Action: MATRIX_VECTOR_PRODUCT

Module	matrixtools
Description	Usage
Calculate the product of the matrix and the vector
output value	type
the vector that is obtained by taking the product between the matrix and the vector that were input	vector

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Description
.#!custom	scalar	the names of the output components for this action depend on the actions input file see the example inputs below for details

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	scalar/vector/matrix	the label for the matrix and the vector/scalar that are being multiplied

Further details and examples

Calculate the product of the matrix and the vector

Thiis action allows you to multiply a matrix and a vector together. This action is primarily used to calculate coordination numbers and symmetry functions, which is what is done by the example 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=1-7 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=2.6 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=7
# PLUMED interprets the command:
# ones: ONES SIZE=7
# 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
# --- 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cc FILEthe name of the file on which to output these quantities=colvar

Notice that you can use this action to multiply multiple matrices by a single vector as 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.w matrix a matrix containing the weights for the bonds between each pair of atoms
c1.x matrix the projection of the bond on the x axis
c1.y matrix the projection of the bond on the y axis
c1.z matrix the projection of the bond on the z axis: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix GROUPspecifies the list of atoms that should be assumed indistinguishable=1-7 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=2.6 NN=6 MM=12 D_MAX=10.0}
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=7
# PLUMED interprets the command:
# ones: ONES SIZE=7
# 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
# --- End of included input --- ccThe MATRIX_VECTOR_PRODUCT action with label cc calculates the following quantities: Quantity    Type    Description  
cc.x vector the product of the matrix c1.x and the vector ones
cc.y vector the product of the matrix c1.y and the vector ones
cc.z vector the product of the matrix c1.z and the vector ones: 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.x,c1.y,c1.z,ones
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cc.x,cc.y,cc.z FILEthe name of the file on which to output these quantities=colvar

Notice that if you use this options all the input matrices must have the same sparsity pattern. This feature was implemented in order to making caluclating Steinhardt parameters such as Q6 straightforward.

You can also multiply a single matrix by multiple vectors:

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=1-7 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=2.6 NN=6 MM=12 D_MAX=10.0}
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=7
# PLUMED interprets the command:
# ones: ONES SIZE=7
# 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
# --- End of included input --- twosThe CONSTANT action with label twos calculates the following quantities: Quantity    Type    Description  
twos vector the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1,2,3,4,5,6,7
twos: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1,2,3,4,5,6,7  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
ccThe MATRIX_VECTOR_PRODUCT action with label cc calculates the following quantities: Quantity    Type    Description  
cc.ones vector the product of the matrix c1 and the vector ones
cc.twos vector the product of the matrix c1 and the vector twos: 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,twos
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cc.ones,cc.twos FILEthe name of the file on which to output these quantities=colvar

This feature was implemented to make calculating local averages of the Steinhard parameters straightforward.

Syntax

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 and the vector/scalar that are being multiplied
SERIAL	optional	false	do the calculation in serial

Keys	Action
`?`	Open this help
`n`	Next page
`p`	Previous page
`s`	Search

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