 steps with 3344 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12843.3588108007 -13197.1859668689 -13197.1945956184 Force two-norm initial, final = 87.233189 0.27963766 Force max component initial, final = 8.1314323 0.032073455 Final line search alpha, max atom move = 1.0000000 0.032073455 Iterations, force evaluations = 1347 2609 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 98.155 | 98.155 | 98.155 | 0.0 | 98.27 Neigh | 0.93672 | 0.93672 | 0.93672 | 0.0 | 0.94 Comm | 0.3415 | 0.3415 | 0.3415 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4541 | | | 0.45 Nlocal: 3344.00 ave 3344 max 3344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11964.0 ave 11964 max 11964 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: 675866.0 ave 675866 max 675866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 675866 Ave neighs/atom = 202.11304 Neighbor list builds = 21 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1347 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.439 | 7.439 | 7.439 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1347 0 -13197.195 0 -13197.195 -79336.164 41129.548 1412 0 -13344.54 0 -13344.54 -31.272848 39140.757 Loop time of 2.78353 on 1 procs for 65 steps with 3344 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 = -13197.1945956186 -13344.5369101243 -13344.5399026293 Force two-norm initial, final = 4300.4267 11.779194 Force max component initial, final = 3144.0105 7.3190634 Final line search alpha, max atom move = 0.00025982495 0.0019016753 Iterations, force evaluations = 65 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5581 | 2.5581 | 2.5581 | 0.0 | 91.90 Neigh | 0.1714 | 0.1714 | 0.1714 | 0.0 | 6.16 Comm | 0.0074535 | 0.0074535 | 0.0074535 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04658 | | | 1.67 Nlocal: 3344.00 ave 3344 max 3344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11962.0 ave 11962 max 11962 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: 729460.0 ave 729460 max 729460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 729460 Ave neighs/atom = 218.13995 Neighbor list builds = 4 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.956 | 7.956 | 7.956 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13344.54 0 -13344.54 -31.272848 Loop time of 2.38e-06 on 1 procs for 0 steps with 3344 atoms 210.1% 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 | | 2.38e-06 | | |100.00 Nlocal: 3344.00 ave 3344 max 3344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11861.0 ave 11861 max 11861 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: 732518.0 ave 732518 max 732518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732518 Ave neighs/atom = 219.05443 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.956 | 7.956 | 7.956 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 -13344.54 -13344.54 50.948227 82.17306 9.349119 -31.272848 -31.272848 247.04228 -28.295955 -312.56487 2.3330184 4007.7967 Loop time of 2.659e-06 on 1 procs for 0 steps with 3344 atoms 300.9% 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 | | 2.659e-06 | | |100.00 Nlocal: 3344.00 ave 3344 max 3344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11861.0 ave 11861 max 11861 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 366259.0 ave 366259 max 366259 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 732518.0 ave 732518 max 732518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732518 Ave neighs/atom = 219.05443 Neighbor list builds = 0 Dangerous builds = 0 3344 -13344.5399026292 eV 2.33301837597869 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:43