Purpose:
Create patchy or rigid particles for LAMMPS input.
Description:
The patch tool creates large multi-atom particles and writes them out as a LAMMPS data file. They need to be simulated with a soft potential in LAMMPS to un-overlap them before they form a proper ensemble.
The individual particles consist of a collection of Lennard-Jones atoms of various types. By defining force field coefficients appropriately, specific atoms can be made attractive or repulsive, so that "patches" of atoms on the particle surface are reactive. The Pizza.py WWW site has example images and movies of simulations using such particles. A paper by Sharon Glotzer's group at U Michigan describing a variety of patchy particle models was the motivation for this tool.
The patch constructor takes a volume fraction as an argument to determine how densely to fill the simulation box. Optionally, the box shape can also be specified.
The build() method creates N particles, each of speficied style and with specified atom types. Several styles are available and new ones can easily be added to patch.py. You will need to look in patch.py for the details of what each style represents. For example, "hex2" uses a C60 bucky ball as a template and creates hexagonal 6-atom patches (atoms of a different type) on either side of the ball.
The build() method can be invoked multiple times to create collections of particles. The position and orientation of each particle is chosen randomly. The seed value sets the random number generator used for coordinate generation.
The ensemble of chains is written to a LAMMPS data file via the write() method.
Usage:
p = patch(vfrac) setup box with a specified volume fraction p = patch(vfrac,1,1,2) x,y,z = aspect ratio of box (def = 1,1,1)
p.seed = 48379 set random # seed (def = 12345) p.randomized = 0 1 = choose next mol randomly (def), 0 = as generated p.dim = 2 set dimension of created box (def = 3) p.blen = 0.97 set length of tether bonds (def = 0.97) p.dmin = 1.02 set min r from i-1 to i+1 tether site (def = 1.02) p.lattice = [Nx,Ny,Nz] generate Nx by Ny by Nz lattice of particles p.displace = [Dx,Dy,Dz] displace particles randomly by +/- Dx,Dy,Dz p.style = "sphere" atom-style of data file, molecular or sphere p.extra = "Molecules" add extra Molecules section to data file p.extratype = 1 add extra atom types when write data file
randomized means choose molecules in random order when creating output if lattice is set, Nx*Ny*Nz must equal N for build (Nz = 1 for 2d) lattice = [0,0,0] = generate N particles randomly = default displace = [0,0,0] = default displacement applied when writing molecule to data file style = molecular by default style is auto-set to line,tri,box by corresponding keywords extratype = 0 by default
p.build(100,"hex2",1,2,3) create 100 "hex2" particles with params 1,2,3
can be invoked multiple times
keywords:
c60hex2: diam,1,2,3 = C-60 with 2 hex patches and ctr part, types 1,2,3
hex2: diam,1,2 = one large particle with 2 7-mer hex patches, types 1,2
hex4: diam,1,2 = one large particle with 4 7-mer hex patches, types 1,2
ring: diam,N,1,2 = one large part with equatorial ring of N, types 1,2
ball: diam,m1,m2,1,2,3 = large ball with m12-len tethers, types 1,2,3
tri5: 1,2 = 3-layer 5-size hollow tri, types 1,2
rod: N,m1,m2,1,2,3 = N-length rod with m12-len tethers, types 1,2,3
tri: N,m1,m2,m3,1,2,3,4 = N-size tri with m123-len tethers, types 1-4
trid2d: N,r,1 = 3d equilateral tri, N beads r apart, type 1, no bonds
hex: m1,m2,m3,m4,m5,m6,1,2,3,4,5,6,7 = 7-atom hex with m-len tethers, t 1-7
dimer: r,1 = two particles r apart, type 1, no bond
star2d: N,r,1 = 2d star of length N (odd), beads r apart, type 1, no bonds
box2d: N,M,r,1 = 2d NxM hollow box, beads r apart, type 1, no bonds
pgon2d: Nlo,Nhi,m = 2d hollow polygons with random N beads from Nlo to Nhi
sphere3d: Nlo,Nhi,m = 3d hollow spheres with random N beads/cube-edge
from Nlo to Nhi
tritet: A,m = 4-tri tet with edge length A, tri type m
tribox: Alo,Ahi,Blo,Bhi,Clo,Chi,m = 12-tri box with side lengths A,B,C & m
linebox: Alo,Ahi,Blo,Bhi,m = 4-line 2d rectangle with random side lengths
from Alo to Ahi and Blo to Bhi, line type m
built of line particles
linetri: Alo,Ahi,Blo,Bhi,m = 3-line 2d triangle with random base
from Alo to Ahi and height Blo to Bhi, type m
built of triangle particles
bodypgon: Nlo,Nhi,m = 2d polygons with random N particles from Nlo to Nhi
built of body particles
p.write("data.patch") write out system to LAMMPS data file
Related tools:
Prerequisites: none
(Glotzer) Zhang and Glotzer, NanoLetters, 4, 1407-1413 (2004).