Action: TOPOLOGY_MATRIX

Module adjmat
Description Usage
Adjacency matrix in which two atoms are adjacent if they are connected topologically used in 0 tutorialsused in 0 eggs
output value type
a matrix containing the weights for the bonds between each pair of atoms matrix

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action’s label followed by a dot and the name of the value required from the list below.

Name Type Keyword Description
w matrix COMPONENTS a matrix containing the weights for the bonds between each pair of atoms
x matrix COMPONENTS the projection of the bond on the x axis
y matrix COMPONENTS the projection of the bond on the y axis
z matrix COMPONENTS the projection of the bond on the z axis

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword Type Description
GROUP atoms the atoms for which you would like to calculate the adjacency matrix
GROUPA atoms when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB atoms when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
ATOMS atoms the atoms for which you would like to calculate the adjacency matrix
BACKGROUND_ATOMS atoms the list of atoms that should be considered as part of the background density

Further details and examples

Text from manual goes here

References

More information about how this action can be used is available in the following articles:

Syntax

The following table describes the keywords and options that can be used with this action

Keyword Type Default Description
GROUP input none the atoms for which you would like to calculate the adjacency matrix
GROUPA input none when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB input none when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
ATOMS input none the atoms for which you would like to calculate the adjacency matrix
BACKGROUND_ATOMS input none the list of atoms that should be considered as part of the background density
NL_CUTOFF compulsory 0.0 The cutoff for the neighbor list
NL_STRIDE compulsory 1 The frequency with which we are updating the atoms in the neighbor list
SWITCH compulsory none switching function that acts upon the distance between the two atoms that define our cylinder. Options for this keyword are explained in the documentation for LESS_THAN.
RADIUS compulsory none swtiching function that acts upon the radial distance of the atom from the center of the cylinder. Options for this keyword are explained in the documentation for LESS_THAN.
CYLINDER_SWITCH compulsory none a switching function on ( r_ij . Options for this keyword are explained in the documentation for LESS_THAN.
BIN_SIZE compulsory none the size to use for the bins
DENSITY_THRESHOLD compulsory none a switching function that acts upon the maximum density in the cylinder. Options for this keyword are explained in the documentation for LESS_THAN.
SIGMA compulsory none the width of the function to be used for kernel density estimation
KERNEL compulsory gaussian the type of kernel function to be used
SERIAL optional false do the calculation in serial
COMPONENTS optional false also calculate the components of the vectors connecting the atoms in the contact matrix
NOPBC optional false don’t use pbc