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 -46.673151 0.0000000) to (28.581351 46.673151 8.6176016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1966093 5.3037672 5.7450677 Created 1045 atoms using lattice units in orthogonal box = (0.0000000 -46.673151 0.0000000) to (28.581351 46.673151 8.6176016) create_atoms CPU = 0.002 seconds 1045 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1966093 5.3037672 5.7450677 Created 1069 atoms using lattice units in orthogonal box = (0.0000000 -46.673151 0.0000000) to (28.581351 46.673151 8.6176016) create_atoms CPU = 0.002 seconds 1069 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 = 6 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2112 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 = 6 20 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) = 7.324 | 7.324 | 7.324 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9237.4348 0 -9237.4348 2181.9274 13 0 -9245.0675 0 -9245.0675 4441.0223 Loop time of 0.965412 on 1 procs for 13 steps with 2112 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 = -9237.43483204708 -9245.06432573539 -9245.06754311318 Force two-norm initial, final = 14.390038 0.15491821 Force max component initial, final = 1.4799356 0.0083221831 Final line search alpha, max atom move = 1.0000000 0.0083221831 Iterations, force evaluations = 13 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95756 | 0.95756 | 0.95756 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0039662 | 0.0039662 | 0.0039662 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003888 | | | 0.40 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11852.0 ave 11852 max 11852 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: 678742.0 ave 678742 max 678742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 678742 Ave neighs/atom = 321.37405 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 20 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 : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.323 | 7.323 | 7.323 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -9245.0675 0 -9245.0675 4441.0223 22991.446 19 0 -9245.4937 0 -9245.4937 -117.39332 23054.362 Loop time of 0.286561 on 1 procs for 6 steps with 2112 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 = -9245.06754311317 -9245.49313255059 -9245.49366260562 Force two-norm initial, final = 168.01884 3.1534655 Force max component initial, final = 164.42741 2.3297037 Final line search alpha, max atom move = 0.00018921521 0.00044081537 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28242 | 0.28242 | 0.28242 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069161 | 0.00069161 | 0.00069161 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00345 | | | 1.20 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11721.0 ave 11721 max 11721 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: 687134.0 ave 687134 max 687134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 687134 Ave neighs/atom = 325.34754 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 = 6 20 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) = 7.460 | 7.460 | 7.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9245.4937 0 -9245.4937 -117.39332 Loop time of 2.418e-06 on 1 procs for 0 steps with 2112 atoms 165.4% 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 | | 2.418e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11590.0 ave 11590 max 11590 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: 677376.0 ave 677376 max 677376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 677376 Ave neighs/atom = 320.72727 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 = 6 20 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) = 7.460 | 7.460 | 7.460 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 -9245.4937 -9245.4937 28.520725 93.829888 8.6149218 -117.39332 -117.39332 -161.56071 -54.823075 -135.79617 2.3480638 596.70469 Loop time of 2.476e-06 on 1 procs for 0 steps with 2112 atoms 282.7% 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 | | 2.476e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11590.0 ave 11590 max 11590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338688.0 ave 338688 max 338688 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 677376.0 ave 677376 max 677376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 677376 Ave neighs/atom = 320.72727 Neighbor list builds = 0 Dangerous builds = 0 2112 -9245.49366260562 eV 2.34806380122167 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02