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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -44.352095 0.0000000) to (36.213334 44.352095 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1733334 5.1291538 5.9736509 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -44.352095 0.0000000) to (36.213334 44.352095 8.9604763) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1733334 5.1291538 5.9736509 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -44.352095 0.0000000) to (36.213334 44.352095 8.9604763) create_atoms CPU = 0.001 seconds 1184 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 25 3 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2352 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.988 | 5.988 | 5.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8473.7677 0 -8473.7677 73319.277 871 0 -9258.9298 0 -9258.9298 -55808.306 Loop time of 28.8728 on 1 procs for 871 steps with 2352 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 = -8473.76772442592 -9258.92128367297 -9258.92983652002 Force two-norm initial, final = 1021.6856 0.29370072 Force max component initial, final = 176.41710 0.053918584 Final line search alpha, max atom move = 0.54358974 0.029309589 Iterations, force evaluations = 871 1709 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.108 | 28.108 | 28.108 | 0.0 | 97.35 Neigh | 0.41034 | 0.41034 | 0.41034 | 0.0 | 1.42 Comm | 0.14742 | 0.14742 | 0.14742 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2065 | | | 0.72 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7662.00 ave 7662 max 7662 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: 325584.0 ave 325584 max 325584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325584 Ave neighs/atom = 138.42857 Neighbor list builds = 17 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 871 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.986 | 5.986 | 5.986 Mbytes Step Temp E_pair E_mol TotEng Press Volume 871 0 -9258.9298 0 -9258.9298 -55808.306 28783.509 914 0 -9306.0757 0 -9306.0757 -24.714112 27827.769 Loop time of 0.798141 on 1 procs for 43 steps with 2352 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9258.92983652004 -9306.07274699352 -9306.0757276974 Force two-norm initial, final = 2114.0039 7.6721629 Force max component initial, final = 1544.9409 4.3440593 Final line search alpha, max atom move = 0.00016756514 0.00072791290 Iterations, force evaluations = 43 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.708 | 0.708 | 0.708 | 0.0 | 88.71 Neigh | 0.067622 | 0.067622 | 0.067622 | 0.0 | 8.47 Comm | 0.0035068 | 0.0035068 | 0.0035068 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01901 | | | 2.38 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7671.00 ave 7671 max 7671 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: 334108.0 ave 334108 max 334108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334108 Ave neighs/atom = 142.05272 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.123 | 6.123 | 6.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9306.0757 0 -9306.0757 -24.714112 Loop time of 2.529e-06 on 1 procs for 0 steps with 2352 atoms 158.2% 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 | | 2.529e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7660.00 ave 7660 max 7660 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: 334228.0 ave 334228 max 334228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334228 Ave neighs/atom = 142.10374 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.123 | 6.123 | 6.123 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 -9306.0757 -9306.0757 35.207707 85.72657 9.2198785 -24.714112 -24.714112 68.22803 114.97824 -257.3486 2.1649023 5124.541 Loop time of 2.609e-06 on 1 procs for 0 steps with 2352 atoms 345.0% 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 | | 2.609e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7660.00 ave 7660 max 7660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167114.0 ave 167114 max 167114 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 334228.0 ave 334228 max 334228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334228 Ave neighs/atom = 142.10374 Neighbor list builds = 0 Dangerous builds = 0 2352 -8973.45206825347 eV 2.16490227115803 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:30