pyiron.atomistics.nma.nma module

class pyiron.atomistics.nma.nma.NMA(job, atomic_units=False)

Bases: tamkin.nma.NMA

This is a generic module to do a Normal Mode Analysis on a job type, which calculates the gradient and the hessian using TAMkin based on a job object. With the NMA object you can animate a certain mode and plot the IR spectrum.

animate_nma_mode(index, amplitude=1.0, frames=24, spacefill=False, particle_size=0.5)

Visualize the normal mode corresponding to an index

Arguments

index index corresponding to a normal mode

amplitude size of the deviation of the normal mode

frames number of frames that constitute the full mode (lower means faster movement)

spacefill remove atom bonds

particle size

size of the atoms in the structure

plot_IR_spectrum(width=7.251632778591094e-06, scale=1.0, intensities=None, charges=None)

Plot IR spectrum based on Lorentzian width, freqs can be scaled through scale Intensities can be provided (e.g. from a Gaussian job) or calculated from the charges

Arguments

width width of the Lorentzian function

scale scales the frequencies with this factor

intensities

IR intensities for spectrum, can be read from Gaussian job

charges charges to calculate IR intensities, from e.g. Yaff simulation