Chemical Kinetics / Pandemia Simulation

Install with*

] add https://github.com/m3g/CKP

and then

using CKP

*This is a Julia package, so install Julia first, from: http://julialang.org.

If this is your first time using Julia, the two steps above may take a while, since all dependencies will be automatically installed.

"Atomistic" simulations

Run "MD" sird simulation with default parameters

mdinput = CKP.MDInput()
trajectory = CKP.md()

Write and read the trajectory to a file

CKP.write(mdinput,trajectory,"md.CKP")
mdinput, trajectory = CKP.read("md.CKP")

Simulate with a different average kinetic energy

equivalent to change temperature (default is 5.):

mdinput = CKP.MDInput(kavg_target=0.5)
trajectory = CKP.md(mdinput)

Create animated gif

CKP.animate(mdinput,trajectory,"animation.gif)

Example output plot:

SIRD simulation with default parameters

input = CKP.SIRDInput()
trajectory = CKP.sird(input)

Simulate with a different rate constant for contamination

input = CKP.SIRDInput(kc=0.8)
trajectory = CKP.sird(input)

Create plot

CKP.plotsird(input,trajectory,"sird.pdf)

Example output plot:

Fit SIRD kinetic simulation to MD simulation data

sirdinput, sirdtraj = CKP.fit(mdtrajectory)

where mdtrajectory is a trajectory obtained with CKP.md.

Plot the fit

CKP.plotfit(mdinput,mdtraj,sirdinput,sirdtraj,"fitplot.pdf")

Example output plot of the fit:

Plot the energy function used in MD simulation

mdinput = CKP.MDInput()
CKP.plotU(mdinput,"energy.pdf")

Example output plot of the fit: