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)