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

Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule.

Examples

Glossary of keywords and components

Description of components

When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in regular collective variables. The label is used to reference the full set of vectors calculated by the action. This is usual when using MultiColvar functions. Generally when doing this the previously calculated multicolvar will be referenced using the DATA keyword rather than ARG.

This Action can be used to calculate the following scalar quantities directly. These quantities are calculated by employing the keywords listed below. These quantities can then be referenced elsewhere in the input file by using this Action's label followed by a dot and the name of the quantity. All of them can be calculated multiple times with different parameters. In this case the quantities calculated can be referenced elsewhere in the input by using the name of the quantity followed by a numerical identifier e.g. label.lessthan-1, label.lessthan-2 etc. When doing this and, for clarity we have made it so that the user can set the label for the components. As such by using the LABEL keyword in the description of the keyword input you can customize the component name. In addition, you can calculate all of these scalar functions for one particular component of the calculated vector by making use of the COMPONENT keyword. The first component is used to refer to the norm of the vector. The individual components can then be referenced using the numbers 2, 3, and so on. So as an example MEAN1={COMPONENT=1} calculates the average vector norm. MEAN2={COMPONENT=2} by contrast calculates the mean for all of the first components of the vectors.

Quantity	Keyword	Description
vmean	VMEAN	the norm of the mean vector. The output component can be referred to elsewhere in the input file by using the label.vmean

The atoms involved can be specified using

MOL

The numerical indices of the atoms in the molecule. If three atoms are specified the orientation of the molecule is taken as the normal to the plane containing the vector connecting the first and second atoms and the vector connecting the second and third atoms. If four atoms are specified the orientation of the molecule is taken as the normal to the plane containing the vector connecting the first and second atoms and the vector connecting the third and fourth atoms. The molecule is always assumed to lie at the geometric center for the three/four atoms.. You can use multiple instances of this keyword i.e. MOL1, MOL2, MOL3...

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL	( default=off ) do the calculation in serial. Do not use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
VMEAN	calculate the norm of the mean vector. The final value can be referenced using label.vmean. You can use multiple instances of this keyword i.e. VMEAN1, VMEAN2, VMEAN3... The corresponding values are then referenced using label.vmean-1, label.vmean-2, label.vmean-3...