AROUND

This is part of the volumes module

This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.

Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three dimensional space. For example, if we have the coordination numbers for all the atoms in the system each coordination number can be assumed to lie on the position of the central atom. Because each base quantity can be assigned to a particular point in space we can calculate functions of the distribution of base quantities in a particular part of the box by using:

\[ \overline{s}_{\tau} = \frac{ \sum_i f(s_i) w(x_i,y_i,z_i) }{ \sum_i w(x_i,y_i,z_i) } \]

where the sum is over the collective variables, \(s_i\), each of which can be thought to be at \( (x_i,y_i,z_i)\). The function \( w(x_i,y_i,z_i) \) measures whether or not the system is in the subregion of interest. It is equal to:

\[ w(x_i,y_i,z_i) = \int_{xl}^{xu} \int_{yl}^{yu} \int_{zl}^{zu} \textrm{d}x\textrm{d}y\textrm{d}z K\left( \frac{x - x_i}{\sigma} \right)K\left( \frac{y - y_i}{\sigma} \right)K\left( \frac{z - z_i}{\sigma} \right) \]

where \(K\) is one of the kernel functions described on histogrambead and \(\sigma\) is a bandwidth parameter. The function \((s_i)\) can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.

When AROUND is used with the DENSITY action the number of atoms in the specified region is calculated

Examples

The following commands tell plumed to calculate the average coordination number for the atoms that have x (in fractional coordinates) within 2.0 nm of the com of mass c1. The final value will be labeled s.mean.

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

contract shortcuts

c1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=1-100 The COM action with label c1 calculates the following quantities:

 Quantity   
 Description  
c1.x
the x coordinate of the virtual atom
c1.y
the y coordinate of the virtual atom
c1.z
the z coordinate of the virtual atom
c1.mass
the mass of the virtual atom
c1.charge
the charge of the virtual atom


c: COORDINATIONNUMBER 
SPECIES
this keyword is used for colvars such as coordination number. 
=1-100 
R_0
 could not find this keyword 
=1.0 The COORDINATIONNUMBER action with label c calculates a single scalar value
s: AROUND 
DATA
the label of an action that calculates multicolvars. 
=c 
ATOM
an alternative to ORIGIN 
=c1 
XLOWER
compulsory keyword ( default=0.0 )
the lower boundary in x relative to the x coordinate of the atom (0 indicates use
full extent of box). 
=-2.0 
XUPPER
compulsory keyword ( default=0.0 )
the upper boundary in x relative to the x coordinate of the atom (0 indicates use
full extent of box). 
=2.0 
SIGMA
compulsory keyword 
the width of the function to be used for kernel density estimation 
=0.1 
MEAN
( default=off ) calculate the average value of the colvar inside the region of interest
 The AROUND action with label s calculates a single scalar value

c1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=1-100 The COM action with label c1 calculates the following quantities:

 Quantity   
 Description  
c1.x
the x coordinate of the virtual atom
c1.y
the y coordinate of the virtual atom
c1.z
the z coordinate of the virtual atom
c1.mass
the mass of the virtual atom
c1.charge
the charge of the virtual atom


c_grp: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=1-100 The GROUP action with label c_grp defines a group of atoms so that they can be referred to later in the input
c_mat: CONTACT_MATRIX 
GROUP
specifies the list of atoms that should be assumed indistinguishable. 
=1-100 
R_0
 could not find this keyword 
=1.0 
D_0
 could not find this keyword 
=0.0 
NN
compulsory keyword ( default=6 )
The n parameter of the switching function 
=6 
MM
compulsory keyword ( default=0 )
The m parameter of the switching function; 0 implies 2*NN 
=0 The CONTACT_MATRIX action with label c_mat calculates a single scalar value
c_ones: ONES 
SIZE
compulsory keyword 
the number of ones that you would like to create 
=100 The ONES action with label c_ones calculates a single scalar value
c: MATRIX_VECTOR_PRODUCT 
ARG
the input for this action is the scalar output from one or more other actions. 
=c_mat,c_ones The MATRIX_VECTOR_PRODUCT action with label c calculates a single scalar value
c_caverage: MEAN 
ARG
the input to this function. 
=c 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The MEAN action with label c_caverage calculates a single scalar value
s_grp: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=c The GROUP action with label s_grp defines a group of atoms so that they can be referred to later in the input
s: AROUND_CALC 
ATOM
an alternative to ORIGIN 
=c1 
XLOWER
compulsory keyword ( default=0.0 )
the lower boundary in x relative to the x coordinate of the atom (0 indicates use
full extent of box). 
=-2.0 
XUPPER
compulsory keyword ( default=0.0 )
the upper boundary in x relative to the x coordinate of the atom (0 indicates use
full extent of box). 
=2.0 
SIGMA
compulsory keyword 
the width of the function to be used for kernel density estimation 
=0.1 
ATOMS
the group of atoms that you would like to investigate. 
=c The AROUND_CALC action with label s calculates a single scalar value
s_prod: CUSTOM 
ARG
the input to this function. 
=c,s 
FUNC
compulsory keyword 
the function you wish to evaluate 
=x*y 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The CUSTOM action with label s_prod calculates a single scalar value
s_numer: SUM 
ARG
the input to this function. 
=s_prod 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The SUM action with label s_numer calculates a single scalar value
s_norm: SUM 
ARG
the input to this function. 
=s 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The SUM action with label s_norm calculates a single scalar value
s_mean: CUSTOM 
ARG
the input to this function. 
=s_numer,s_norm 
FUNC
compulsory keyword 
the function you wish to evaluate 
=x/y 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The CUSTOM action with label s_mean calculates a single scalar value

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	Keyword	Description
lessthan	LESS_THAN	the number of cvs in the region of interest that are less than a certain threshold
morethan	MORE_THAN	the number of cvs in the region of interest that are more than a certain threshold
between	BETWEEN	the number of cvs in the region of interest that are within a certain range
sum	SUM	the sum of all the colvars weighted by the function that determines if we are in the region
mean	MEAN	the average values of the colvar in the region of interest

The atoms involved can be specified using

ATOMS	the group of atoms that you would like to investigate. For more information on how to specify lists of atoms see Groups and Virtual Atoms
ORIGIN	the atom whose vicinity we are interested in examining. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Or alternatively by using

ATOM	an alternative to ORIGIN

Compulsory keywords

SIGMA	the width of the function to be used for kernel density estimation
KERNEL	( default=gaussian ) the type of kernel function to be used
XLOWER	( default=0.0 ) the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).
XUPPER	( default=0.0 ) the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).
YLOWER	( default=0.0 ) the lower boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).
YUPPER	( default=0.0 ) the upper boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).
ZLOWER	( default=0.0 ) the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).
ZUPPER	( default=0.0 ) the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).

Options

SERIAL	( default=off ) do the calculation in serial. Do not parallelize
OUTSIDE	( default=off ) calculate quantities for colvars that are on atoms outside the region of interest
SUM	( default=off ) calculate the sum of all the quantities.
MEAN	( default=off ) calculate the average value of the colvar inside the region of interest
DATA	the label of an action that calculates multicolvars. Weighted sums based on the location of the colvars calculated by this action will be calcualted
LESS_THAN	calcualte the number of colvars that are inside the region of interest and that are less than a certain threshold
MORE_THAN	calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold
BETWEEN	calculate the number of colvars that are inside the region of interest and that have a CV value that is between a particular set of bounds