Trajectory Analysis¶

Description¶

A radial distribution function \(g(r)\), or pair correlation function, is a density of distances between particles, relative to the average distance density. The x-axis variable represents a distance \(r\), while the y-axis represents the relative density of that distance. For a complete homogeneous system of particles the \(g(r)\) values for the distances between all particles equals 1 everywhere.

Two sets of atoms \(\mathbb{S}_{\textrm{from}}\) and \(\mathbb{S}_{\textrm{to}}\), of length \(n_{\textrm{from}}\) and \(n_{\textrm{to}}\) respectively, are specified with the keywords AtomsFrom and AtomsTo in the RadialDistribution block. As a result the program computes \(n_{\textrm{from}}*n_{\textrm{to}}\) distances \(r_{ij}^s\) between atom \(i\) in \(\mathbb{S}_{\textrm{from}}\) and atom \(j\) in \(\mathbb{S}_{\textrm{to}}\) for each trajectory frame \(s\) out of a total of \(n_{\textrm{frames}}\) frames.

A normalized histogram is then computed from these distances, resulting in a function \(N(r)\).

\(N(r)=\frac{1}{n_{\textrm{frames}}} \sum_{s=1}^{n_{\textrm{frames}}} \sum_{i=1}^{n_{\textrm{from}}}\sum_{j=1}^{n_{\textrm{to}}} \delta(r_{ij}^s-r)\).

This histogram is converted to a density, by dividing all values \(N(r)\) with the volume \(V(r)= 4 \pi r^2 dr\) of a sphere-slice at radius \(r\) with thickness \(dr\).

The density is further converted to a relative density by dividing with the total density of the system \(\rho_{\textrm{tot}} = \frac{n_{\textrm{from}}*n_{\textrm{to}}}{V_{\textrm{tot}}}\), yielding the final radial distribution function \(g(r)\).

\(g(r) = \frac{N(r)}{V(r)*\rho_{\textrm{tot}}}\)

Options¶

Non-periodic systems The above equation assumes that the volume \(V_{\textrm{tot}}\) of the system is a well-defined quantity. This assumption is correct for systems with 3D periodicity, where the \(V_{\textrm{tot}}\) is defined as the volume of the periodic cell. In such a system the value of \(r\) can be no larger than \(r_{\textrm{max}}\), the radius of the largest sphere that can be placed inside the periodic cell.

If a system is non-periodic in one or more direction, then the program still computes a \(g(r)\), only if the radius \(r_{max}\) is supplied by the user with the Range keyword in the RadialDistribution block. The radius is the second value supplied.

RadialDistribution
   Range float_list
End

RadialDistribution

Type:	Block
Recurring:	True
Description:	All input related to radial distribution functions.

Range

Type:	Float List
Description:	Either one, two, or three real values. If one it is the stepsize. If two, it is the minimum value and the maximum value. If three, it is the minimum value, the maximum value, and the stepsize. The stepsize overrides NBins.

In this case the volume \(V_{\textrm{tot}}\) is assumed to be the volume of a sphere with radius \(r_{\textrm{max}}\).

NPT simulations The above equation further assumes that the volume \(V_{\textrm{tot}}\) is constant throughout the simulation. The \(g(r)\) of the trajectory from an NPT simulation can still be computed, and in this case \(V_{\textrm{tot}}\) is the average value of the volume of the periodic cell.

Simulations with varying numbers of atoms The above equation also assumes that \(n_{\textrm{from}}\) and \(n_{\textrm{to}}\) remain constant throughout the simulation. However, in a Molecular Gun simulation particles can be added to the system, and in a GCMC simulation particles can be both added and removed from the system. Nonetheless, the program still computes a \(g(r)\) in these situations.

If the AtomsFrom and AtomsTo blocks contain element names (supplied with the recurring Element keyword), then every time atoms are added to or removed from the system, the sets of atoms \(\mathbb{S}_{\textrm{from}}\) and \(\mathbb{S}_{\textrm{to}}\) are re-evaluated.

If the AtomsFrom and AtomsTo blocks contain atom numbers (supplied with the recurring Atom keyword), these numbers are updated in the sets \(\mathbb{S}_{from}\) and \(\mathbb{S}_{to}\) every time atoms are added to or removed from the system. If one of the atoms from the set disappears, the number of distances contributing to the \(g(r)\) decreases.

Note: Currently, the values of \(n_{from}\) and \(n_{to}\) in the normalization factor are taken from the last frame of the simulation.

Warning: If multiple trajectories are supplied, and the number of atoms changes between the end of one trajectory and the beginning of another, this may result in an error in the atom numbers used by the program internally.

Description¶

An autocorrelation function \(C(t)\) describes the average correlation (overlap) of a (vector) property \(\textbf{A}\) with itself as a function of time.

\(C(t) = \langle \textbf{A}(0) \cdot \textbf{A}(t)) \rangle\)

The average runs over all time-intervals \(\left( t_{0}, t_{0}+t \right),\left( t_{1}, t_{1}+t \right),...,\left( t_{N}, t_{N}+t \right)\), with \(t_{N} = t_{n} - t_{m}\). Here \(n\) is the total number of simulation steps in the trajectory, and \(m\) is the number of discrete \(t\) values for which \(C(t)\) is computed. The value \(m\) can be set with the keyword MaxStep, and defaults to half the total number of simulation steps. If applicable, the average also runs over all possible contributions to \(\textbf{A}\) at each simulation timestep. The normalized autocorrelation function \(c(t)\) describes the decorrelation of the property with time, and always starts at 1.0 at \(t=0\).

\(c(t) = \frac{\langle \textbf{A}(0) \cdot \textbf{A}(t)) \rangle}{\langle \textbf{A}(0) \cdot \textbf{A}(0)) \rangle}\)

In most cases short timescale fluctuations are important, so frequent storage of the desired property is required (when preparing the molecular dynamics simulation, set the Frequency keyword in the Trajectory block of the MolecularDynanimcs settings low, preferably to 1).

A power spectrum is automatically computed by Fourier transform of the autocorrelation function, and provides information on the frequencies of the signal. When the selected property is the dipole moment, the power spectrum matches the IR spectrum.

Options¶

Autocorrelation functions can be computed for different simulation properties: 1) Dipole moments from atomic charges 2) Velocities 3) User provided values.

AutoCorrelation
   Property [Velocities | DipoleMomentFromCharges | InputValues | DiffusionCoefficient]
End

AutoCorrelation

Type:	Block
Recurring:	True
Description:	All input related to auto correlation functions.

Property

Type:	Multiple Choice
Default value:	DipoleMomentFromCharges
Options:	[Velocities, DipoleMomentFromCharges, InputValues, DiffusionCoefficient]
Description:	Compute the ACF either from velocities (from rkf), the dipole moment (from atomic charges in rkf), or from values specified in input. If DiffusionCoefficient is selected the unnormalized velocity autocorrelation function is computed and integrated.

With the keyword Normalized a normalized ACF is computed, and with the keyword MaxStep the number of values \(n\) in the autocorrelation function (\(t = [0,t_{1},t_{2},....,t_{n}]\)) can be set. The default value is half of the total number of simulation steps used.

A subset of atoms for which the property \(\textbf{A}\) should be selected/computed can be provided in the block Atoms. The block can contain element names (recurring keyword Element), or individual atom numbers (recurring keyword Atom).

AutoCorrelation
   Atoms
      Atom integer
      Element string
   End
End

AutoCorrelation

Type:	Block
Recurring:	True
Description:	All input related to auto correlation functions.

Atoms

Type:	Block
Description:	Relevant if Property is set to Velocities, DipoleMomentFromCharges, or DiffusionCoefficient. Atom numbers or elements for the set of atoms for which the property is read/computed. By default all atoms are used.

Atom

Type:	Integer
Recurring:	True
Description:	Atom number.

Element

Type:	String
Recurring:	True
Description:	Element Symbol Atom.