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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -40.734352 0.0000000) to (28.803536 40.734352 5.7039502) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0829770 6.3897023 5.7039502 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.734352 0.0000000) to (28.803536 40.734352 5.7039502) create_atoms CPU = 0.003 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0829770 6.3897023 5.7039502 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.734352 0.0000000) to (28.803536 40.734352 5.7039502) create_atoms CPU = 0.002 seconds 410 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 808 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2618.6772 0 -2618.6772 17020.01 75 0 -2713.4759 0 -2713.4759 -423.48214 Loop time of 2.09415 on 1 procs for 75 steps with 808 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 = -2618.67722913484 -2713.47334909303 -2713.47588184035 Force two-norm initial, final = 162.70873 0.11992475 Force max component initial, final = 49.014915 0.020168661 Final line search alpha, max atom move = 1.0000000 0.020168661 Iterations, force evaluations = 75 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0085 | 2.0085 | 2.0085 | 0.0 | 95.91 Neigh | 0.052568 | 0.052568 | 0.052568 | 0.0 | 2.51 Comm | 0.017549 | 0.017549 | 0.017549 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01555 | | | 0.74 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5382.00 ave 5382 max 5382 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: 115304.0 ave 115304 max 115304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115304 Ave neighs/atom = 142.70297 Neighbor list builds = 3 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.960 | 4.960 | 4.960 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -2713.4759 0 -2713.4759 -423.48214 13384.814 79 0 -2713.5143 0 -2713.5143 -19.676061 13378.034 Loop time of 0.108985 on 1 procs for 4 steps with 808 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 = -2713.47588184034 -2713.51420887426 -2713.51433925102 Force two-norm initial, final = 20.350618 0.62370086 Force max component initial, final = 17.609671 0.59040577 Final line search alpha, max atom move = 0.00065338832 0.00038576423 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10601 | 0.10601 | 0.10601 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063901 | 0.00063901 | 0.00063901 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002333 | | | 2.14 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5039.00 ave 5039 max 5039 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: 114600.0 ave 114600 max 114600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114600 Ave neighs/atom = 141.83168 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.098 | 5.098 | 5.098 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2713.5143 0 -2713.5143 -19.676061 Loop time of 6.615e-06 on 1 procs for 0 steps with 808 atoms 181.4% 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 | | 6.615e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5023.00 ave 5023 max 5023 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: 114844.0 ave 114844 max 114844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114844 Ave neighs/atom = 142.13366 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.098 | 5.098 | 5.098 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 -2713.5143 -2713.5143 28.717739 81.658073 5.7048327 -19.676061 -19.676061 -70.497399 -3.3344637 14.80368 2.6042553 655.65205 Loop time of 6.996e-06 on 1 procs for 0 steps with 808 atoms 285.9% 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 | | 6.996e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5023.00 ave 5023 max 5023 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57422.0 ave 57422 max 57422 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114844.0 ave 114844 max 114844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114844 Ave neighs/atom = 142.13366 Neighbor list builds = 0 Dangerous builds = 0 808 -2713.51433925102 eV 2.60425525204769 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02