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

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 FILEthe name of the file on which to output these quantities=index.ndx 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

Obviously, if you want to print the indices of the atoms that have a coordination number that is equal to 4 you use a command like the one shown below:

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 equal to 4
# on every 10th step of the simulation
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 FILEthe name of the file on which to output these quantities=index.ndx
   LESS_THAN_OR_EQUALwhen printing with arguments that are vectors only print components of vectors have a value less than or equal to this value=4
   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
   STRIDE the frequency with which the quantities of interest should be output=10
...

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

RESTART, UPDATE_FROM and UPDATE_UNTIL

Notice that the RESTART, UPDATE_FROM and UPDATE_UNTIL keywords keywords can be used in this action in the same way as they are used for PRINT. Consequently, if you would like to append to an existing file called index.ndx instead of backing that file up at the start of the calculation and outputting the data from the calculation on a new file called index.ndx you would use an input like the one shown below:

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 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

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 FILEthe name of the file on which to output these quantities=index.ndx
  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 RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
...

Similarly, if you want to only output the index.ndx file during the 400 ps time interval after the first 100 ps of the simulation you would use an input like the one shown below:

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 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

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 FILEthe name of the file on which to output these quantities=index.ndx
  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
  UPDATE_FROMOnly update this action from this time=100 UPDATE_UNTILOnly update this action until this time=500
...

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.

Keyword	Type	Description
ARG	vector	the labels of vectors that should be used when printind the NDX file
ATOMS	atoms	the list of atoms that have the corresponding arguments

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 labels of vectors that should be used when printind the NDX file
ATOMS	input	none	the list of atoms that have the corresponding arguments
STRIDE	compulsory	1	the frequency with which the quantities of interest should be output
FILE	optional	not used	the name of the file on which to output these quantities
LESS_THAN_OR_EQUAL	optional	not used	when printing with arguments that are vectors only print components of vectors have a value less than or equal to this value
GREATER_THAN_OR_EQUAL	optional	not used	when printing with arguments that are vectors only print components of vectors have a value greater than or equal to this value
RESTART	optional	not used	allows per-action setting of restart (YES/NO/AUTO)
UPDATE_FROM	optional	not used	Only update this action from this time
UPDATE_UNTIL	optional	not used	Only update this action until this time

Quantity	Type	Description
c1	matrix	a matrix containing the weights for the bonds between each pair of atoms