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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -41.630490 0.0000000) to (50.982420 41.630490 8.6176019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8265623 5.3520392 5.7450679 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -41.630490 0.0000000) to (50.982420 41.630490 8.6176019) create_atoms CPU = 0.003 seconds 1687 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8265623 5.3520392 5.7450679 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -41.630490 0.0000000) to (50.982420 41.630490 8.6176019) create_atoms CPU = 0.002 seconds 1687 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 62 atoms, new total = 3312 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 12.17 | 12.17 | 12.17 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14332.379 0 -14332.379 16999.766 43 0 -14463.417 0 -14463.417 -15451.398 Loop time of 3.32722 on 1 procs for 43 steps with 3312 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14332.3794171806 -14463.4036664158 -14463.4165411632 Force two-norm initial, final = 156.64309 0.32109805 Force max component initial, final = 12.924597 0.023720271 Final line search alpha, max atom move = 1.0000000 0.023720271 Iterations, force evaluations = 43 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2581 | 3.2581 | 3.2581 | 0.0 | 97.92 Neigh | 0.044974 | 0.044974 | 0.044974 | 0.0 | 1.35 Comm | 0.010811 | 0.010811 | 0.010811 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01334 | | | 0.40 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12970.0 ave 12970 max 12970 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: 809952.0 ave 809952 max 809952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 809952 Ave neighs/atom = 244.55072 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.16 | 12.16 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -14463.417 0 -14463.417 -15451.398 36580.395 47 0 -14464.149 0 -14464.149 -6033.6518 36374.77 Loop time of 0.299494 on 1 procs for 4 steps with 3312 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 = -14463.416541163 -14464.1489276439 -14464.1489341062 Force two-norm initial, final = 365.53216 0.63468215 Force max component initial, final = 268.41766 0.45340850 Final line search alpha, max atom move = 0.0036622822 0.0016605099 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29532 | 0.29532 | 0.29532 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062122 | 0.00062122 | 0.00062122 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003553 | | | 1.19 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12708.0 ave 12708 max 12708 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: 813692.0 ave 813692 max 813692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 813692 Ave neighs/atom = 245.67995 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.68 | 11.68 | 11.68 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14464.149 0 -14464.149 -6033.6518 Loop time of 2.244e-06 on 1 procs for 0 steps with 3312 atoms 178.3% 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 | | 2.244e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12708.0 ave 12708 max 12708 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: 814548.0 ave 814548 max 814548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 814548 Ave neighs/atom = 245.93841 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.68 | 11.68 | 11.68 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 -14464.149 -14464.149 50.834036 83.26098 8.5941741 -6033.6518 -6033.6518 -8.4611049 -18112.411 19.916705 2.3201304 1605.3668 Loop time of 2.33e-06 on 1 procs for 0 steps with 3312 atoms 343.3% 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 | | 2.33e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12708.0 ave 12708 max 12708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 407274.0 ave 407274 max 407274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 814548.0 ave 814548 max 814548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 814548 Ave neighs/atom = 245.93841 Neighbor list builds = 0 Dangerous builds = 0 3312 -14464.1489341062 eV 2.3201303547447 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04