PDFCylinder

class maicos.modules.pdfcylinder.PDFCylinder(g1: AtomGroup, g2: AtomGroup | None = None, bin_width_pdf_z: float = 0.3, bin_width_pdf_phi: float = 0.1, drwidth: float = 0.1, dmin: float | None = None, dmax: float | None = None, density: bool = False, origin: ndarray | None = None, dim: int = 2, zmin: float | None = None, zmax: float | None = None, rmin: float = 0, rmax: float | None = None, bin_width: float = 1, bin_method: str = 'com', refgroup: AtomGroup | None = None, unwrap: bool = False, pack: bool = True, jitter: float = 0.0, concfreq: int = 0, output: str = 'pdf.dat')

Bases: CylinderBase

Shell-wise one-dimensional (cylindrical) pair distribution functions.

The one-dimensional pair distribution functions \(g_{\text{1d}}(\phi)\) and \(g_{\text{1d}}(z)\) describes the pair distribution to particles which lie on the same cylinder along the angular and axial directions respectively. These functions can be used in cylindrical systems that are inhomogeneous along radial coordinate, and homogeneous in the angular and axial directions. It gives the average number density of \(g2\) as a function of angular and axial distances respectively from a \(g1\) atom. Then the angular pair distribution function is

\[g_{\text{1d}}(\phi) = \left \langle \sum_{i}^{N_{g_1}} \sum_{j}^{N_{g2}} \delta(\phi - \phi_{ij}) \delta(R_{ij}) \delta(z_{ij}) \right \rangle\]

And the axial pair distribution function is

\[g_{\text{1d}}(z) = \left \langle \sum_{i}^{N_{g_1}} \sum_{j}^{N_{g2}} \delta(z - z_{ij}) \delta(R_{ij}) \delta(\phi_{ij}) \right \rangle\]

Even though due to consistency reasons the results are called pair distribution functions the output is not unitless. The default output is is in dimension of number/volume in \(Å^{-3}\). If density is set to True, the output is normalised by the density of \(g2\).

Parameters:

• atomgroup (MDAnalysis.core.groups.AtomGroup) – A AtomGroup for which the calculations are performed.

• g1 (MDAnalysis.core.groups.AtomGroup) – First AtomGroup.

• g2 (MDAnalysis.core.groups.AtomGroup) – Second AtomGroup.

• bin_width_pdf_z (float) – Binwidth of bins in the histogram of the axial PDF (Å).

• bin_width_pdf_phi (float) – Binwidth of bins in the histogram of the angular PDF (Å).

• drwidth (float) – radial width of a PDF cylindrical shell (Å), and axial or angular (arc) slices.

• dmin (float) – the minimum pairwise distance between ‘g1’ and ‘g2’ (Å).

• dmax (float) – the maximum pairwise distance between ‘g1’ and ‘g2’ (Å).

• density (bool) – normalise the PDF by the density of ‘g2’ (\(Å^{-3}\)).

• origin (numpy.ndarray) – Set origin of the cylindrical coordinate system (x,y,z). If None the origin will be set according to the refgroup parameter.

• dim ({0, 1, 2}) – Dimension for binning (x=0, y=1, z=1).

• zmin (float) – Minimal coordinate for evaluation (in Å) with respect to the center of mass of the refgroup. If zmin=None, all coordinates down to the lower cell boundary are taken into account.

• zmax (float) – Maximal coordinate for evaluation (in Å) with respect to the center of mass of the refgroup. If zmax = None, all coordinates up to the upper cell boundary are taken into account.

• rmin (float) – Minimal radial coordinate relative to the center of mass of the refgroup for evaluation (in Å).

• rmax (float) –

  Maximal radial coordinate relative to the center of mass of the refgroup for evaluation (in Å).

  If rmax=None, the box extension is taken.

• bin_width (float) – Width of the bins (in Å).

• bin_method ({"com", "cog", "coc"}) –

  Method for the position binning.

  The possible options are center of mass ("com"), center of geometry ("cog"), and center of charge ("coc").

• refgroup (MDAnalysis.core.groups.AtomGroup) – Reference AtomGroup used for the calculation. If refgroup is provided, the calculation is performed relative to the center of mass of the AtomGroup. If refgroup is None the calculations are performed with respect to the center of the (changing) box.

• unwrap (bool) –

  When True, molecules that are broken due to the periodic boundary conditions are made whole.

  If the input contains molecules that are already whole, speed up the calculation by disabling unwrap. To do so, use the flag -no-unwrap when using MAICoS from the command line, or use unwrap=False when using MAICoS from the Python interpreter.

  Note: Molecules containing virtual sites (e.g. TIP4P water models) are not currently supported in MDAnalysis. In this case, you need to provide unwrapped trajectory files directly, and disable unwrap. Trajectories can be unwrapped, for example, using the trjconv command of GROMACS.

• pack (bool) –

  When True, molecules are put back into the unit cell. This is required because MAICoS only takes into account molecules that are inside the unit cell.

  If the input contains molecules that are already packed, speed up the calculation by disabling packing with pack=False.

• jitter (float) –

  Magnitude of the random noise to add to the atomic positions.

  A jitter can be used to stabilize the aliasing effects sometimes appearing when histogramming data. The jitter value should be about the precision of the trajectory. In that case, using jitter will not alter the results of the histogram. If jitter = 0.0 (default), the original atomic positions are kept unchanged.

  You can estimate the precision of the positions in your trajectory with maicos.lib.util.trajectory_precision(). Note that if the precision is not the same for all frames, the smallest precision should be used.

• concfreq (int) – When concfreq (for conclude frequency) is larger than 0, the conclude function is called and the output files are written every concfreq frames.

• output (str) – Output filename.

results.bin_pos

Bin positions (in Å) ranging from rmin to rmax.

Type:

numpy.ndarray

results.phi_bins

Angular distances to which the PDF is calculated with shape (pdf_nbins) (Å)

Type:

numpy.ndarray

results.z_bins

axial distances to which the PDF is calculated with shape (pdf_nbins) (Å)

Type:

numpy.ndarray

results.phi_pdf

Angular PDF with shape (pdf_nbins, n_bins) (\(\text{Å}^{-3}\))

Type:

numpy.ndarray

results.z_pdf

Axial PDF with shape (pdf_nbins, n_bins) (\(\text{Å}^{-3}\))

Type:

numpy.ndarray

run(start: int | None = None, stop: int | None = None, step: int | None = None, frames: int | None = None, verbose: bool | None = None, progressbar_kwargs: dict | None = None) → Self

Iterate over the trajectory.

Parameters:

• start (int) – start frame of analysis

• stop (int) – stop frame of analysis

• step (int) – number of frames to skip between each analysed frame

• frames (array_like) – array of integers or booleans to slice trajectory; frames can only be used instead of start, stop, and step. Setting both frames and at least one of start, stop, step to a non-default value will raise a ValueError.

• verbose (bool) – Turn on verbosity

• progressbar_kwargs (dict) – ProgressBar keywords with custom parameters regarding progress bar position, etc; see MDAnalysis.lib.log.ProgressBar for full list.

Returns:

self – analysis object

Return type:

object

save() → None

Save results of analysis to file specified by output.