sample.orbital.density: Sample the wave function's density using a choice of...

In npetraco/che302r: Handy functions for CHEM 302, Physical Chemistry II

Sample the wave function's density using a choice of algorithms and schemes

Description

Sample the wave function's density

Usage

sample.orbital.density(
  nqn,
  lqn,
  mqn,
  orb.func.info,
  printQ = FALSE,
  algorithm = "ais",
  type = "serial",
  num.processes = 1
)

Arguments

nqn	n quantum number
lqn	l quantum number
mqn	m quantum number
orb.func.info	Orbital pdfs info generated by splined.sqorb.functs()
algorithm	Can be "ais" or "mcmc"
type	Can be "serial" or "parallel"

Details

Sample the wave function's density and plot corresponding r,theta, phi (x,y,z) values. Can do MCMC, or AIS. MCMC and AIS chains can be run in parallel for extra speed.

Value

orbital sample matrix (num.sample-rows by 3-columns)

References

XXXXX

Examples

library(che302r)
library(parallel)
library(doSNOW)
library(rgl)

#Pick an orbital:
n <- 1
l <- 0
m <- (0)

# Create squared orbital functions for sampling
orb.sq.funcs  <- splined.sqorb.functs(n, l, m, r.max = 320, num.knots = 1000)
rax           <- orb.sq.funcs$r.axis
R.sq          <- orb.sq.funcs$R.sq.func
plot(rax, rax^2 * R.sq(rax), typ="l")

#Sample the orbital density:
#detectCores() # Number of processors available

#density.samples <- sample.orbital.density(n, l, m, printQ = T, orb.func.info = orb.sq.funcs, algorithm="ais", type="parallel", num.processes = 4)

# Sample in cartesian coordinates
x               <- density.samples[,1]
y               <- density.samples[,2]
z               <- density.samples[,3]

#Plot the sampled orbital density:
#2D
plot(x,y)
plot(x,z)
plot(y,z)

#3D
plot3d(x,y,z,type="s",radius=1.5,xlab="x",ylab="y",zlab="z")

# 3D slices
plot3d(x,y,rep(0,length(z)),type="s",radius=0.5,xlab="x",ylab="y",zlab="z")
plot3d(x,rep(0,length(y)),z,type="s",radius=0.5,xlab="x",ylab="y",zlab="z")
plot3d(rep(0,length(x)), y, z,type="s",radius=0.5,xlab="x",ylab="y",zlab="z")

npetraco/che302r documentation built on April 17, 2025, 10:34 p.m.