DensityCylinder#

class maicos.modules.densitycylinder.DensityCylinder(atomgroups, dens='mass', dim=2, zmin=None, zmax=None, bin_width=1, rmin=0, rmax=None, refgroup=None, grouping='atoms', unwrap=True, bin_method='com', output='density.dat', concfreq=0)[source]#

Bases: ProfileCylinderBase

Compute cylindrical partial density profiles.

Calculations are carried out for mass \((\rm u \cdot Å^{-3})\), number \((\rm Å^{-3})\) or charge \((\rm e \cdot Å^{-3})\) density profiles along a certain cartesian axes [x, y, z] of the simulation cell. Cell dimensions are allowed to fluctuate in time.

For grouping with respect to molecules, residues etc., the corresponding centers (i.e., center of mass) taking into account periodic boundary conditions are calculated. For these calculations molecules will be unwrapped/made whole. Trajectories containing already whole molecules can be run with unwrap=False to gain a speedup. For grouping with respect to atoms the unwrap option is always ignored.

Parameters:

  • atomgroups (list[AtomGroup]) – a list of AtomGroup objects for which the calculations are performed.

  • refgroup (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 to the center of the (changing) box.

  • unwrap (bool) –

    When unwrap = 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.

  • 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

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

  • 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.

  • jitter (float) –

    If jitter is not None, random numbers of the order of jitter (Å) are added to the atom positions.

    The appilication of a jitter is rationalized in possible aliasing effects when histogramming data, i.e., for spatial profiles. These aliasing effects can be stabilized with the application of a numerical jitter. The jitter value should be about the precision of the trajectory and will not alter the results of the histogram.

    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.

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

  • 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.

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

    Atom grouping for the calculations of profiles.

    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').

  • bin_method (str {'cog', 'com', 'coc'}) –

    Method for the position binning.

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

  • output (str) – Output filename.

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

results.bin_pos#

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

Type:

numpy.ndarray

results.profile#

Calculated profile.

Type:

numpy.ndarray

results.dprofile#

Estimated profile’s uncertainity.

Type:

numpy.ndarray