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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -57.485352 0.0000000) to (33.187528 57.485352 4.9657304) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4580262 4.5757202 4.9657304 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -57.485352 0.0000000) to (33.187528 57.485352 4.9657304) create_atoms CPU = 0.006 seconds 806 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4580262 4.5757202 4.9657304 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -57.485352 0.0000000) to (33.187528 57.485352 4.9657304) create_atoms CPU = 0.005 seconds 806 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 31 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1606 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.552 | 5.552 | 5.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6235.8535 0 -6235.8535 49693.269 242 0 -6476.3846 0 -6476.3846 -62442.743 Loop time of 13.3435 on 1 procs for 242 steps with 1606 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 = -6235.85349986946 -6476.37900579321 -6476.38458254533 Force two-norm initial, final = 369.62291 0.30650566 Force max component initial, final = 118.62008 0.085864309 Final line search alpha, max atom move = 0.60182296 0.051675112 Iterations, force evaluations = 242 471 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.082 | 13.082 | 13.082 | 0.0 | 98.04 Neigh | 0.071673 | 0.071673 | 0.071673 | 0.0 | 0.54 Comm | 0.10321 | 0.10321 | 0.10321 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08617 | | | 0.65 Nlocal: 1606.00 ave 1606 max 1606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9168.00 ave 9168 max 9168 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: 253296.0 ave 253296 max 253296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253296 Ave neighs/atom = 157.71856 Neighbor list builds = 2 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 242 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.550 | 5.550 | 5.550 Mbytes Step Temp E_pair E_mol TotEng Press Volume 242 0 -6476.3846 0 -6476.3846 -62442.743 18947.209 276 0 -6493.5205 0 -6493.5205 -19270.392 18031.494 Loop time of 1.11081 on 1 procs for 34 steps with 1606 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6476.38458254534 -6493.51488277082 -6493.52047043389 Force two-norm initial, final = 945.96715 13.435229 Force max component initial, final = 743.52617 11.972051 Final line search alpha, max atom move = 0.00027662043 0.0033117140 Iterations, force evaluations = 34 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0379 | 1.0379 | 1.0379 | 0.0 | 93.43 Neigh | 0.036037 | 0.036037 | 0.036037 | 0.0 | 3.24 Comm | 0.0082629 | 0.0082629 | 0.0082629 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02864 | | | 2.58 Nlocal: 1606.00 ave 1606 max 1606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9347.00 ave 9347 max 9347 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: 260980.0 ave 260980 max 260980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260980 Ave neighs/atom = 162.50311 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.689 | 5.689 | 5.689 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6493.5205 0 -6493.5205 -19270.392 Loop time of 6.485e-06 on 1 procs for 0 steps with 1606 atoms 169.6% 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 | | 6.485e-06 | | |100.00 Nlocal: 1606.00 ave 1606 max 1606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9347.00 ave 9347 max 9347 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: 261272.0 ave 261272 max 261272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261272 Ave neighs/atom = 162.68493 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.689 | 5.689 | 5.689 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 -6493.5205 -6493.5205 32.184341 114.9707 4.8730391 -19270.392 -19270.392 -1031.6133 -56767.24 -12.323246 2.2724146 6544.8808 Loop time of 6.966e-06 on 1 procs for 0 steps with 1606 atoms 287.1% 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 | | 6.966e-06 | | |100.00 Nlocal: 1606.00 ave 1606 max 1606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9347.00 ave 9347 max 9347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130636.0 ave 130636 max 130636 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 261272.0 ave 261272 max 261272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261272 Ave neighs/atom = 162.68493 Neighbor list builds = 0 Dangerous builds = 0 1606 -6493.52047043389 eV 2.27241457349973 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15