QUATERNION

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

Calculate quaternions for molecules.

The reference frame for the molecule is defined using the positions of three user selected atoms. From the positions of these atoms, \(\mathbf{x}_1\), \(\mathbf{x}_2\) and \(\mathbf{x}_3\), we define the vectors of the reference frame as:

\[\begin{aligned} \mathbf{x} & = \mathbf{x}_2 - \mathbf{x}_1 \\ \mathbf{y} & = (\mathbf{x}_2 - \mathbf{x}_1) \times (\mathbf{x}_3 - \mathbf{x}_1) \\ \mathbf{z} & \mathbf{x} \times \mathbf{y} \]

Examples

This calculates the quaternions for a molecule with 10 atoms

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

q1: QUATERNION ATOMS1the three atom that we are using to calculate the quaternion. =1,2,3 The QUATERNION action with label q1 calculates the following quantities:

 Quantity   
 Description  
q1.w
the real component of quaternion
q1.i
the i component of the quaternion
q1.j
the j component of the quaternion
q1.k
the k component of the quaternion


PRINT ARGthe input for this action is the scalar output from one or more other actions. =q1.w,q1.i,q1.j,q1.k FILEthe name of the file on which to output these quantities =colvar The PRINT action with label 

This calculate the quaternions for two molecules with 10 atoms

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

q1: QUATERNION ATOMS1the three atom that we are using to calculate the quaternion. =1,2,3 ATOMSthe three atom that we are using to calculate the quaternion. =4,5,6  You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT ARGthe input for this action is the scalar output from one or more other actions. =q1.w,q1.i,q1.j,q1.k FILEthe name of the file on which to output these quantities =colvar  You cannot view the components that are calculated by each action for this input file. Sorry 

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
w	the real component of quaternion
i	the i component of the quaternion
j	the j component of the quaternion
k	the k component of the quaternion

The atoms involved can be specified using

ATOMS

the three atom that we are using to calculate the quaternion. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances