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 = 2.8509989 2.8509989 2.8509989 Created orthogonal box = (0.0000000 -40.117110 0.0000000) to (9.4556936 40.117110 4.0319213) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2980425 4.8626801 4.0319213 Created 132 atoms using lattice units in orthogonal box = (0.0000000 -40.117110 0.0000000) to (9.4556936 40.117110 4.0319213) create_atoms CPU = 0.001 seconds 132 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2980425 4.8626801 4.0319213 Created 134 atoms using lattice units in orthogonal box = (0.0000000 -40.117110 0.0000000) to (9.4556936 40.117110 4.0319213) create_atoms CPU = 0.000 seconds 134 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 ghost atom cutoff = 7 binsize = 3.5, bins = 3 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 264 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_262519520678_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 3 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1093.7713 0 -1093.7713 66722.214 21 0 -1126.9758 0 -1126.9758 4110.0949 Loop time of 0.611436 on 1 procs for 21 steps with 264 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 = -1093.77125860474 -1126.97474207704 -1126.97575231826 Force two-norm initial, final = 98.003283 0.10810680 Force max component initial, final = 29.731627 0.020313101 Final line search alpha, max atom move = 1.0000000 0.020313101 Iterations, force evaluations = 21 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60985 | 0.60985 | 0.60985 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094772 | 0.00094772 | 0.00094772 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006427 | | | 0.11 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3163.00 ave 3163 max 3163 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: 35664.0 ave 35664 max 35664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35664 Ave neighs/atom = 135.09091 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 3 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.434 | 4.434 | 4.434 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -1126.9758 0 -1126.9758 4110.0949 3058.8986 29 0 -1127.1107 0 -1127.1107 7.7356563 3065.6687 Loop time of 0.172577 on 1 procs for 8 steps with 264 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 = -1126.97575231826 -1127.11063140776 -1127.11065142108 Force two-norm initial, final = 33.742113 0.19422038 Force max component initial, final = 29.402419 0.073780381 Final line search alpha, max atom move = 0.0040589715 0.00029947246 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17093 | 0.17093 | 0.17093 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032024 | 0.00032024 | 0.00032024 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001327 | | | 0.77 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2955.00 ave 2955 max 2955 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: 33820.0 ave 33820 max 33820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33820 Ave neighs/atom = 128.10606 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 ghost atom cutoff = 7 binsize = 3.5, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1127.1107 0 -1127.1107 7.7356563 Loop time of 1.761e-06 on 1 procs for 0 steps with 264 atoms 170.4% 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 | | 1.761e-06 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2824.00 ave 2824 max 2824 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: 33516.0 ave 33516 max 33516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33516 Ave neighs/atom = 126.95455 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 ghost atom cutoff = 7 binsize = 3.5, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.571 | 4.571 | 4.571 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 -1127.1107 -1127.1107 9.4003278 80.691494 4.0416106 7.7356563 7.7356563 8.9711876 38.778781 -24.543 2.3944398 247.57578 Loop time of 1.615e-06 on 1 procs for 0 steps with 264 atoms 123.8% 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 | | 1.615e-06 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2824.00 ave 2824 max 2824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16758.0 ave 16758 max 16758 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33516.0 ave 33516 max 33516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33516 Ave neighs/atom = 126.95455 Neighbor list builds = 0 Dangerous builds = 0 264 -1127.11065142108 eV 2.39443976702712 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01