Action: CONCATENATE

Module	valtools
Description	Usage
Join vectors or matrices together
output value	type
the concatenated vector/matrix that was constructed from the input values	vector/matrix

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

Join vectors or matrices together

This action can be used to join sets of scalars, vector or matrices together into a single output value. The following example shows how this works with vectors and scalars:

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

d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
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=3,4 ATOMS2the pair of atom that we are calculating the distance between=5,6
vThe CONCATENATE action with label v calculates the following quantities:
 Quantity   
 Type   
 Description  
v
vector
the concatenated vector/matrix that was constructed from the input values: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=d1,d2

The output vector here, v, has three components. The first of these is the distance between atoms 1 and 2 and the second and third are the distances between atoms 3 and 4 and 5 and 6 respectively.

Concatenating two or more vectors is similarly straightfoward. Concatenating matrices is a little more difficult as the user must explain the axes that each matrix should be joined to. The following input should give some idea as to how the joining of matrices is done in practise. In this example, we define two groups of atoms and calculate the contact matrix between all the atoms in the two groups by first calculating three contact matrices that describe the inter and intra group contacts.

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

# Define two groups of atoms
gThe GROUP action with label g calculates the following quantities:
 Quantity   
 Type   
 Description  
g
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-5
hThe GROUP action with label h calculates the following quantities:
 Quantity   
 Type   
 Description  
h
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6-20

# Calculate the CONTACT_MATRIX for the atoms in group g
cgThe CONTACT_MATRIX action with label cg calculates the following quantities:
 Quantity   
 Type   
 Description  
cg
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=g 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}

# Calculate the CONTACT_MATRIX for the atoms in group h
chThe CONTACT_MATRIX action with label ch calculates the following quantities:
 Quantity   
 Type   
 Description  
ch
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=h 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=0.2}

# Calculate the CONTACT_MATRIX between the atoms in group g and group h
cghThe CONTACT_MATRIX action with label cgh calculates the following quantities:
 Quantity   
 Type   
 Description  
cgh
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 GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=g GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=h 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=0.15}

# Now calculate the contact matrix between the atoms in group h and group h
# Notice this is just the transpose of cgh
cghTThe TRANSPOSE action with label cghT calculates the following quantities:
 Quantity   
 Type   
 Description  
cghT
matrix
the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=cgh

# And concatenate the matrices together to construct the adjacency matrix between the
# adjacency matrices
mThe CONCATENATE action with label m calculates the following quantities:
 Quantity   
 Type   
 Description  
m
matrix
the concatenated vector/matrix that was constructed from the input values: CONCATENATEJoin vectors or matrices together More details ...
 MATRIX11specify the matrices that you wish to join together into a single matrix=cg MATRIX12specify the matrices that you wish to join together into a single matrix=cgh
 MATRIX21specify the matrices that you wish to join together into a single matrix=cghT MATRIX22specify the matrices that you wish to join together into a single matrix=ch
...

Syntax

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