PROJECT_POINTS

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

Find the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input

Examples

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. 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
coord	the coordinates of the points in the low dimensional space

Compulsory keywords

CGTOL

( default=1E-6 ) the tolerance for the conjugate gradient minimization

Options

SERIAL	( default=off ) do the calculation in serial. Do not parallelize
ARG	the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag.. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...
TARGET	the matrix of target quantities that you would like to match. You can use multiple instances of this keyword i.e. TARGET1, TARGET2, TARGET3...
FUNC	a function that is applied on the distances between the points in the low dimensional space. You can use multiple instances of this keyword i.e. FUNC1, FUNC2, FUNC3...
WEIGHTS	the matrix with the weights of the target quantities. You can use multiple instances of this keyword i.e. WEIGHTS1, WEIGHTS2, WEIGHTS3...