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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -54.949015 0.0000000) to (38.854821 54.949015 5.1464468) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1349717 6.2661157 5.1464468 Created 911 atoms using lattice units in orthogonal box = (0.0000000 -54.949015 0.0000000) to (38.854821 54.949015 5.1464468) create_atoms CPU = 0.007 seconds 911 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1349717 6.2661157 5.1464468 Created 915 atoms using lattice units in orthogonal box = (0.0000000 -54.949015 0.0000000) to (38.854821 54.949015 5.1464468) create_atoms CPU = 0.007 seconds 915 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 = 9 23 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 3 atoms, new total = 1823 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_609260676108_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 = 9 23 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) = 6.809 | 6.809 | 6.809 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5435.2894 0 -5435.2894 79203.105 80 0 -5969.4529 0 -5969.4529 3849.0816 Loop time of 9.64372 on 1 procs for 80 steps with 1823 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 = -5435.28942759141 -5969.44732159364 -5969.45294746838 Force two-norm initial, final = 997.72084 0.19792296 Force max component initial, final = 196.89713 0.013365534 Final line search alpha, max atom move = 1.0000000 0.013365534 Iterations, force evaluations = 80 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.4356 | 9.4356 | 9.4356 | 0.0 | 97.84 Neigh | 0.13483 | 0.13483 | 0.13483 | 0.0 | 1.40 Comm | 0.042637 | 0.042637 | 0.042637 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03066 | | | 0.32 Nlocal: 1823.00 ave 1823 max 1823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13357.0 ave 13357 max 13357 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: 579698.0 ave 579698 max 579698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579698 Ave neighs/atom = 317.99122 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 = 9 23 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 : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.809 | 6.809 | 6.809 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -5969.4529 0 -5969.4529 3849.0816 21975.679 84 0 -5969.5942 0 -5969.5942 -24.595321 22035.138 Loop time of 0.468454 on 1 procs for 4 steps with 1823 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5969.4529474684 -5969.59413024257 -5969.59424284709 Force two-norm initial, final = 107.40412 1.1785063 Force max component initial, final = 98.785673 0.99734850 Final line search alpha, max atom move = 0.00038178951 0.00038077720 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46044 | 0.46044 | 0.46044 | 0.0 | 98.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020479 | 0.0020479 | 0.0020479 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005964 | | | 1.27 Nlocal: 1823.00 ave 1823 max 1823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13363.0 ave 13363 max 13363 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: 579638.0 ave 579638 max 579638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579638 Ave neighs/atom = 317.95831 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 = 9 23 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) = 6.947 | 6.947 | 6.947 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5969.5942 0 -5969.5942 -24.595321 Loop time of 6.986e-06 on 1 procs for 0 steps with 1823 atoms 200.4% 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 | | 6.986e-06 | | |100.00 Nlocal: 1823.00 ave 1823 max 1823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13363.0 ave 13363 max 13363 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: 579214.0 ave 579214 max 579214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579214 Ave neighs/atom = 317.72573 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 = 9 23 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) = 6.947 | 6.947 | 6.947 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 -5969.5942 -5969.5942 38.854007 110.22277 5.1452753 -24.595321 -24.595321 29.172024 -30.457211 -72.500778 2.3135122 654.10025 Loop time of 7.026e-06 on 1 procs for 0 steps with 1823 atoms 256.2% 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 | | 7.026e-06 | | |100.00 Nlocal: 1823.00 ave 1823 max 1823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13363.0 ave 13363 max 13363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 289607.0 ave 289607 max 289607 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 579214.0 ave 579214 max 579214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579214 Ave neighs/atom = 317.72573 Neighbor list builds = 0 Dangerous builds = 0 1823 -5969.59424284709 eV 2.31351215820494 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11