4.9.2. Linear Density — MDAnalysis.analysis.lineardensity

A tool to compute mass and charge density profiles along the three cartesian axes [xyz] of the simulation cell. Works only for orthorombic, fixed volume cells (thus for simulations in canonical NVT ensemble).

class MDAnalysis.analysis.lineardensity.LinearDensity(select, grouping='atoms', binsize=0.25, **kwargs)[source]

Linear density profile

Parameters:

  • select (AtomGroup) – any atomgroup

  • grouping (str {'atoms', 'residues', 'segments', 'fragments'}) – Density profiles will be computed either on the atom positions (in the case of ‘atoms’) or on the center of mass of the specified grouping unit (‘residues’, ‘segments’, or ‘fragments’).

  • binsize (float) – Bin width in Angstrom used to build linear density histograms. Defines the resolution of the resulting density profile (smaller –> higher resolution)

  • verbose (bool, optional) – Show detailed progress of the calculation if set to True

results.x.dim

index of the [xyz] axes

Type:

int

results.x.mass_density

mass density in \(g \cdot cm^{-3}\) in [xyz] direction

Type:

numpy.ndarray

results.x.mass_density_stddev

standard deviation of the mass density in [xyz] direction

Type:

numpy.ndarray

results.x.charge_density

charge density in \(\mathrm{e} \cdot mol \cdot cm^{-3}\) in [xyz] direction

Type:

numpy.ndarray

results.x.charge_density_stddev

standard deviation of the charge density in [xyz] direction

Type:

numpy.ndarray

results.x.pos

Alias to the results.x.mass_density attribute.

Deprecated since version 2.2.0: Will be removed in MDAnalysis 3.0.0. Please use results.x.mass_density instead.

Type:

numpy.ndarray

results.x.pos_std

Alias to the results.x.mass_density_stddev attribute.

Deprecated since version 2.2.0: Will be removed in MDAnalysis 3.0.0. Please use results.x.mass_density_stddev instead.

Type:

numpy.ndarray

results.x.char

Alias to the results.x.charge_density attribute.

Deprecated since version 2.2.0: Will be removed in MDAnalysis 3.0.0. Please use results.x.charge_density instead.

Type:

numpy.ndarray

results.x.char_std

Alias to the results.x.charge_density_stddev attribute.

Deprecated since version 2.2.0: Will be removed in MDAnalysis 3.0.0. Please use results.x.charge_density_stddev instead.

Type:

numpy.ndarray

results.x.slice_volume

volume of bin in [xyz] direction

Type:

float

results.x.hist_bin_edges

edges of histogram bins for mass/charge densities, useful for, e.g., plotting of histogram data.

Type:

numpy.ndarray

Note
Type:

These density units are likely to be changed in the future.

Example

First create a LinearDensity object by supplying a selection, then use the run() method. Finally access the results stored in results, i.e. the mass density in the x direction.

ldens = LinearDensity(selection)
ldens.run()
print(ldens.results.x.mass_density)

Alternatively, other types of grouping can be selected using the grouping keyword. For example to calculate the density based on a grouping of the ResidueGroup of the input AtomGroup.

ldens = LinearDensity(selection, grouping='residues', binsize=1.0)
ldens.run()

Added in version 0.14.0.

Changed in version 1.0.0: Support for the start, stop, and step keywords has been removed. These should instead be passed to LinearDensity.run(). The save() method was also removed, you can use np.savetxt() or np.save() on the LinearDensity.results dictionary contents instead.

Changed in version 1.0.0: Changed selection keyword to select

Changed in version 2.0.0: Results are now instances of Results allowing access via key and attribute.

Changed in version 2.2.0:

  • Fixed a bug that caused LinearDensity to fail if grouping=”residues” or grouping=”segments” were set.

  • Residues, segments, and fragments will be analysed based on their centre of mass, not centre of geometry as previously stated.

  • LinearDensity now works with updating atom groups.

  • Added new result container results.x.hist_bin_edges. It contains the bin edges of the histrogram bins for calculated densities and can be used for easier plotting of histogram data.

Deprecated since version 2.2.0: The results dictionary has been changed and the attributes results.x.pos, results.x.pos_std, results.x.char and results.x.char_std are now deprecated. They will be removed in 3.0.0. Please use results.x.mass_density, results.x.mass_density_stddev, results.x.charge_density, and results.x.charge_density_stddev instead.

class MDAnalysis.analysis.lineardensity.Results(*args, **kwargs)[source]

From version 3.0.0 onwards, some entries in Results will be renamed. See the docstring for LinearDensity for details. The Results class is defined here to implement deprecation warnings for the user.