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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -59.855366 0.0000000) to (48.871701 59.855366 9.9073306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0252782 5.7395556 6.6048871 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -59.855366 0.0000000) to (48.871701 59.855366 9.9073306) create_atoms CPU = 0.002 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0252782 5.7395556 6.6048871 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -59.855366 0.0000000) to (48.871701 59.855366 9.9073306) create_atoms CPU = 0.002 seconds 1755 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 15 36 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 3491 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_618133763375_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 15 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.707 | 5.707 | 5.707 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11064.416 0 -11064.416 24621.399 82 0 -11694.421 0 -11694.421 938.34051 Loop time of 16.545 on 1 procs for 82 steps with 3491 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 = -11064.415910213 -11694.4122836658 -11694.4214210723 Force two-norm initial, final = 498.62399 0.27780109 Force max component initial, final = 58.514329 0.10627079 Final line search alpha, max atom move = 1.0000000 0.10627079 Iterations, force evaluations = 82 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.461 | 16.461 | 16.461 | 0.0 | 99.49 Neigh | 0.043454 | 0.043454 | 0.043454 | 0.0 | 0.26 Comm | 0.015472 | 0.015472 | 0.015472 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02537 | | | 0.15 Nlocal: 3491.00 ave 3491 max 3491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8468.00 ave 8468 max 8468 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: 270910.0 ave 270910 max 270910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270910 Ave neighs/atom = 77.602406 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 15 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.712 | 5.712 | 5.712 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -11694.421 0 -11694.421 938.34051 57962.512 87 0 -11694.693 0 -11694.693 102.15258 58023.296 Loop time of 0.836228 on 1 procs for 5 steps with 3491 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 = -11694.4214210724 -11694.6915227759 -11694.6934074794 Force two-norm initial, final = 118.92818 6.6660336 Force max component initial, final = 117.29737 5.0791124 Final line search alpha, max atom move = 0.00014099641 0.00071613660 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83209 | 0.83209 | 0.83209 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000502 | 0.000502 | 0.000502 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003632 | | | 0.43 Nlocal: 3491.00 ave 3491 max 3491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8255.00 ave 8255 max 8255 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: 271022.0 ave 271022 max 271022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271022 Ave neighs/atom = 77.634489 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.851 | 5.851 | 5.851 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11694.693 0 -11694.693 102.15258 Loop time of 2.79e-06 on 1 procs for 0 steps with 3491 atoms 179.2% 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 | | 2.79e-06 | | |100.00 Nlocal: 3491.00 ave 3491 max 3491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8312.00 ave 8312 max 8312 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: 270940.0 ave 270940 max 270940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270940 Ave neighs/atom = 77.611000 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.851 | 5.851 | 5.851 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 -11694.693 -11694.693 48.763447 120.21696 9.8978815 102.15258 102.15258 69.710137 140.84079 95.9068 2.520037 1885.9856 Loop time of 2.732e-06 on 1 procs for 0 steps with 3491 atoms 292.8% 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 | | 2.732e-06 | | |100.00 Nlocal: 3491.00 ave 3491 max 3491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8312.00 ave 8312 max 8312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135470.0 ave 135470 max 135470 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270940.0 ave 270940 max 270940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270940 Ave neighs/atom = 77.611000 Neighbor list builds = 0 Dangerous builds = 0 3491 -11694.6934074794 eV 2.52003699267972 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18