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 = 4.0501996 4.0501996 4.0501996 Created orthogonal box = (0.0000000 -43.054213 0.0000000) to (43.054213 43.054213 4.0501996) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7151610 5.7151610 4.0501996 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -43.054213 0.0000000) to (43.054213 43.054213 4.0501996) create_atoms CPU = 0.003 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7151610 5.7151610 4.0501996 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -43.054213 0.0000000) to (43.054213 43.054213 4.0501996) create_atoms CPU = 0.002 seconds 454 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 21 1 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 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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_060567868558_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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 4.981 | 4.981 | 4.981 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3196.9877 0 -3196.9877 11114.12 55 0 -3238.9352 0 -3238.9352 6635.4486 Loop time of 1.60266 on 1 procs for 55 steps with 906 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 = -3196.98771907877 -3238.93269331985 -3238.93520509431 Force two-norm initial, final = 37.803923 0.10085484 Force max component initial, final = 11.595768 0.0094265916 Final line search alpha, max atom move = 1.0000000 0.0094265916 Iterations, force evaluations = 55 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5559 | 1.5559 | 1.5559 | 0.0 | 97.08 Neigh | 0.017871 | 0.017871 | 0.017871 | 0.0 | 1.12 Comm | 0.01667 | 0.01667 | 0.01667 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01222 | | | 0.76 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7335.00 ave 7335 max 7335 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: 128208.0 ave 128208 max 128208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128208 Ave neighs/atom = 141.50993 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.981 | 4.981 | 4.981 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -3238.9352 0 -3238.9352 6635.4486 15015.428 67 0 -3239.4751 0 -3239.4751 11.766364 15150.674 Loop time of 0.250139 on 1 procs for 12 steps with 906 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 = -3238.93520509432 -3239.47238369841 -3239.47508925791 Force two-norm initial, final = 119.72042 0.39594455 Force max component initial, final = 104.84268 0.35307064 Final line search alpha, max atom move = 0.00027237680 9.6168250e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22215 | 0.22215 | 0.22215 | 0.0 | 88.81 Neigh | 0.017914 | 0.017914 | 0.017914 | 0.0 | 7.16 Comm | 0.002616 | 0.002616 | 0.002616 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007456 | | | 2.98 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7371.00 ave 7371 max 7371 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: 127172.0 ave 127172 max 127172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127172 Ave neighs/atom = 140.36645 Neighbor list builds = 1 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.119 | 5.119 | 5.119 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3239.4751 0 -3239.4751 11.766364 Loop time of 6.595e-06 on 1 procs for 0 steps with 906 atoms 151.6% 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 | | 6.595e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7371.00 ave 7371 max 7371 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: 127180.0 ave 127180 max 127180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127180 Ave neighs/atom = 140.37528 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.119 | 5.119 | 5.119 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 -3239.4751 -3239.4751 43.035886 87.131616 4.04041 11.766364 11.766364 37.321157 2.673066 -4.6951316 2.581431 183.27403 Loop time of 7.146e-06 on 1 procs for 0 steps with 906 atoms 237.9% 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 | | 7.146e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7371.00 ave 7371 max 7371 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63590.0 ave 63590 max 63590 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127180.0 ave 127180 max 127180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127180 Ave neighs/atom = 140.37528 Neighbor list builds = 0 Dangerous builds = 0 906 -3239.47508925791 eV 2.58143103673668 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02