Weighting functions

Weight functions used for spatial binned analysis modules.

maicos.lib.weights.density_weights(atomgroup: AtomGroup, grouping: str, dens: str) → ndarray

Weights for density calculations.

Parameters:

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

• grouping ({"atoms", "residues", "segments", "molecules", "fragments"}) –

  Atom grouping for the calculations.

  The possible grouping options are the atom positions (in the case where grouping="atoms") or the center of mass of the specified grouping unit (in the case where grouping="residues", "segments", "molecules" or "fragments").

• dens ({"mass", "number", "charge", "electron"}) – density type to be calculated.

Returns:

1D array of calculated weights. The length depends on the grouping.

Return type:

numpy.ndarray

Raises:

ValueError – if grouping or dens parameter is not supported.

maicos.lib.weights.diporder_pair_weights(g1: AtomGroup, g2: AtomGroup, compound: str) → ndarray

Normalized dipole moments as weights for general diporder RDF calculations.

maicos.lib.weights.diporder_weights(atomgroup: AtomGroup, grouping: str, order_parameter: str, get_unit_vectors: Unit_vector) → ndarray

Weights for general diporder calculations.

Parameters:

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

• grouping ({"atoms", "residues", "segments", "molecules", "fragments"}) –

  Atom grouping for the calculations.

  The possible grouping options are the atom positions (in the case where grouping="atoms") or the center of mass of the specified grouping unit (in the case where grouping="residues", "segments", "molecules" or "fragments").

• order_parameter ({"P0", "cos_theta", "cos_2_theta"}) –

  Order parameter to be calculated:

  • "P0": total dipole moment projected on an axis

  • "cos_theta": cosine of the dipole moment with an axis

  • "cos_2_theta": squred cosine with an axis.

• get_unit_vectors (Callable) – Callable that returns unit vectors on which the projection is performed. Returned unit_vectors can either be of shape (3,) or of shape (n, 3). For a shape of (3,) the same unit vector is used for all calculations.

maicos.lib.weights.temperature_weights(atomgroup: AtomGroup, grouping: str) → ndarray

Weights for temperature calculations.

Parameters:

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

• grouping ({"atoms", "residues", "segments", "molecules", "fragments"}) –

  Atom grouping for the calculations.

  The possible grouping options are the atom positions (in the case where grouping="atoms") or the center of mass of the specified grouping unit (in the case where grouping="residues", "segments", "molecules" or "fragments").

Returns:

1D array of calculated weights. The length depends on the grouping.

Return type:

numpy.ndarray

Raises:

NotImplementedError – Currently only works for grouping=’atoms’

maicos.lib.weights.velocity_weights(atomgroup: AtomGroup, grouping: str, vdim: int) → ndarray

Weights for velocity calculations.

The function normalises by the number of compounds.

Parameters:

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

• grouping ({"atoms", "residues", "segments", "molecules", "fragments"}) –

  Atom grouping for the calculations.

  The possible grouping options are the atom positions (in the case where grouping="atoms") or the center of mass of the specified grouping unit (in the case where grouping="residues", "segments", "molecules" or "fragments").

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

Returns:

1D array of calculated weights. The length depends on the grouping.

Return type:

numpy.ndarray