DipoleAngle

class maicos.DipoleAngle(atomgroup: AtomGroup, unwrap: bool = False, pack: bool = True, refgroup: AtomGroup | None = None, concfreq: int = 0, grouping: str = 'residues', pdim: int = 2, output: str = 'dipangle.dat', jitter: float = 0.0)

Bases: AnalysisBase

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

• 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.

• 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.

• 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.

• 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").

• pdim ({0, 1, 2}) – direction of the projection

• output (str) – Output filename.

results.t

time (ps).

Type:

numpy.ndarray

results.cos_theta_i

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

Type:

numpy.ndarray

results.cos_theta_ii

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

Type:

numpy.ndarray

results.cos_theta_ij

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

Type:

numpy.ndarray

References

[1]

Hossam Elgabarty, Tobias Kampfrath, Douwe Jan Bonthuis, Vasileios Balos, Naveen Kumar Kaliannan, Philip Loche, Roland R. Netz, Martin Wolf, Thomas D. Kühne, and Mohsen Sajadi. Energy transfer within the hydrogen bonding network of water following resonant terahertz excitation. Science Advances, 6(17):eaay7074, April 2020. doi:10.1126/sciadv.aay7074.

save() → None

Save results of analysis to file specified by output.