SKETCHMAP_READ

	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.

Read in a sketch-map projection from an input file

Examples

Glossary of keywords and components

Description of components

The names of the components in this action can be customized by the user in the actions input file. However, in addition to the components that can be customized the following quantities will always be output

Quantity	Description
coord	the low-dimensional projections of the various input configurations

In addition the following quantities can be calculated by employing the keywords listed below

Quantity	Keyword	Description
gradient	GRADIENT	the gradient
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
vsum	VSUM	the norm of sum of vectors. The output component can be referred to elsewhere in the input file by using the label.vsum
spath	SPATH	the position on the path
gspath	GPATH	the position on the path calculated using trigonometry
gzpath	GPATH	the distance from the path calculated using trigonometry
zpath	ZPATH	the distance from the path
altmin	ALT_MIN	the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
between	BETWEEN	the number/fraction of values within a certain range. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
highest	HIGHEST	the highest of the quantities calculated by this action
lessthan	LESS_THAN	the number of values less than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
lowest	LOWEST	the lowest of the quantities calculated by this action
max	MAX	the maximum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
mean	MEAN	the mean value. The output component can be referred to elsewhere in the input file by using the label.mean
min	MIN	the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
moment	MOMENTS	the central moments of the distribution of values. The second moment would be referenced elsewhere in the input file using label.moment-2, the third as label.moment-3, etc.
morethan	MORE_THAN	the number of values more than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
sum	SUM	the sum of values

Compulsory keywords

HIGH_DIM_FUNCTION	( default=as in input action ) the parameters of the switching function in the high dimensional space
LOW_DIM_FUNCTION	( default=as in input action ) the parameters of the switching function in the low dimensional space
MIXPARAM	( default=0.0 ) the amount of the pure distances to mix into the stress function
TYPE	( default=OPTIMAL-FAST ) the manner in which distances are calculated. More information on the different metrics that are available in PLUMED can be found in the section of the manual on Distances from reference configurations
REFERENCE	the file containing the sketch-map projection
PROPERTY	the property to be used in the index. This should be in the REMARK of the reference

Options

SERIAL	( default=off ) do the calculation in serial. Do not use MPI
LOWMEM	( default=off ) lower the memory requirements
DISABLE_CHECKS	( default=off ) disable checks on reference input structures.