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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -63.704815 0.0000000) to (39.011073 63.704815 9.9088223) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2921085 6.1649821 6.6058816 Created 1488 atoms using lattice units in orthogonal box = (0.0000000 -63.704815 0.0000000) to (39.011073 63.704815 9.9088223) create_atoms CPU = 0.007 seconds 1488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2921085 6.1649821 6.6058816 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -63.704815 0.0000000) to (39.011073 63.704815 9.9088223) create_atoms CPU = 0.006 seconds 1494 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 = 10 30 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 6 atoms, new total = 2976 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_106969701023_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 = 10 30 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) = 6.518 | 6.518 | 6.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9340.457 0 -9340.457 43064.152 78 0 -10128.409 0 -10128.409 3767.1515 Loop time of 7.20247 on 1 procs for 78 steps with 2976 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 = -9340.4570133029 -10128.3990379556 -10128.4087294483 Force two-norm initial, final = 878.93218 0.22143303 Force max component initial, final = 151.03907 0.034917760 Final line search alpha, max atom move = 1.0000000 0.034917760 Iterations, force evaluations = 78 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9297 | 6.9297 | 6.9297 | 0.0 | 96.21 Neigh | 0.19731 | 0.19731 | 0.19731 | 0.0 | 2.74 Comm | 0.033167 | 0.033167 | 0.033167 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04225 | | | 0.59 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10224.0 ave 10224 max 10224 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: 423804.0 ave 423804 max 423804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423804 Ave neighs/atom = 142.40726 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 30 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.521 | 6.521 | 6.521 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -10128.409 0 -10128.409 3767.1515 49250.675 85 0 -10129.022 0 -10129.022 -8.4289724 49479.959 Loop time of 0.470623 on 1 procs for 7 steps with 2976 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10128.4087294482 -10129.018499303 -10129.0224759834 Force two-norm initial, final = 231.59740 0.57291195 Force max component initial, final = 209.31754 0.38366710 Final line search alpha, max atom move = 0.00010160159 3.8981186e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45964 | 0.45964 | 0.45964 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020016 | 0.0020016 | 0.0020016 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008983 | | | 1.91 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10327.0 ave 10327 max 10327 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: 422410.0 ave 422410 max 422410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 422410 Ave neighs/atom = 141.93884 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 = 10 31 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) = 6.660 | 6.660 | 6.660 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10129.022 0 -10129.022 -8.4289724 Loop time of 6.275e-06 on 1 procs for 0 steps with 2976 atoms 207.2% 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 | | 6.275e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10327.0 ave 10327 max 10327 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: 421524.0 ave 421524 max 421524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 421524 Ave neighs/atom = 141.64113 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 = 10 31 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) = 6.660 | 6.660 | 6.660 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 -10129.022 -10129.022 38.99642 128.24479 9.89384 -8.4289724 -8.4289724 -12.418594 -8.7206859 -4.1476376 2.5316778 1169.8734 Loop time of 6.675e-06 on 1 procs for 0 steps with 2976 atoms 299.6% 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 | | 6.675e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10327.0 ave 10327 max 10327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210762.0 ave 210762 max 210762 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 421524.0 ave 421524 max 421524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 421524 Ave neighs/atom = 141.64113 Neighbor list builds = 0 Dangerous builds = 0 2976 -10129.0224759834 eV 2.53167778818838 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08