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 -63.695224 0.0000000) to (39.005200 63.695224 9.9073306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2911612 6.1640539 6.6048871 Created 1487 atoms using lattice units in orthogonal box = (0.0000000 -63.695224 0.0000000) to (39.005200 63.695224 9.9073306) create_atoms CPU = 0.002 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2911612 6.1640539 6.6048871 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -63.695224 0.0000000) to (39.005200 63.695224 9.9073306) create_atoms CPU = 0.002 seconds 1493 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 38 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2975 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_618133763375_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.609 | 5.609 | 5.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9405.7242 0 -9405.7242 24913.832 81 0 -9969.8296 0 -9969.8296 2894.3903 Loop time of 14.2632 on 1 procs for 81 steps with 2975 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9405.72419532452 -9969.81969451655 -9969.82960423744 Force two-norm initial, final = 500.14760 0.26650073 Force max component initial, final = 91.118423 0.070667482 Final line search alpha, max atom move = 1.0000000 0.070667482 Iterations, force evaluations = 81 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.167 | 14.167 | 14.167 | 0.0 | 99.32 Neigh | 0.059974 | 0.059974 | 0.059974 | 0.0 | 0.42 Comm | 0.014606 | 0.014606 | 0.014606 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0219 | | | 0.15 Nlocal: 2975.00 ave 2975 max 2975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7734.00 ave 7734 max 7734 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: 231094.0 ave 231094 max 231094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231094 Ave neighs/atom = 77.678655 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.609 | 5.609 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -9969.8296 0 -9969.8296 2894.3903 49228.435 88 0 -9970.3445 0 -9970.3445 98.892485 49400.765 Loop time of 0.924168 on 1 procs for 7 steps with 2975 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 = -9969.82960423745 -9970.34297980849 -9970.34445719926 Force two-norm initial, final = 191.44260 5.4973350 Force max component initial, final = 181.34345 4.2863572 Final line search alpha, max atom move = 0.00019935809 0.00085451996 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91908 | 0.91908 | 0.91908 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063705 | 0.00063705 | 0.00063705 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004455 | | | 0.48 Nlocal: 2975.00 ave 2975 max 2975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7731.00 ave 7731 max 7731 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: 231022.0 ave 231022 max 231022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231022 Ave neighs/atom = 77.654454 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.747 | 5.747 | 5.747 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9970.3445 0 -9970.3445 98.892485 Loop time of 2.13e-06 on 1 procs for 0 steps with 2975 atoms 187.8% 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 | | 2.13e-06 | | |100.00 Nlocal: 2975.00 ave 2975 max 2975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7736.00 ave 7736 max 7736 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: 230930.0 ave 230930 max 230930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230930 Ave neighs/atom = 77.623529 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.747 | 5.747 | 5.747 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 -9970.3445 -9970.3445 38.966899 128.18371 9.8901978 98.892485 98.892485 79.893732 139.88174 76.901983 2.54387 1219.359 Loop time of 2.457e-06 on 1 procs for 0 steps with 2975 atoms 244.2% 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 | | 2.457e-06 | | |100.00 Nlocal: 2975.00 ave 2975 max 2975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7736.00 ave 7736 max 7736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115465.0 ave 115465 max 115465 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 230930.0 ave 230930 max 230930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230930 Ave neighs/atom = 77.623529 Neighbor list builds = 0 Dangerous builds = 0 2975 -9970.34445719926 eV 2.54387003853474 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15