Q3
This is part of the symfunc module
It is only available if you configure PLUMED with ./configure –enable-modules=symfunc . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Calculate 3rd order Steinhardt parameters.

The 3rd order Steinhardt parameters allow us to measure the degree to which the first coordination shell around an atom is ordered. The Steinhardt parameter for atom, \(i\) is complex vector whose components are calculated using the following formula:

\[ q_{3m}(i) = \frac{\sum_j \sigma( r_{ij} ) Y_{3m}(\mathbf{r}_{ij}) }{\sum_j \sigma( r_{ij} ) } \]

where \(Y_{3m}\) is one of the 3rd order spherical harmonics so \(m\) is a number that runs from \(-3\) to \(+3\). The function \(\sigma( r_{ij} )\) is a switchingfunction that acts on the distance between atoms \(i\) and \(j\). The parameters of this function should be set so that it the function is equal to one when atom \(j\) is in the first coordination sphere of atom \(i\) and is zero otherwise.

The Steinhardt parameters can be used to measure the degree of order in the system in a variety of different ways. The simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.

\[ Q_3(i) = \sqrt{ \sum_{m=-3}^3 q_{3m}(i)^{*} q_{3m}(i) } \]

This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, when the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with this colvar it is the distribution of these normed quantities that is investigated.

Other measures of order can be taken by averaging the components of the individual \(q_3\) vectors individually or by taking dot products of the \(q_{3}\) vectors on adjacent atoms. More information on these variables can be found in the documentation for LOCAL_Q3, LOCAL_AVERAGE and NLINKS.

Examples

The following command calculates the average Q3 parameter for the 64 atoms in a box of Lennard Jones and prints this quantity to a file called colvar:

Click on the labels of the actions for more information on what each action computes
tested on master




The following command calculates the histogram of Q3 parameters for the 64 atoms in a box of Lennard Jones and prints these quantities to a file called colvar:

Click on the labels of the actions for more information on what each action computes
tested on master