Action: BRIDGE_MATRIX

Module	adjmat
Description	Usage
Calculate the number of atoms that bridge two parts of a structure
output value	type
a matrix containing the weights for the bonds between each pair of atoms	matrix

Details and examples

Calculate the number of atoms that bridge two parts of a structure

This adjacency matrix is used to implement the BRIDGE shortcut. The action outputs a adjacency matrix in the same way as CONTACT_MATRIX. However, the $j,k$ element of the adjacency matrix is calculated using:

$$M_{jk} = \sum_i s_A(r_{ij})s_B(r_{ik})$$

In this expression, the sum runs over all the atoms that were specified using the BRIDGING_ATOMS keyword, $s_A$ and $s_B$ are switching functions, and $r_{ij}$ and $r_{ik}$ are the distances between atom $i$ and $j$ and between atoms $i$ and $k$. Less formally, this formula ensures that $j,k$ element of the output matrix is one if there is a bridging atom between atom $j$ and $k$.

In the following example input atoms 100-200 can serve as bridging atoms between the atoms in GROUPA and GROUPB and the two switching functions $s_A$ and $s_B$ in the formula above are identical.

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

w1The BRIDGE_MATRIX action with label w1 calculates the following quantities:
 Quantity   
 Type   
 Description  
w1
matrix
a matrix containing the weights for the bonds between each pair of atoms: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action has hidden defaults. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200
   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=1-10 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=11-20
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
...
w1: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action uses the defaults shown here. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200
   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=1-10 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=11-20
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
 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
...

If you use a single GROUP keyword as in the input below as a single SWITCH keyword the output matrix is symmetric.

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

w2The BRIDGE_MATRIX action with label w2 calculates the following quantities:
 Quantity   
 Type   
 Description  
w2
matrix
a matrix containing the weights for the bonds between each pair of atoms: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action has hidden defaults. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
...
w2: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action uses the defaults shown here. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
 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
...

However, if the two switching functions are not identical, as in the following example, then the output matrix is not symmetric even if GROUP is used rather than GROUPA/GROUPB.

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

w2The BRIDGE_MATRIX action with label w2 calculates the following quantities:
 Quantity   
 Type   
 Description  
w2
matrix
a matrix containing the weights for the bonds between each pair of atoms: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action has hidden defaults. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10
   SWITCHAThe switching function on the distance between bridging atoms and the atoms in group A. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
   SWITCHBThe switching function on the distance between the bridging atoms and the atoms in group B. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.4}
...
w2: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action uses the defaults shown here. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10
   SWITCHAThe switching function on the distance between bridging atoms and the atoms in group A. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
   SWITCHBThe switching function on the distance between the bridging atoms and the atoms in group B. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.4}
 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
...

Notice that in all the inputs above the $r_{ij}$ and $r_{ik}$ values that enter the formula above are calculated in a way that takes the periodic boundary conditions into account. If you want to ignore the periodic boundary conditions you can use the NOPBC flag as shown below.

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

w2The BRIDGE_MATRIX action with label w2 calculates the following quantities:
 Quantity   
 Type   
 Description  
w2
matrix
a matrix containing the weights for the bonds between each pair of atoms: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action has hidden defaults. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
   NOPBC don't use pbc
...
w2: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action uses the defaults shown here. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
   NOPBC don't use pbc
 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
...

COMPONENTS flag

If you add the flag COMPONENTS to the input as shown below:

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

c4The BRIDGE_MATRIX action with label c4 calculates the following quantities:
 Quantity   
 Type   
 Description  
c4.w
matrix
a matrix containing the weights for the bonds between each pair of atoms
c4.x
matrix
the projection of the bond on the x axis
c4.y
matrix
the projection of the bond on the y axis
c4.z
matrix
the projection of the bond on the z axis: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action has hidden defaults. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
   COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
...
c4: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action uses the defaults shown here. More details ...
   BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
   COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
 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
...

then four matrices with the labels c4.w, c4.x, c4.y and c4.z are output by the action. The matrix with the label c4.w is the adjacency matrix that would be output if you had not added the COMPONENTS flag. The $i,j$ component of the matrices c4.x, c4.y and c4.z contain the $x$, $y$ and $z$ components of the vector connecting atoms $j$ and $k$. Importantly, however, the components of these vectors are only stored in c4.x, c4.y and c4.z if the elements of c4.w are non-zero. Using the COMPONENTS flag in this way ensures that you can use BRIDGE_MATRIX in tandem with many of the functionalities that are part of the symfunc module.

The MASK keyword

You use the MASK keyword with BRIDGE_MATRIX in the same way that is used in CONTACT_MATRIX. This keyword thus expects a vector in input, which tells BRIDGE_MATRIX that it is safe to not calculate certain rows of the output matrix. An example where this keyword is used is shown below:

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

# The atoms that are of interest
owThe GROUP action with label ow calculates the following quantities:
 Quantity   
 Type   
 Description  
ow
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=1-1650
# Fixed virtual atom which serves as the probe volume's center (pos. in nm)
centerThe FIXEDATOM action with label center calculates the following quantities:
 Quantity   
 Type   
 Description  
center
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.5,2.5,2.5
center: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.5,2.5,2.5  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
# Vector in which element i is one if atom i is in sphere of interest and zero otherwise
sphereThe INSPHERE action with label sphere calculates the following quantities:
 Quantity   
 Type   
 Description  
sphere
vector
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest: INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details ATOMSthe group of atoms that you would like to investigate=ow CENTERthe atom whose vicinity we are interested in examining=center RADIUSthe switching function that tells us the extent of the sphereical region of interest. Options for this keyword are explained in the documentation for LESS_THAN.={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52}
# Calculates cooordination numbers
cmapThe BRIDGE_MATRIX action with label cmap calculates the following quantities:
 Quantity   
 Type   
 Description  
cmap
matrix
a matrix containing the weights for the bonds between each pair of atoms: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action has hidden defaults. More details ...
   GROUPthe atoms for which you would like to calculate the adjacency matrix=ow BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=1650-3000
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={GAUSSIAN D_0=0.32 R_0=0.01 D_MAX=0.34} MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=sphere
...
cmap: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action uses the defaults shown here. More details ...
   GROUPthe atoms for which you would like to calculate the adjacency matrix=ow BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=1650-3000
   SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={GAUSSIAN D_0=0.32 R_0=0.01 D_MAX=0.34} MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=sphere
 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
...
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=1650
# PLUMED interprets the command:
# ones: ONES SIZE=1650
# 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=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
# --- 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=cmap,ones
# Multiply coordination numbers by sphere vector
prodThe CUSTOM action with label prod calculates the following quantities:
 Quantity   
 Type   
 Description  
prod
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cc,sphere FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Sum of coordination numbers for atoms that are in the sphere of interest
numerThe SUM action with label numer calculates the following quantities:
 Quantity   
 Type   
 Description  
numer
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=prod PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Number of atoms that are in sphere of interest
denomThe SUM action with label denom calculates the following quantities:
 Quantity   
 Type   
 Description  
denom
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=sphere PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Average coordination number for atoms in sphere of interest
avThe CUSTOM action with label av calculates the following quantities:
 Quantity   
 Type   
 Description  
av
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=prod,sphere FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And print out final CV to a file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=av FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1

This input calculates the average for a type of coordination number for those atoms that are within a spherical region that is centered on the point $(2.5,2.5,2.5)$. The coordination number for the atoms that is evaluated here counts an atom $k$ in the coordination sphere of atom $j$ if there is a bridging atom within 0.34 nm of atoms $j$ and $k$.

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
MASK	vector	a vector that is used to used to determine which rows of the adjancency matrix to compute
GROUP	atoms	the atoms for which you would like to calculate the adjacency matrix
GROUPA	atoms	when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB	atoms	when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
BRIDGING_ATOMS	atoms	The list of atoms that can form the bridge between the two interesting parts of the structure

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. 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	Keyword	Description
w	matrix	COMPONENTS	a matrix containing the weights for the bonds between each pair of atoms
x	matrix	COMPONENTS	the projection of the bond on the x axis
y	matrix	COMPONENTS	the projection of the bond on the y axis
z	matrix	COMPONENTS	the projection of the bond on the z axis

Full list of keywords

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

Keyword	Type	Default	Description
MASK	input	none	a vector that is used to used to determine which rows of the adjancency matrix to compute
GROUP	input	none	the atoms for which you would like to calculate the adjacency matrix
GROUPA	input	none	when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB	input	none	when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
BRIDGING_ATOMS	input	none	The list of atoms that can form the bridge between the two interesting parts of the structure
NL_CUTOFF	compulsory	0.0	The cutoff for the neighbor list
NL_STRIDE	compulsory	1	The frequency with which we are updating the atoms in the neighbor list
COMPONENTS	optional	false	also calculate the components of the vector connecting the atoms in the contact matrix
NOPBC	optional	false	don't use pbc
SWITCH	optional	not used	The parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.
SWITCHA	optional	not used	The switching function on the distance between bridging atoms and the atoms in group A. Options for this keyword are explained in the documentation for LESS_THAN.
SWITCHB	optional	not used	The switching function on the distance between the bridging atoms and the atoms in group B. Options for this keyword are explained in the documentation for LESS_THAN.
SERIAL	optional	false	do the calculation in serial. Further information about this flag can be found here.
USEGPU	optional	false	run this calculation on the GPU. Further information about this flag can be found here.

deprecated keywords

The keywords in the following table can still be used with this action but have been deprecated

Keyword	Description
ATOMS	You should use GROUP instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only

References

More information about how this action can be used is available in the following articles:

• G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017)