Shortcut: SELECT_COMPONENTS

Module	valtools
Description	Usage
Create a new value to hold a subset of the components that are in a vector or matrix
output value	type
a vector containing the selected components	vector

Details and examples

Create a new value to hold a subset of the components that are in a vector or matrix

Output a scalar or vector that contains a subset of the elements in the input vector or matrix. In the example below the value s is a scalar that contains the distance between atoms 3 and 4.

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
sThe SELECT_COMPONENTS action with label s calculates the following quantities: Quantity    Type    Description  
s vector a vector containing the selected components: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix This action is a shortcut. More details ARGthe value from which we are selecting components=d COMPONENTSthe components in the input value that you woul like to build a new vector from=2
# PLUMED interprets the command:
# s: SELECT_COMPONENTS ARG=d COMPONENTS=2
# as follows (Click the red comment above to revert to the short version of the input):
s_maskThe CONSTANT action with label s_mask calculates the following quantities: Quantity    Type    Description  
s_mask vector the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,0,1,1
sThe SELECT_WITH_MASK action with label s calculates the following quantities: Quantity    Type    Description  
s vector a vector/matrix of values that is obtained using a mask to select elements of interest: SELECT_WITH_MASKUse a mask to select elements of an array More details ARGthe label for the value upon which you are going to apply the mask=d MASKan array with ones in the components that you want to discard=s_mask
# --- End of included input ---

In this example the output z is a 2 dimensional vector containing the distances between atoms 3 and 4 and 7 and 8.

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
sThe SELECT_COMPONENTS action with label s calculates the following quantities: Quantity    Type    Description  
s vector a vector containing the selected components: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix This action is a shortcut. More details ARGthe value from which we are selecting components=d COMPONENTSthe components in the input value that you woul like to build a new vector from=2,4
# PLUMED interprets the command:
# s: SELECT_COMPONENTS ARG=d COMPONENTS=2,4
# as follows (Click the red comment above to revert to the short version of the input):
s_maskThe CONSTANT action with label s_mask calculates the following quantities: Quantity    Type    Description  
s_mask vector the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,0,1,0
sThe SELECT_WITH_MASK action with label s calculates the following quantities: Quantity    Type    Description  
s vector a vector/matrix of values that is obtained using a mask to select elements of interest: SELECT_WITH_MASKUse a mask to select elements of an array More details ARGthe label for the value upon which you are going to apply the mask=d MASKan array with ones in the components that you want to discard=s_mask
# --- End of included input ---

Lastly, in this example we calculate a matrix of distances. The scalar s that is output from the SELECT_COMPONENTS action contains the distance between atoms 1 and 3 and 3 and 4.

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

dThe DISTANCE_MATRIX action with label d calculates the following quantities: Quantity    Type    Description  
d matrix a matrix containing the weights for the bonds between each pair of atoms: DISTANCE_MATRIXCalculate a matrix of distances between atoms. This action has hidden defaults. More details GROUPthe atoms for which you would like to calculate the adjacency matrix=1-5
d: DISTANCE_MATRIXCalculate a matrix of distances between atoms. This action uses the defaults shown here. More details GROUPthe atoms for which you would like to calculate the adjacency matrix=1-5  NL_CUTOFF The cutoff for the neighbor list=0.0 NL_STRIDE The frequency with which we are updating the atoms in the neighbor list=1 CUTOFF ignore distances that have a value larger than this cutoff=-1
sThe SELECT_COMPONENTS action with label s calculates the following quantities: Quantity    Type    Description  
s vector a vector containing the selected components: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix This action is a shortcut. More details ARGthe value from which we are selecting components=d COMPONENTSthe components in the input value that you woul like to build a new vector from=1.3,3.4
# PLUMED interprets the command:
# s: SELECT_COMPONENTS ARG=d COMPONENTS=1.3,3.4
# as follows (Click the red comment above to revert to the short version of the input):
s_flatThe FLATTEN action with label s_flat calculates the following quantities: Quantity    Type    Description  
s_flat vector a vector containing all the elements of the input matrix: FLATTENConvert a matrix into a vector More details ARGthe label for the matrix that you would like to flatten to a vector=d
s_maskThe CONSTANT action with label s_mask calculates the following quantities: Quantity    Type    Description  
s_mask vector the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,0,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1
sThe SELECT_WITH_MASK action with label s calculates the following quantities: Quantity    Type    Description  
s vector a vector/matrix of values that is obtained using a mask to select elements of interest: SELECT_WITH_MASKUse a mask to select elements of an array More details ARGthe label for the value upon which you are going to apply the mask=s_flat MASKan array with ones in the components that you want to discard=s_mask
# --- End of included input ---

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 value from which we are selecting components

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 value from which we are selecting components
COMPONENTS	compulsory	none	the components in the input value that you woul like to build a new vector from

Quantity	Type	Description
d	vector	the DISTANCE for each set of specified atoms