Action: MATRIX_PRODUCT_DIAGONAL

Module	refdist
Description	Usage
Calculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector
output value	type
a vector containing the diagonal elements of the matrix that obtaned by multiplying the two input matrices together	scalar/vector

Details and examples

Calculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector

This action allows you to multiply two matrices and recover the diagonal of the product of the matrices. The following input shows an example where two contact matrices are multiplied together.

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=1-100 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}
c2The CONTACT_MATRIX action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
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=1-100 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=0.2}
mThe MATRIX_PRODUCT_DIAGONAL action with label m calculates the following quantities:
 Quantity   
 Type   
 Description  
m
vector
a vector containing the diagonal elements of the matrix that obtaned by multiplying the two input matrices together: MATRIX_PRODUCT_DIAGONALCalculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector More details ARGthe two vectors/matrices whose product are to be taken=c1,c2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=m FILEthe name of the file on which to output these quantities=colvar

As you can see from the documentation for the shortcut EUCLIDEAN_DISTANCE this action is useful for computing distances between vectors.

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	vector/matrix	the two vectors/matrices whose product are to be taken

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 two vectors/matrices whose product are to be taken
SERIAL	optional	false	do the calculation in serial. Further information about this flag can be found here.
USEGPU	optional	false	run this calculation on the GPU. Further information about this flag can be found here.