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 = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -63.715883 0.0000000) to (22.526967 63.715883 4.9753746) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0438203 5.4391608 4.9753746 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -63.715883 0.0000000) to (22.526967 63.715883 4.9753746) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0438203 5.4391608 4.9753746 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.715883 0.0000000) to (22.526967 63.715883 4.9753746) create_atoms CPU = 0.002 seconds 658 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 27 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_149104665840_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.361 | 6.361 | 6.361 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5336.0202 0 -5336.0202 84617.991 74 0 -5741.8887 0 -5741.8887 4534.6994 Loop time of 3.29941 on 1 procs for 74 steps with 1312 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5336.02015309899 -5741.88405027892 -5741.88872991498 Force two-norm initial, final = 801.78522 0.21336877 Force max component initial, final = 227.54305 0.040907659 Final line search alpha, max atom move = 1.0000000 0.040907659 Iterations, force evaluations = 74 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2261 | 3.2261 | 3.2261 | 0.0 | 97.78 Neigh | 0.047022 | 0.047022 | 0.047022 | 0.0 | 1.43 Comm | 0.015615 | 0.015615 | 0.015615 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0107 | | | 0.32 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12688.0 ave 12688 max 12688 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: 428192.0 ave 428192 max 428192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428192 Ave neighs/atom = 326.36585 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.362 | 6.362 | 6.362 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -5741.8887 0 -5741.8887 4534.6994 14282.565 78 0 -5742.0037 0 -5742.0037 -13.876803 14320.903 Loop time of 0.182559 on 1 procs for 4 steps with 1312 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 = -5741.88872991498 -5742.00240110838 -5742.00367078683 Force two-norm initial, final = 82.728953 1.0956421 Force max component initial, final = 68.832169 0.97712929 Final line search alpha, max atom move = 9.5988273e-05 9.3792953e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.179 | 0.179 | 0.179 | 0.0 | 98.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006349 | 0.0006349 | 0.0006349 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002921 | | | 1.60 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12688.0 ave 12688 max 12688 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: 430052.0 ave 430052 max 430052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 430052 Ave neighs/atom = 327.78354 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.499 | 6.499 | 6.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5742.0037 0 -5742.0037 -13.876803 Loop time of 1.785e-06 on 1 procs for 0 steps with 1312 atoms 168.1% 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 | | 1.785e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12688.0 ave 12688 max 12688 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: 426944.0 ave 426944 max 426944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 426944 Ave neighs/atom = 325.41463 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.499 | 6.499 | 6.499 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 -5742.0037 -5742.0037 22.549184 127.79166 4.969779 -13.876803 -13.876803 -109.42589 28.608702 39.186783 2.273655 390.96772 Loop time of 2.551e-06 on 1 procs for 0 steps with 1312 atoms 235.2% 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 | | 2.551e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12688.0 ave 12688 max 12688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 213472.0 ave 213472 max 213472 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 426944.0 ave 426944 max 426944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 426944 Ave neighs/atom = 325.41463 Neighbor list builds = 0 Dangerous builds = 0 1312 -5742.00367078683 eV 2.27365495647324 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04