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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -30.575370 0.0000000) to (21.620051 30.575370 4.0498067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1722906 4.8276900 4.0498067 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -30.575370 0.0000000) to (21.620051 30.575370 4.0498067) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1722906 4.8276900 4.0498067 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.575370 0.0000000) to (21.620051 30.575370 4.0498067) create_atoms CPU = 0.001 seconds 230 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 = 7 18 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 452 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_260546967793_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 = 7 18 2 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) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1745.2412 0 -1745.2412 70227.686 78 0 -1926.9775 0 -1926.9775 -5385.5278 Loop time of 6.22623 on 1 procs for 78 steps with 452 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 = -1745.24118147712 -1926.97610040398 -1926.977528093 Force two-norm initial, final = 384.85684 0.11997168 Force max component initial, final = 133.42286 0.028523809 Final line search alpha, max atom move = 1.0000000 0.028523809 Iterations, force evaluations = 78 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2055 | 6.2055 | 6.2055 | 0.0 | 99.67 Neigh | 0.010295 | 0.010295 | 0.010295 | 0.0 | 0.17 Comm | 0.0052851 | 0.0052851 | 0.0052851 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005128 | | | 0.08 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3124.00 ave 3124 max 3124 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: 50464.0 ave 50464 max 50464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50464 Ave neighs/atom = 111.64602 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 18 2 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -1926.9775 0 -1926.9775 -5385.5278 5354.1771 83 0 -1927.0391 0 -1927.0391 2.2196382 5337.1117 Loop time of 0.386999 on 1 procs for 5 steps with 452 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 = -1926.977528093 -1927.03883466748 -1927.03914560089 Force two-norm initial, final = 36.085736 0.24728032 Force max component initial, final = 31.516809 0.14992965 Final line search alpha, max atom move = 0.00030181159 4.5250505e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38568 | 0.38568 | 0.38568 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023853 | 0.00023853 | 0.00023853 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001079 | | | 0.28 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3124.00 ave 3124 max 3124 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: 50416.0 ave 50416 max 50416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50416 Ave neighs/atom = 111.53982 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 = 7 18 2 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1927.0391 0 -1927.0391 2.2196382 Loop time of 2.505e-06 on 1 procs for 0 steps with 452 atoms 199.6% 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 | | 2.505e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3156.00 ave 3156 max 3156 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: 50432.0 ave 50432 max 50432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50432 Ave neighs/atom = 111.57522 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 = 7 18 2 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) = 4.597 | 4.597 | 4.597 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 -1927.0391 -1927.0391 21.536503 61.122154 4.0544549 2.2196382 2.2196382 -4.3232289 44.987154 -34.00501 2.2563975 425.90126 Loop time of 2.27e-06 on 1 procs for 0 steps with 452 atoms 220.3% 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 | | 2.27e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3156.00 ave 3156 max 3156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25216.0 ave 25216 max 25216 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50432.0 ave 50432 max 50432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50432 Ave neighs/atom = 111.57522 Neighbor list builds = 0 Dangerous builds = 0 452 -1927.03914560089 eV 2.25639754858732 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07