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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -45.057453 0.0000000) to (31.857943 45.057453 4.9753748) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4391610 6.0438205 4.9753748 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.057453 0.0000000) to (31.857943 45.057453 4.9753748) create_atoms CPU = 0.002 seconds 660 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4391610 6.0438205 4.9753748 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.057453 0.0000000) to (31.857943 45.057453 4.9753748) create_atoms CPU = 0.001 seconds 660 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1308 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_222110751402_000#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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 5.889 | 5.889 | 5.889 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5670.3351 0 -5670.3351 29144.881 62 0 -5716.4836 0 -5716.4836 1360.0023 Loop time of 2.08311 on 1 procs for 62 steps with 1308 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 = -5670.33513935668 -5716.47852814989 -5716.48358546207 Force two-norm initial, final = 101.82089 0.23815167 Force max component initial, final = 19.773186 0.024582542 Final line search alpha, max atom move = 1.0000000 0.024582542 Iterations, force evaluations = 62 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.068 | 2.068 | 2.068 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0083155 | 0.0083155 | 0.0083155 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006795 | | | 0.33 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8904.00 ave 8904 max 8904 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: 324032.0 ave 324032 max 324032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324032 Ave neighs/atom = 247.73089 Neighbor list builds = 0 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.892 | 5.892 | 5.892 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -5716.4836 0 -5716.4836 1360.0023 14283.682 63 0 -5716.4877 0 -5716.4877 865.39768 14287.757 Loop time of 0.0543789 on 1 procs for 1 steps with 1308 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 = -5716.48358546205 -5716.48358546205 -5716.48767282103 Force two-norm initial, final = 12.224059 4.7629617 Force max component initial, final = 10.842951 4.2067541 Final line search alpha, max atom move = 9.2225816e-05 0.00038797133 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053529 | 0.053529 | 0.053529 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001906 | 0.0001906 | 0.0001906 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006589 | | | 1.21 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8911.00 ave 8911 max 8911 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: 323376.0 ave 323376 max 323376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323376 Ave neighs/atom = 247.22936 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.030 | 6.030 | 6.030 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5716.4877 0 -5716.4877 865.39768 Loop time of 1.728e-06 on 1 procs for 0 steps with 1308 atoms 115.7% 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 | | 1.728e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8911.00 ave 8911 max 8911 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: 323408.0 ave 323408 max 323408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323408 Ave neighs/atom = 247.25382 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.030 | 6.030 | 6.030 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 -5716.4877 -5716.4877 31.848085 90.114906 4.9783349 865.39768 865.39768 -471.58395 3316.931 -249.15404 2.2357429 564.44537 Loop time of 1.81e-06 on 1 procs for 0 steps with 1308 atoms 221.0% 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 | | 1.81e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8911.00 ave 8911 max 8911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 161704.0 ave 161704 max 161704 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 323408.0 ave 323408 max 323408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323408 Ave neighs/atom = 247.25382 Neighbor list builds = 0 Dangerous builds = 0 1308 -5716.48767282103 eV 2.23574286514266 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02