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 = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -36.898366 0.0000000) to (45.191084 36.898366 8.6176016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7515925 5.3670350 5.7450677 Created 1318 atoms using lattice units in orthogonal box = (0.0000000 -36.898366 0.0000000) to (45.191084 36.898366 8.6176016) create_atoms CPU = 0.002 seconds 1318 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7515925 5.3670350 5.7450677 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -36.898366 0.0000000) to (45.191084 36.898366 8.6176016) create_atoms CPU = 0.002 seconds 1324 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2628 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_306032198193_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 8.159 | 8.159 | 8.159 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8629.9636 0 -8629.9636 232293.35 64 0 -11467.938 0 -11467.938 1585.798 Loop time of 4.60573 on 1 procs for 64 steps with 2628 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8629.96356352196 -11467.9278816249 -11467.9375179733 Force two-norm initial, final = 3388.4387 0.31322362 Force max component initial, final = 462.67632 0.055691033 Final line search alpha, max atom move = 1.0000000 0.055691033 Iterations, force evaluations = 64 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4877 | 4.4877 | 4.4877 | 0.0 | 97.44 Neigh | 0.087676 | 0.087676 | 0.087676 | 0.0 | 1.90 Comm | 0.015834 | 0.015834 | 0.015834 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01455 | | | 0.32 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12646.0 ave 12646 max 12646 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: 863238.0 ave 863238 max 863238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 863238 Ave neighs/atom = 328.47717 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.156 | 8.156 | 8.156 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -11467.938 0 -11467.938 1585.798 28739.307 67 0 -11468.009 0 -11468.009 -5.4967793 28767.707 Loop time of 0.268254 on 1 procs for 3 steps with 2628 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 = -11467.9375179732 -11468.0080761695 -11468.0090627012 Force two-norm initial, final = 78.595967 0.98952258 Force max component initial, final = 78.299998 0.75337763 Final line search alpha, max atom move = 8.1320003e-05 6.1264671e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26514 | 0.26514 | 0.26514 | 0.0 | 98.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053205 | 0.00053205 | 0.00053205 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002583 | | | 0.96 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12314.0 ave 12314 max 12314 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: 857310.0 ave 857310 max 857310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 857310 Ave neighs/atom = 326.22146 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 8.294 | 8.294 | 8.294 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11468.009 0 -11468.009 -5.4967793 Loop time of 2.021e-06 on 1 procs for 0 steps with 2628 atoms 148.4% 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 | | 2.021e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12317.0 ave 12317 max 12317 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: 855946.0 ave 855946 max 855946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 855946 Ave neighs/atom = 325.70244 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 8.294 | 8.294 | 8.294 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 -11468.009 -11468.009 45.168439 73.934535 8.6143561 -5.4967793 -5.4967793 29.530323 -4.0781679 -41.942493 2.1934267 1336.4364 Loop time of 2.349e-06 on 1 procs for 0 steps with 2628 atoms 255.4% 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 | | 2.349e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12317.0 ave 12317 max 12317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 427973.0 ave 427973 max 427973 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 855946.0 ave 855946 max 855946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 855946 Ave neighs/atom = 325.70244 Neighbor list builds = 0 Dangerous builds = 0 2628 -11468.0090627012 eV 2.19342665412225 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05