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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -42.836993 0.0000000) to (52.464388 42.836993 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9959300 5.5076134 5.9120667 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -42.836993 0.0000000) to (52.464388 42.836993 8.8681001) create_atoms CPU = 0.003 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9959300 5.5076134 5.9120667 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -42.836993 0.0000000) to (52.464388 42.836993 8.8681001) create_atoms CPU = 0.003 seconds 1690 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3356 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_390178379548_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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.608 | 5.608 | 5.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10688.338 0 -10688.338 67358.608 64 0 -11826.786 0 -11826.786 6025.4342 Loop time of 6.64863 on 1 procs for 64 steps with 3356 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 = -10688.3377553704 -11826.7743868652 -11826.7856710793 Force two-norm initial, final = 546.47819 0.31520416 Force max component initial, final = 52.575527 0.089604931 Final line search alpha, max atom move = 1.0000000 0.089604931 Iterations, force evaluations = 64 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5687 | 6.5687 | 6.5687 | 0.0 | 98.80 Neigh | 0.046491 | 0.046491 | 0.046491 | 0.0 | 0.70 Comm | 0.012109 | 0.012109 | 0.012109 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02131 | | | 0.32 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7586.00 ave 7586 max 7586 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: 259142.0 ave 259142 max 259142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259142 Ave neighs/atom = 77.217521 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.608 | 5.608 | 5.608 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -11826.786 0 -11826.786 6025.4342 39860.631 70 0 -11827.471 0 -11827.471 -14.843032 40028.594 Loop time of 0.458198 on 1 procs for 6 steps with 3356 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 = -11826.7856710793 -11827.4701757935 -11827.4708986973 Force two-norm initial, final = 301.20212 1.7377135 Force max component initial, final = 264.09326 1.1842943 Final line search alpha, max atom move = 9.8402988e-05 0.00011653809 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45344 | 0.45344 | 0.45344 | 0.0 | 98.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056237 | 0.00056237 | 0.00056237 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004196 | | | 0.92 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7573.00 ave 7573 max 7573 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: 259046.0 ave 259046 max 259046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259046 Ave neighs/atom = 77.188915 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.746 | 5.746 | 5.746 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11827.471 0 -11827.471 -14.843032 Loop time of 2.513e-06 on 1 procs for 0 steps with 3356 atoms 199.0% 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 | | 2.513e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7573.00 ave 7573 max 7573 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: 258924.0 ave 258924 max 258924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258924 Ave neighs/atom = 77.152563 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.746 | 5.746 | 5.746 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 -11827.471 -11827.471 52.509701 86.111175 8.8526088 -14.843032 -14.843032 -47.443267 34.413081 -31.498911 2.2841772 1889.7478 Loop time of 3.061e-06 on 1 procs for 0 steps with 3356 atoms 261.4% 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 | | 3.061e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7573.00 ave 7573 max 7573 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129462.0 ave 129462 max 129462 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258924.0 ave 258924 max 258924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258924 Ave neighs/atom = 77.152563 Neighbor list builds = 0 Dangerous builds = 0 3356 -11827.4708986973 eV 2.28417719641193 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07