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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -38.931832 0.0000000) to (19.465916 38.931832 3.6147299) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6986694 4.6986694 3.6147299 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -38.931832 0.0000000) to (19.465916 38.931832 3.6147299) create_atoms CPU = 0.001 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6986694 4.6986694 3.6147299 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -38.931832 0.0000000) to (19.465916 38.931832 3.6147299) create_atoms CPU = 0.000 seconds 233 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 8 29 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 459 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_887933271505_002#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1557.782 0 -1557.782 26634.718 15 0 -1615.2428 0 -1615.2428 896.79956 Loop time of 0.293387 on 1 procs for 15 steps with 459 atoms 15.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1557.78196303183 -1615.24202902298 -1615.24284467709 Force two-norm initial, final = 153.22624 0.096440377 Force max component initial, final = 54.074459 0.031270654 Final line search alpha, max atom move = 1.0000000 0.031270654 Iterations, force evaluations = 15 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29152 | 0.29152 | 0.29152 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096751 | 0.00096751 | 0.00096751 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009038 | | | 0.31 Nlocal: 459.000 ave 459 max 459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3235.00 ave 3235 max 3235 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: 24642.0 ave 24642 max 24642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24642 Ave neighs/atom = 53.686275 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -1615.2428 0 -1615.2428 896.79956 5478.8011 19 0 -1615.271 0 -1615.271 14.637606 5482.3595 Loop time of 0.0710811 on 1 procs for 4 steps with 459 atoms 16.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1615.24284467709 -1615.26979756209 -1615.27104353749 Force two-norm initial, final = 14.043029 0.80467285 Force max component initial, final = 8.5696100 0.56562858 Final line search alpha, max atom move = 0.00016669090 9.4285136e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.069874 | 0.069874 | 0.069874 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019815 | 0.00019815 | 0.00019815 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001009 | | | 1.42 Nlocal: 459.000 ave 459 max 459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3235.00 ave 3235 max 3235 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: 24694.0 ave 24694 max 24694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24694 Ave neighs/atom = 53.799564 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 1617.361 0 1617.361 14.637606 Loop time of 2.254e-06 on 1 procs for 0 steps with 459 atoms 88.7% 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 | | 2.254e-06 | | |100.00 Nlocal: 459.000 ave 459 max 459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3235.00 ave 3235 max 3235 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: 24698.0 ave 24698 max 24698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24698 Ave neighs/atom = 53.808279 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.591 | 4.591 | 4.591 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 1617.361 -1615.271 19.403132 77.992504 3.622787 14.637606 14.637606 57.077133 -165.57403 152.40972 2.2325663 253.1607 Loop time of 2.205e-06 on 1 procs for 0 steps with 459 atoms 90.7% 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 | | 2.205e-06 | | |100.00 Nlocal: 459.000 ave 459 max 459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3235.00 ave 3235 max 3235 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12349.0 ave 12349 max 12349 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24698.0 ave 24698 max 24698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24698 Ave neighs/atom = 53.808279 Neighbor list builds = 0 Dangerous builds = 0 459 1617.36095454426 eV 2.23256627240514 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00