DipoleAngle#

class maicos.modules.dipoleangle.DipoleAngle(atomgroup, dim=2, output='dipangle.dat', concfreq=0)[source]#

Bases: AnalysisBase

Calculate angle timeseries of dipole moments with respect to an axis.

The analysis can be applied to study the orientational dynamics of water molecules during an excitation pulse. For more details read Elgabarty et al.[1].

Parameters:

  • atomgroup (AtomGroup) – A AtomGroup 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) – Reference vector for angle (x=0, y=1, z=2).

  • output (str) – Prefix for output filenames.

  • concfreq – Default number of frames after which results are calculated and files refreshed. If 0 results are only calculated at the end of the analysis and not saved by default.

results.t#

time (ps).

Type:

numpy.ndarray

resulst.cos_theta_i#

Average \(\cos\) between dipole and axis.

Type:

numpy.ndarray

resulst.cos_theta_ii#

Average \(\cos²\) of the dipoles and axis.

Type:

numpy.ndarray

resulst.cos_theta_ij#

Product \(\cos\) of dipole i and cos of dipole j (i != j).

Type:

numpy.ndarray

References

save()[source]#

Save result.