Action: PRINT_NDX

Module	generic
Description	Usage
Print an ndx file
This action outputs data to a file. You can read more about how PLUMED manages output files here

Input

The arguments and atoms 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

Print an ndx file

The following example shows how you can use this command to print out the indices of all the atoms that have a coordination number that is greater than or equal to 4.

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

# These three lines calculate the coordination numbers of 100 atoms
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 NN=6 MM=12}
onesThe ONES action with label ones calculates the following quantities:
 Quantity   
 Type   
 Description  
ones
vector
a vector of ones with the required number of elements: ONESCreate a constant vector with all elements equal to one This action is a shortcut. More details SIZEthe number of ones that you would like to create=100
# PLUMED interprets the command:
# ones: ONES SIZE=100
# as follows (Click the red comment above to revert to the short version of the input):
onesThe CONSTANT action with label ones calculates the following quantities:
 Quantity   
 Type   
 Description  
ones
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details NOLOG do not report all the read in scalars in the log VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
# --- End of included input --- ccThe MATRIX_VECTOR_PRODUCT action with label cc calculates the following quantities:
 Quantity   
 Type   
 Description  
cc
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=c1,ones

# This command then prints the indices of the atoms that have a coordination number that is greater than 4
# every step
PRINT_NDXPrint an ndx file More details ATOMSthe list of atoms that have the corresponding arguments=1-100 ARGthe labels of vectors that should be used when printind the NDX file=cc GREATER_THAN_OR_EQUALwhen printing with arguments that are vectors only print components of vectors have a value greater than or equal to this value=4

This command is used in the OUTPUT_CLUSTER command that you can use to output the indices of the atoms that are in a particular cluster.

Syntax

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