1LAMMPS (15 Jun 2020) 2# Demonstrate MLIAP interface to ChemSNAP potential 3 4# Initialize simulation 5 6variable nsteps index 100 7variable nrep equal 4 8variable a equal 5.83 9units metal 10 11# generate the box and atom positions using a FCC lattice 12 13variable nx equal ${nrep} 14variable nx equal 4 15variable ny equal ${nrep} 16variable ny equal 4 17variable nz equal ${nrep} 18variable nz equal 4 19 20boundary p p p 21 22lattice diamond $a 23lattice diamond 5.83 24Lattice spacing in x,y,z = 5.83 5.83 5.83 25region box block 0 ${nx} 0 ${ny} 0 ${nz} 26region box block 0 4 0 ${ny} 0 ${nz} 27region box block 0 4 0 4 0 ${nz} 28region box block 0 4 0 4 0 4 29create_box 2 box 30Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32) 31 1 by 2 by 2 MPI processor grid 32create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 33Created 512 atoms 34 create_atoms CPU = 0.000 seconds 35 36mass 1 114.76 37mass 2 30.98 38 39# choose potential 40 41include InP_JCPA2020.mliap 42# DATE: 2020-06-01 UNITS: metal 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) 43 44# Definition of SNAP+ZBL potential. 45 46variable zblcutinner index 4 47variable zblcutouter index 4.2 48variable zblz1 index 49 49variable zblz2 index 15 50 51# Specify hybrid with SNAP and ZBL 52 53pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor 54pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor 55pair_style hybrid/overlay zbl 4 4.2 mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor 56Reading potential file InP_JCPA2020.mliap.model with DATE: 2020-06-01 57Reading potential file InP_JCPA2020.mliap.descriptor with DATE: 2020-06-01 58SNAP keyword rcutfac 1.0 59SNAP keyword twojmax 6 60SNAP keyword nelems 2 61SNAP keyword elems In 62SNAP keyword radelems 3.81205 63SNAP keyword welems 1 64SNAP keyword rfac0 0.99363 65SNAP keyword rmin0 0.0 66SNAP keyword bzeroflag 1 67SNAP keyword wselfallflag 1 68SNAP keyword chemflag 1 69SNAP keyword bnormflag 1 70pair_coeff 1 1 zbl ${zblz1} ${zblz1} 71pair_coeff 1 1 zbl 49 ${zblz1} 72pair_coeff 1 1 zbl 49 49 73pair_coeff 1 2 zbl ${zblz1} ${zblz2} 74pair_coeff 1 2 zbl 49 ${zblz2} 75pair_coeff 1 2 zbl 49 15 76pair_coeff 2 2 zbl ${zblz2} ${zblz2} 77pair_coeff 2 2 zbl 15 ${zblz2} 78pair_coeff 2 2 zbl 15 15 79pair_coeff * * mliap In P 80 81 82# Setup output 83 84thermo 10 85thermo_modify norm yes 86 87# Set up NVE run 88 89timestep 0.5e-3 90neighbor 1.0 bin 91neigh_modify once no every 1 delay 0 check yes 92 93# Run MD 94 95velocity all create 300.0 4928459 loop geom 96fix 1 all nve 97run ${nsteps} 98run 100 99Neighbor list info ... 100 update every 1 steps, delay 0 steps, check yes 101 max neighbors/atom: 2000, page size: 100000 102 master list distance cutoff = 8.6589 103 ghost atom cutoff = 8.6589 104 binsize = 4.32945, bins = 6 6 6 105 2 neighbor lists, perpetual/occasional/extra = 2 0 0 106 (1) pair zbl, perpetual, half/full from (2) 107 attributes: half, newton on 108 pair build: halffull/newton 109 stencil: none 110 bin: none 111 (2) pair mliap, perpetual 112 attributes: full, newton on 113 pair build: full/bin/atomonly 114 stencil: full/bin/3d 115 bin: standard 116Per MPI rank memory allocation (min/avg/max) = 4.591 | 4.591 | 4.591 Mbytes 117Step Temp E_pair E_mol TotEng Press 118 0 300 -3.4805794 0 -3.4418771 1353.5968 119 10 285.84677 -3.4787531 0 -3.4418766 1611.7131 120 20 248.14649 -3.4738884 0 -3.4418756 2312.0308 121 30 198.94136 -3.4675394 0 -3.4418744 3168.1543 122 40 152.74831 -3.4615791 0 -3.4418734 3903.5749 123 50 121.9796 -3.4576091 0 -3.4418728 4387.1254 124 60 113.27555 -3.4564863 0 -3.4418729 4556.3003 125 70 125.68089 -3.4580873 0 -3.4418735 4431.2083 126 80 151.47475 -3.4614159 0 -3.4418745 4107.2369 127 90 179.18708 -3.4649919 0 -3.4418754 3739.5881 128 100 197.50662 -3.4673559 0 -3.441876 3492.7778 129Loop time of 5.01913 on 4 procs for 100 steps with 512 atoms 130 131Performance: 0.861 ns/day, 27.884 hours/ns, 19.924 timesteps/s 13299.7% CPU use with 4 MPI tasks x no OpenMP threads 133 134MPI task timing breakdown: 135Section | min time | avg time | max time |%varavg| %total 136--------------------------------------------------------------- 137Pair | 4.9328 | 4.9409 | 4.952 | 0.3 | 98.44 138Neigh | 0 | 0 | 0 | 0.0 | 0.00 139Comm | 0.065669 | 0.076754 | 0.084728 | 2.5 | 1.53 140Output | 0.000173 | 0.00028775 | 0.000617 | 0.0 | 0.01 141Modify | 0.000256 | 0.00026675 | 0.000281 | 0.0 | 0.01 142Other | | 0.0009633 | | | 0.02 143 144Nlocal: 128 ave 128 max 128 min 145Histogram: 4 0 0 0 0 0 0 0 0 0 146Nghost: 1099 ave 1099 max 1099 min 147Histogram: 4 0 0 0 0 0 0 0 0 0 148Neighs: 7808 ave 7808 max 7808 min 149Histogram: 4 0 0 0 0 0 0 0 0 0 150FullNghs: 15616 ave 15616 max 15616 min 151Histogram: 4 0 0 0 0 0 0 0 0 0 152 153Total # of neighbors = 62464 154Ave neighs/atom = 122 155Neighbor list builds = 0 156Dangerous builds = 0 157 158Total wall time: 0:00:05 159