pyMolDyn Documentation



Keyboard Shortcuts

In pyMolDyn, several keyboard shortcuts are available. Note, on Linux machines, use "Ctrl" (Control) instead of "Cmd" (Command).

Shortcut Action
Alt+1 Open Most Recent File
Cmd+1 Export Bonds
Cmd+2 Export Bond angles
Cmd+3 Export Bond dihedral angles
Cmd+4 Export Cavity Information (domains)
Cmd+5 Export Cavity Information (surface method)
Cmd+6 Export Cavity Information (center method)
Cmd+I Open Settings
Cmd+O Open Files for calculation
d Show Domains
c Show cavities (surface method)
f Show cavities (center method)
r Reset camera
arrow Keys Rotate camera

Cell Shape Description

pyMolDyn supports cell shapes corresponding to all seven 3D Bravais lattice systems. The cell shape and size are set using the Bravais lattice parameters as shown below, with angles given in radians. The application reads these settings from the second line of the .xyz file and uses them for all frames.

The following snippet shows the second line for a hexgonal cell:

HEX 17.68943 22.61158

Additional comments on this line will be ignored.

Bravais cell shape: TRI cell shape: MON Bravais cell shape: ORT Bravais cell shape: TET Bravais cell shape: RHO cell shape: CUB cell shape: HEX

Full resolution images of cell shape information: TRI, MON, ORT, TET, RHO, CUB, HEX

Pair Distribution Function Smoothing Kernels

The PDF plotting widget in pyMolDyn uses one of seven selectable smoothing kernels to create a graph. The kernels, their formulas with a bandwidth σ and their plots for σ=1, are given here. Please note that for a bandwidth of 0, the data is not smoothened, but individual peaks of height 1 are rendered. This can be useful, but visually overlapping peaks might be misleading.

Gaussian

$$\frac{1}{\sqrt{2 \pi\sigma^2}} \cdot \exp\left(-\frac{x^2}{2\sigma^2}\right)$$ Gaussian

Epanechnikov

$$\frac{3}{4\sigma} \cdot \left(1 - \frac{x^2}{\sigma^2}\right) \text{ for all } -\sigma < x < \sigma$$ Epanechnikov

Compact

$$\frac{2.25228362104}{\sigma} \cdot \exp\left(\left(\frac{x^2}{\sigma^2}-1\right)^{-1}\right) \text{ for all } -\sigma < x < \sigma$$ Compact

Triangular

$$\frac{1}{\sigma}-\left|\frac{x}{\sigma^2}\right| \text{ for all } -\sigma < x < \sigma$$ Triangular

Box

$$\frac{1}{2\sigma} \text{ for all } -\sigma < x < \sigma$$ Box

Right Box

$$\frac{1}{\sigma} \text{ for all } 0 < x < \sigma$$ Right Box

Left Box

$$\frac{1}{\sigma} \text{ for all } -\sigma < x < 0$$ Left Box