simPart {nanop} | R Documentation |
Functions to simulate the deterministic atomic positions in a nanoparticle and displace those positions stochastically to model thermal effects
simPart(sym="fcc", latticep=4.08, r=10, latticepshell=NA, rcore=NA, rcenter=FALSE, center=c(0,0,0), foranalcs=FALSE) displacePart(nanop, sigma=NA, sigmacore=NA, sigmashell=NA, rcore=NA, rcenter=FALSE, center=c(0,0,0), latticep = 4.08)
sym |
character vector describing the structure to be used; currently only "fcc" for face-centered cubic is available. |
latticep |
numeric indicating the lattice parameter(s). |
r |
numeric indicating the radius of the nanoparticle. (Currently, only spherical nanoparticle models are implemented). |
nanop |
numeric matrix in which each row represents the position
of an atom, e.g., as returned by simPart .
|
sigma |
numeric which, if not NA , determines the variance
of the Gaussian displacements from the mean atomic position
throughout the nanoparticle. If this argument is not NA then
the following three arguments should be NA .
|
sigmacore |
numeric which, if not NA , determines the variance
of the Gaussian displacements from the mean atomic position
in the core of the nanoparticle; if this argument is not
NA then both
rcore and sigmashell must also be not NA .
|
sigmashell |
numeric which, if not NA , determines the variance
of the Gaussian displacements from the mean atomic position
in the shell of the nanoparticle; if this argument is not
NA then both
rcore and sigmacore must also be not NA .
|
rcore |
numeric which, if not NA , determines the radius of
the core; if this argument is not NA then both
sigmacore and sigmashell must also be not NA .
|
latticepshell |
numeric indicating the lattice parameter(s) associated with the shell. |
rcenter |
logical value indicating whether to choose the center of the particle at random within the unit cell |
center |
If rcenter=FALSE , the position at the particle center. |
foranalcs |
logical indicating whether the result will be used in
combination with calculating analytical broadening for a core-shell
particle using the function broadPDF . |
numeric matrix with three columns in which each row represents an atomic position.
## Deterministic particle aa <- simPart() ## if the package 'rgl' is installed, the lines calling ## 'spheres3d' can be uncommented; they will provide a 3D ## visualization of a particle. # spheres3d(aa, radius=.4) ## Particle with uniform displacements aa <- simPart(r=11, latticep=5) ax <- displacePart(aa, sigma=.02) # spheres3d(ax, radius=.4) ## Particle with displacements in the core different from displacements ## in the shell aa <- simPart(r=10, latticep=5) ax <- displacePart(aa, sigmacore=.001, sigmashell=.1, rcore=10) # spheres3d(ax, radius=.4)