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 = 3.6406460 3.6406460 3.6406460 Created orthogonal box = (0.0000000 -53.876641 0.0000000) to (43.990093 53.876641 8.9177251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4234361 5.1662532 5.9451500 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -53.876641 0.0000000) to (43.990093 53.876641 8.9177251) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4234361 5.1662532 5.9451500 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -53.876641 0.0000000) to (43.990093 53.876641 8.9177251) create_atoms CPU = 0.002 seconds 1758 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 23 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 4 atoms, new total = 3504 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_945018740343_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 23 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) = 13.39 | 13.39 | 13.39 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8277.7374 0 -8277.7374 184526.7 66 0 -11432.428 0 -11432.428 6197.1766 Loop time of 13.8959 on 1 procs for 66 steps with 3504 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 = -8277.73738022654 -11432.4170029022 -11432.4278997719 Force two-norm initial, final = 3718.2728 0.27210552 Force max component initial, final = 534.65731 0.011085133 Final line search alpha, max atom move = 1.0000000 0.011085133 Iterations, force evaluations = 66 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.726 | 13.726 | 13.726 | 0.0 | 98.77 Neigh | 0.11519 | 0.11519 | 0.11519 | 0.0 | 0.83 Comm | 0.029248 | 0.029248 | 0.029248 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02581 | | | 0.19 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15269.0 ave 15269 max 15269 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: 1.11366e+06 ave 1.11366e+06 max 1.11366e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1113658 Ave neighs/atom = 317.82477 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 = 10 23 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.39 | 13.39 | 13.39 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -11432.428 0 -11432.428 6197.1766 42270.703 73 0 -11433.285 0 -11433.285 185.92021 42446.328 Loop time of 1.13447 on 1 procs for 7 steps with 3504 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 = -11432.4278997718 -11433.2834615655 -11433.2849828399 Force two-norm initial, final = 335.23586 9.6323056 Force max component initial, final = 307.83370 7.7171198 Final line search alpha, max atom move = 8.9440269e-05 0.00069022127 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.127 | 1.127 | 1.127 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011029 | 0.0011029 | 0.0011029 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006334 | | | 0.56 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15266.0 ave 15266 max 15266 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: 1.11289e+06 ave 1.11289e+06 max 1.11289e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1112888 Ave neighs/atom = 317.60502 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 = 10 23 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) = 12.91 | 12.91 | 12.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11433.285 0 -11433.285 185.92021 Loop time of 2.267e-06 on 1 procs for 0 steps with 3504 atoms 0.0% 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 | | 2.267e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15266.0 ave 15266 max 15266 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: 1.11204e+06 ave 1.11204e+06 max 1.11204e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1112038 Ave neighs/atom = 317.36244 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 = 10 23 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) = 12.91 | 12.91 | 12.91 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 -11433.285 -11433.285 43.949678 108.40719 8.9089459 185.92021 185.92021 55.181281 293.05765 209.52171 2.2416812 1598.1516 Loop time of 1.1595e-05 on 1 procs for 0 steps with 3504 atoms 172.5% 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 | | 1.16e-05 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15266.0 ave 15266 max 15266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 556019.0 ave 556019 max 556019 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.11204e+06 ave 1.11204e+06 max 1.11204e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1112038 Ave neighs/atom = 317.36244 Neighbor list builds = 0 Dangerous builds = 0 3504 -11433.2849828399 eV 2.24168116006268 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16