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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -47.172258 0.0000000) to (22.237216 47.172258 5.1015671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6815191 5.7930843 5.1015671 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -47.172258 0.0000000) to (22.237216 47.172258 5.1015671) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6815191 5.7930843 5.1015671 Created 464 atoms using lattice units in orthogonal box = (0.0000000 -47.172258 0.0000000) to (22.237216 47.172258 5.1015671) create_atoms CPU = 0.001 seconds 464 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 16 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 912 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_151002396060_004#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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.695 | 6.695 | 6.695 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3146.8452 0 -3146.8452 18875.29 21 0 -3202.8365 0 -3202.8365 6008.4207 Loop time of 2.10378 on 1 procs for 21 steps with 912 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 = -3146.84519947407 -3202.83431141561 -3202.83646571546 Force two-norm initial, final = 75.244241 0.18254624 Force max component initial, final = 13.663473 0.011331112 Final line search alpha, max atom move = 1.0000000 0.011331112 Iterations, force evaluations = 21 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0874 | 2.0874 | 2.0874 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010511 | 0.010511 | 0.010511 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005904 | | | 0.28 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12856.0 ave 12856 max 12856 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: 572144.0 ave 572144 max 572144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 572144 Ave neighs/atom = 627.35088 Neighbor list builds = 0 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.695 | 6.695 | 6.695 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -3202.8365 0 -3202.8365 6008.4207 10702.88 27 0 -3203.015 0 -3203.015 -261.30821 10750.989 Loop time of 0.429735 on 1 procs for 6 steps with 912 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 = -3202.83646571548 -3203.01330008609 -3203.01501334653 Force two-norm initial, final = 84.619082 3.6960429 Force max component initial, final = 79.353377 3.3862655 Final line search alpha, max atom move = 0.00016209646 0.00054890165 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.421 | 0.421 | 0.421 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017058 | 0.0017058 | 0.0017058 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007028 | | | 1.64 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12856.0 ave 12856 max 12856 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: 572208.0 ave 572208 max 572208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 572208 Ave neighs/atom = 627.42105 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.833 | 6.833 | 6.833 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3203.015 0 -3203.015 -261.30821 Loop time of 3.828e-06 on 1 procs for 0 steps with 912 atoms 156.7% 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 | | 3.828e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12856.0 ave 12856 max 12856 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: 571408.0 ave 571408 max 571408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 571408 Ave neighs/atom = 626.54386 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.833 | 6.833 | 6.833 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 -3203.015 -3203.015 22.212967 94.787613 5.1061112 -261.30821 -261.30821 -504.09119 -196.82157 -83.011864 2.3078222 502.18285 Loop time of 4.791e-06 on 1 procs for 0 steps with 912 atoms 208.7% 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 | | 4.791e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12856.0 ave 12856 max 12856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 285704.0 ave 285704 max 285704 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 571408.0 ave 571408 max 571408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 571408 Ave neighs/atom = 626.54386 Neighbor list builds = 0 Dangerous builds = 0 912 -3203.01501334653 eV 2.30782217286751 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03