SELECT

This is part of the isdb module

Selects an argument based on the value of a SELECTOR.

You should read the documentation for SELECTOR to understand this action better.

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
compulsory keyword 
the labels of the scalars on which the bias will act 
=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
compulsory keyword 
the labels of the scalars on which the bias will act 
=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
compulsory keyword 
the labels of the scalars on which the bias will act 
=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
compulsory keyword 
the labels of the values from which the function is calculated 
=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
compulsory keyword 
the labels of the values that you would like to print to the file 
=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

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
.#!value	the value of the selected argument

Compulsory keywords

ARG	the labels of the values from which the function is calculated
SELECTOR	name of the variable used to select

Options

NUMERICAL_DERIVATIVES

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