Shortcut: SUM

Module	function
Description	Usage
Calculate the sum of the arguments
output value	type
the sum	scalar

Input

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

Further details and examples

Calculate the sum of the arguments

This action takes a single vector or a single matrix in input. The output is a scalar that contains the sum of all the elements in the input vector/matrix. This action is very useful if you want to do calculations like the one illustrated in this example:

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

dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=3,4 ATOMS3the pair of atom that we are calculating the distance between=5,6 ATOMS4the pair of atom that we are calculating the distance between=7,8
bThe LESS_THAN action with label b calculates the following quantities:
 Quantity   
 Type   
 Description  
b
vector
the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=d SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1}
sThe SUM action with label s calculates the following quantities:
 Quantity   
 Type   
 Description  
s
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=b PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=s FILEthe name of the file on which to output these quantities=colvar

This example calculates and outputs the number of distances that are less than 0.1 nm.

You can do something similar by summing the elements of a matrix as shown below:

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

cThe CONTACT_MATRIX action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
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}
sThe SUM action with label s calculates the following quantities:
 Quantity   
 Type   
 Description  
s
scalar
the sum of all the elements in the input matrix: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=s FILEthe name of the file on which to output these quantities=colvar

Syntax

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