This is part of the adjmat module

Adjacency matrix in which two atoms are adjacent if they are connected topologically

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	Keyword	Description
w	COMPONENTS	the weight of the connection
x	COMPONENTS	the projection of the bond on the x axis
y	COMPONENTS	the projection of the bond on the y axis
z	COMPONENTS	the projection of the bond on the z axis

The atoms involved can be specified using

GROUP	the atoms for which you would like to calculate the adjacency matrix. For more information on how to specify lists of atoms see Groups and Virtual Atoms
GROUPA	. For more information on how to specify lists of atoms see Groups and Virtual Atoms
GROUPB	. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Or alternatively by using

ATOMS

the atoms for which you would like to calculate the adjacency matrix. This is a depracated syntax that is equivalent to GROUP. You are strongly recommened to use GROUP instead of ATOMS.

Or alternatively by using

BACKGROUND_ATOMS

the list of atoms that should be considered as part of the background density. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

NL_CUTOFF	( default=0.0 ) The cutoff for the neighbor list. A value of 0 means we are not using a neighbor list
NL_STRIDE	( default=1 ) The frequency with which we are updating the atoms in the neighbor list
SWITCH	This keyword is used if you want to employ an alternative to the continuous swiching function defined above. The following provides information on the switchingfunction that are available. When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.
RADIUS
CYLINDER_SWITCH	a switching function on ( r_ij . r_ik - 1 )/r_ij
BIN_SIZE	the size to use for the bins
DENSITY_THRESHOLD
SIGMA	the width of the function to be used for kernel density estimation
KERNEL	( default=gaussian ) the type of kernel function to be used

Options

SERIAL

( default=off ) do the calculation in serial. Do not parallelize

COMPONENTS

( default=off ) also calculate the components of the vector connecting the atoms in the contact matrix

NOPBC

( default=off ) don't use pbc