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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -54.503146 0.0000000) to (22.249532 54.503146 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3398876 4.7233333 5.1383093 Created 602 atoms using lattice units in orthogonal box = (0.0000000 -54.503146 0.0000000) to (22.249532 54.503146 7.7074639) create_atoms CPU = 0.004 seconds 602 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3398876 4.7233333 5.1383093 Created 602 atoms using lattice units in orthogonal box = (0.0000000 -54.503146 0.0000000) to (22.249532 54.503146 7.7074639) create_atoms CPU = 0.003 seconds 602 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 38 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1204 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8004.9229 0 -8004.9229 37628.295 35 0 -8160.4975 0 -8160.4975 16799.769 Loop time of 3.76315 on 1 procs for 35 steps with 1204 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 = -8004.92292021395 -8160.49261167298 -8160.49749923469 Force two-norm initial, final = 85.965893 1.0001179 Force max component initial, final = 14.982994 0.26922006 Final line search alpha, max atom move = 1.0000000 0.26922006 Iterations, force evaluations = 35 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7356 | 3.7356 | 3.7356 | 0.0 | 99.27 Neigh | 0.013194 | 0.013194 | 0.013194 | 0.0 | 0.35 Comm | 0.0058621 | 0.0058621 | 0.0058621 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008469 | | | 0.23 Nlocal: 1204.00 ave 1204 max 1204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4184.00 ave 4184 max 4184 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: 69436.0 ave 69436 max 69436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69436 Ave neighs/atom = 57.671096 Neighbor list builds = 1 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -8160.4975 0 -8160.4975 16799.769 18693.213 38 0 -8160.738 0 -8160.738 6945.2373 18761.739 Loop time of 0.388187 on 1 procs for 3 steps with 1204 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 = -8160.49749923469 -8160.73737062636 -8160.73801293528 Force two-norm initial, final = 185.18844 1.0133681 Force max component initial, final = 136.62954 0.26107795 Final line search alpha, max atom move = 0.00024581949 6.4178047e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38543 | 0.38543 | 0.38543 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054249 | 0.00054249 | 0.00054249 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002217 | | | 0.57 Nlocal: 1204.00 ave 1204 max 1204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4021.00 ave 4021 max 4021 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: 69452.0 ave 69452 max 69452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69452 Ave neighs/atom = 57.684385 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.729 | 4.729 | 4.729 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8160.738 0 -8160.738 6945.2373 Loop time of 6.515e-06 on 1 procs for 0 steps with 1204 atoms 168.8% 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 | | 6.515e-06 | | |100.00 Nlocal: 1204.00 ave 1204 max 1204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3973.00 ave 3973 max 3973 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: 69428.0 ave 69428 max 69428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69428 Ave neighs/atom = 57.664452 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.729 | 4.729 | 4.729 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 -8160.738 -8160.738 22.296389 109.00629 7.719461 6945.2373 6945.2373 -11.081944 20836.852 9.9422756 2.3797248 823.69849 Loop time of 7.267e-06 on 1 procs for 0 steps with 1204 atoms 261.5% 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 | | 7.267e-06 | | |100.00 Nlocal: 1204.00 ave 1204 max 1204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3973.00 ave 3973 max 3973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34714.0 ave 34714 max 34714 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69428.0 ave 69428 max 69428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69428 Ave neighs/atom = 57.664452 Neighbor list builds = 0 Dangerous builds = 0 1204 -8160.73801293528 eV 2.37972484168854 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04