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 = 3.6583648 3.6583648 3.6583648 Created orthogonal box = (0.0000000 -73.349986 0.0000000) to (42.348634 73.349986 6.3364737) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6886225 5.8388049 6.3364737 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -73.349986 0.0000000) to (42.348634 73.349986 6.3364737) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6886225 5.8388049 6.3364737 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -73.349986 0.0000000) to (42.348634 73.349986 6.3364737) create_atoms CPU = 0.004 seconds 1610 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_769582363439_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.653 | 6.653 | 6.653 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11866.38 0 -11866.38 69287.42 486 0 -12985.833 0 -12985.833 -49049.258 Loop time of 22.7519 on 1 procs for 486 steps with 3216 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11866.3797392334 -12985.8202587978 -12985.8330709532 Force two-norm initial, final = 1601.1013 0.33854467 Force max component initial, final = 431.26691 0.039382987 Final line search alpha, max atom move = 0.90273911 0.035552562 Iterations, force evaluations = 486 938 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.108 | 22.108 | 22.108 | 0.0 | 97.17 Neigh | 0.29186 | 0.29186 | 0.29186 | 0.0 | 1.28 Comm | 0.17742 | 0.17742 | 0.17742 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1742 | | | 0.77 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12552.0 ave 12552 max 12552 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: 439140.0 ave 439140 max 439140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439140 Ave neighs/atom = 136.54851 Neighbor list builds = 10 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 486 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.652 | 6.652 | 6.652 Mbytes Step Temp E_pair E_mol TotEng Press Volume 486 0 -12985.833 0 -12985.833 -49049.258 39365.618 514 0 -13013.149 0 -13013.149 -30.529309 37961.695 Loop time of 0.912202 on 1 procs for 28 steps with 3216 atoms 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12985.8330709533 -13013.1462024309 -13013.148879538 Force two-norm initial, final = 2156.8387 7.0038179 Force max component initial, final = 1470.7079 3.8774057 Final line search alpha, max atom move = 6.4587124e-05 0.00025043048 Iterations, force evaluations = 28 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82473 | 0.82473 | 0.82473 | 0.0 | 90.41 Neigh | 0.059088 | 0.059088 | 0.059088 | 0.0 | 6.48 Comm | 0.004486 | 0.004486 | 0.004486 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0239 | | | 2.62 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12622.0 ave 12622 max 12622 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: 456192.0 ave 456192 max 456192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 456192 Ave neighs/atom = 141.85075 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.790 | 6.790 | 6.790 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13013.149 0 -13013.149 -30.529309 Loop time of 2.515e-06 on 1 procs for 0 steps with 3216 atoms 159.0% 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 | | 2.515e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12602.0 ave 12602 max 12602 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: 456594.0 ave 456594 max 456594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 456594 Ave neighs/atom = 141.97575 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.790 | 6.790 | 6.790 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 -13013.149 -13013.149 41.42906 144.18896 6.3548971 -30.529309 -30.529309 81.715431 -160.84515 -12.458205 2.2401188 7021.7704 Loop time of 2.97e-06 on 1 procs for 0 steps with 3216 atoms 235.7% 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 | | 2.97e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12602.0 ave 12602 max 12602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 228297.0 ave 228297 max 228297 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 456594.0 ave 456594 max 456594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 456594 Ave neighs/atom = 141.97575 Neighbor list builds = 0 Dangerous builds = 0 3216 -13013.1488795379 eV 2.2401187850307 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24