Action: FLATTEN

Module	valtools
Description	Usage
Convert a matrix into a vector
output value	type
a vector containing all the elements of the input matrix	vector

Details and examples

Convert a matrix into a vector

This action can be used to convert an input matrix to a vector. The input matrix is flattened in row-major order so if the input matrix is $N \times M$ the output vector has $N\times M$ elements. The first $M$ of these elements contain the first row of the input matrix, the second $M$ contain the second row of the input matrix and so on.

The following example illustrates how we can convert a $5\times 5$ contact matrix into a vector with 25 elements:

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

c1The CONTACT_MATRIX action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
matrix
a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1,2,3,4,5 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.1}
fThe FLATTEN action with label f calculates the following quantities:
 Quantity   
 Type   
 Description  
f
vector
a vector containing all the elements of the input matrix: FLATTENConvert a matrix into a vector More details ARGthe label for the matrix that you would like to flatten to a vector=c1
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=f FILEthe name of the file on which to output these quantities=colvar

Input

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

Keyword	Type	Description
ARG	matrix	the label for the matrix that you would like to flatten to a vector

Full list of keywords

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

Keyword	Type	Default	Description
ARG	input	none	the label for the matrix that you would like to flatten to a vector