Timeseries modules

Dipole angle

Description

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

Parameters

atomgroupAtomGroup

Atomgroup on which the analysis is executed

dimint

refernce vector for angle (x=0, y=1, z=2)

outputstr

Prefix for output filenames

concfreqint

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.

verbosebool

Turn on more logging and debugging

Attributes

results.tnp.ndarray

time (ps)

resulst.cos_theta_inp.ndarray

Average cos between dipole and axis

resulst.cos_theta_iinp.ndarray

Average cos^2 of the same between dipole and axis

resulst.cos_theta_ijnp.ndarray

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

Kinetic energy

Description

Calculate the timeseries of energies.

The kinetic energy function computes the translational and rotational kinetic energy with respect to molecular center (center of mass, center of charge) of a molecular dynamics simulation trajectory.

Parameters

atomgroupAtomGroup

Atomgroup on which the analysis is executed

refpointstr

reference point for molecular center: center of mass (COM) or center of charge (COC) Note: The oxygen position only works for systems of pure water

outputstr

Output filename

${VERBOSE_PARAMETER}

Attributes

results.tnp.ndarray

time (ps)

results.transnp.ndarray

translational kinetic energy (kJ/mol)

results.rotnp.ndarray

rotational kinetic energy (kJ/mol)