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 -44.271219 0.0000000) to (5.1120000 44.271219 6.2608958) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1120000 5.9028292 6.2608958 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -44.271219 0.0000000) to (5.1120000 44.271219 6.2608958) create_atoms CPU = 0.004 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1120000 5.9028292 6.2608958 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -44.271219 0.0000000) to (5.1120000 44.271219 6.2608958) create_atoms CPU = 0.003 seconds 122 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 = 2 33 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 242 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_003#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 = 2 33 3 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) = 4.417 | 4.417 | 4.417 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -805.51473 0 -805.51473 61639.083 17 0 -859.52224 0 -859.52224 9899.4543 Loop time of 0.629734 on 1 procs for 17 steps with 242 atoms 31.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -805.514725611436 -859.522237152911 -859.522237152911 Force two-norm initial, final = 118.80596 0.76790045 Force max component initial, final = 37.889196 0.14579280 Final line search alpha, max atom move = 1.8582640e-08 2.7092152e-09 Iterations, force evaluations = 17 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62208 | 0.62208 | 0.62208 | 0.0 | 98.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043967 | 0.0043967 | 0.0043967 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003253 | | | 0.52 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1942.00 ave 1942 max 1942 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: 13256.0 ave 13256 max 13256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13256 Ave neighs/atom = 54.776860 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 = 2 33 3 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.418 | 4.418 | 4.418 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -859.52224 0 -859.52224 9899.4543 2833.8626 24 0 -859.60699 0 -859.60699 -185.94965 2854.1801 Loop time of 0.0813787 on 1 procs for 7 steps with 242 atoms 33.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -859.522237152912 -859.60671841591 -859.606993157758 Force two-norm initial, final = 31.848595 0.94431179 Force max component initial, final = 25.422783 0.43872999 Final line search alpha, max atom move = 0.00072006908 0.00031591590 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.079148 | 0.079148 | 0.079148 | 0.0 | 97.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050992 | 0.00050992 | 0.00050992 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001721 | | | 2.11 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2038.00 ave 2038 max 2038 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: 13396.0 ave 13396 max 13396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13396 Ave neighs/atom = 55.355372 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 = 2 33 3 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) = 4.556 | 4.556 | 4.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -859.60699 0 -859.60699 -185.94965 Loop time of 6.645e-06 on 1 procs for 0 steps with 242 atoms 90.3% 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 | | 6.645e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2032.00 ave 2032 max 2032 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: 13380.0 ave 13380 max 13380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13380 Ave neighs/atom = 55.289256 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 = 2 33 3 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) = 4.556 | 4.556 | 4.556 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 -859.60699 -859.60699 5.1441334 88.556779 6.2653789 -185.94965 -185.94965 -149.45604 -246.31828 -162.07464 2.4613649 4.058824 Loop time of 6.485e-06 on 1 procs for 0 steps with 242 atoms 262.1% 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 | | 6.485e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2032.00 ave 2032 max 2032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6690.00 ave 6690 max 6690 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13380.0 ave 13380 max 13380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13380 Ave neighs/atom = 55.289256 Neighbor list builds = 0 Dangerous builds = 0 242 -859.606993157758 eV 2.46136494816259 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00