pyiron.atomistics.nma.nma module¶
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class
pyiron.atomistics.nma.nma.
NMA
(job, atomic_units=False)[source]¶ 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.
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animate_nma_mode
(index, amplitude=1.0, frames=24, spacefill=False, particle_size=0.5)[source]¶ 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
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plot_IR_spectrum
(width=7.251632778591094e-06, scale=1.0, intensities=None, charges=None)[source]¶ 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
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