SELECT

This is part of the isdb module

Selects an argument based on the value of a SELECTOR.

Examples

In this example we use a simulated-tempering like approach activated by the RESCALE action. For each value of the scale parameter, we perform an independent Parallel Bias Metadynamics simulation (see PBMETAD). At each moment of the simulation, only one of the PBMETAD actions is activated, based on the current value of the associated SELECTOR. The SELECT action can then be used to print out the value of the (active) PBMETAD bias potential.

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

ene: ENERGY The ENERGY action with label ene calculates a single scalar value
d: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label d calculates a single scalar value
SELECTOR 
NAME
compulsory keyword 
name of the SELECTOR 
=GAMMA 
VALUE
compulsory keyword 
set (initial) value of the SELECTOR 
=0 The SELECTOR action with label 
pbmetad0: PBMETAD 
ARG
the input for this action is the scalar output from one or more other actions. 
=d 
SELECTOR
add forces and do update based on the value of SELECTOR 
=GAMMA 
SELECTOR_ID
value of SELECTOR 
=0 
SIGMA
compulsory keyword 
the widths of the Gaussian hills 
=0.1 
PACE
compulsory keyword 
the frequency for hill addition, one for all biases 
=500 
HEIGHT
the height of the Gaussian hills, one for all biases. 
=1 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases. 
=8 
FILE
files in which the lists of added hills are stored, default names are assigned using
arguments if FILE is not found 
=HILLS.0 The PBMETAD action with label pbmetad0 calculates a single scalar value
pbmetad1: PBMETAD 
ARG
the input for this action is the scalar output from one or more other actions. 
=d 
SELECTOR
add forces and do update based on the value of SELECTOR 
=GAMMA 
SELECTOR_ID
value of SELECTOR 
=1 
SIGMA
compulsory keyword 
the widths of the Gaussian hills 
=0.1 
PACE
compulsory keyword 
the frequency for hill addition, one for all biases 
=500 
HEIGHT
the height of the Gaussian hills, one for all biases. 
=1 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases. 
=8 
FILE
files in which the lists of added hills are stored, default names are assigned using
arguments if FILE is not found 
=HILLS.1 The PBMETAD action with label pbmetad1 calculates a single scalar value
res: RESCALE ...
   
ARG
the input for this action is the scalar output from one or more other actions. 
=ene,pbmetad0.bias,pbmetad1.bias 
TEMP
compulsory keyword 
temperature 
=300 
   
SELECTOR
compulsory keyword 
name of the SELECTOR used for rescaling 
=GAMMA 
MAX_RESCALE
compulsory keyword 
maximum values for rescaling 
=1.2 
NOT_RESCALED
these last N arguments will not be scaled 
=2 
NBIN
compulsory keyword 
number of bins for gamma grid 
=2 
   
W0
 could not find this keyword 
=1000 
BIASFACTOR
compulsory keyword 
bias factor 
=100.0 
BSTRIDE
compulsory keyword 
stride for writing bias 
=2000 
BFILE
compulsory keyword 
file name for bias 
=bias.dat 
...The RESCALE action with label res calculates the following quantities:

 Quantity   
 Description  
res.bias
the instantaneous value of the bias potential
res.igamma
gamma parameter
res.accgamma
MC acceptance for gamma
res.wtbias
well-tempered bias


pbactive: SELECT 
ARG
the input for this action is the scalar output from one or more other actions. 
=pbmetad0.bias,pbmetad1.bias 
SELECTOR
compulsory keyword 
name of the variable used to select 
=GAMMA The SELECT action with label pbactive calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=pbactive 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=100 
FILE
the name of the file on which to output these quantities 
=COLVAR The PRINT action with label 

Glossary of keywords and components

Compulsory keywords

SELECTOR

name of the variable used to select

Options

NUMERICAL_DERIVATIVES

( default=off ) calculate the derivatives for these quantities numerically

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...