LAMMPS (15 Jun 2020) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP InP potential # Initialize simulation variable nsteps index 100 variable nrep equal 4 variable a equal 5.83 units metal # generate the box and atom positions using a FCC lattice variable nx equal ${nrep} variable nx equal 4 variable ny equal ${nrep} variable ny equal 4 variable nz equal ${nrep} variable nz equal 4 boundary p p p lattice diamond $a lattice diamond 5.83 Lattice spacing in x,y,z = 5.83 5.83 5.83 region box block 0 ${nx} 0 ${ny} 0 ${nz} region box block 0 4 0 ${ny} 0 ${nz} region box block 0 4 0 4 0 ${nz} region box block 0 4 0 4 0 4 create_box 2 box Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32) 1 by 2 by 2 MPI processor grid create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 Created 512 atoms create_atoms CPU = 0.000 seconds mass 1 114.76 mass 2 30.98 # choose potential include InP_JCPA2020.snap # DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) # Definition of SNAP+ZBL potential. variable zblcutinner index 4 variable zblcutouter index 4.2 variable zblz1 index 49 variable zblz2 index 15 # Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap pair_style hybrid/overlay zbl 4 ${zblcutouter} snap pair_style hybrid/overlay zbl 4 4.2 snap pair_coeff 1 1 zbl ${zblz1} ${zblz1} pair_coeff 1 1 zbl 49 ${zblz1} pair_coeff 1 1 zbl 49 49 pair_coeff 1 2 zbl ${zblz1} ${zblz2} pair_coeff 1 2 zbl 49 ${zblz2} pair_coeff 1 2 zbl 49 15 pair_coeff 2 2 zbl ${zblz2} ${zblz2} pair_coeff 2 2 zbl 15 ${zblz2} pair_coeff 2 2 zbl 15 15 pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01 SNAP Element = In, Radius 3.81205, Weight 1 SNAP Element = P, Radius 3.82945, Weight 0.929316 Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01 SNAP keyword rcutfac 1.0 SNAP keyword twojmax 6 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0.0 SNAP keyword bzeroflag 1 SNAP keyword quadraticflag 0 SNAP keyword wselfallflag 1 SNAP keyword chemflag 1 SNAP keyword bnormflag 1 # Setup output thermo 10 thermo_modify norm yes # Set up NVE run timestep 0.5e-3 neighbor 1.0 bin neigh_modify once no every 1 delay 0 check yes # Run MD velocity all create 300.0 4928459 loop geom fix 1 all nve run ${nsteps} run 100 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.6589 ghost atom cutoff = 8.6589 binsize = 4.32945, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair zbl, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (2) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.587 | 4.587 | 4.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -3.4805794 0 -3.4418771 1353.5968 10 285.84677 -3.4787531 0 -3.4418766 1611.7131 20 248.14649 -3.4738884 0 -3.4418756 2312.0308 30 198.94136 -3.4675394 0 -3.4418744 3168.1543 40 152.74831 -3.4615791 0 -3.4418734 3903.5749 50 121.9796 -3.4576091 0 -3.4418728 4387.1254 60 113.27555 -3.4564863 0 -3.4418729 4556.3003 70 125.68089 -3.4580873 0 -3.4418735 4431.2083 80 151.47475 -3.4614159 0 -3.4418745 4107.2369 90 179.18708 -3.4649919 0 -3.4418754 3739.5881 100 197.50662 -3.4673559 0 -3.441876 3492.7778 Loop time of 3.73974 on 4 procs for 100 steps with 512 atoms Performance: 1.155 ns/day, 20.776 hours/ns, 26.740 timesteps/s 98.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4687 | 3.5182 | 3.5985 | 2.7 | 94.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13897 | 0.21952 | 0.26888 | 10.7 | 5.87 Output | 0.00018191 | 0.00047094 | 0.0012944 | 0.0 | 0.01 Modify | 0.00013065 | 0.00013524 | 0.00014186 | 0.0 | 0.00 Other | | 0.001456 | | | 0.04 Nlocal: 128 ave 128 max 128 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1099 ave 1099 max 1099 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 7808 ave 7808 max 7808 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 15616 ave 15616 max 15616 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62464 Ave neighs/atom = 122 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:03