Shortcut: NEIGHBORS

Module	adjmat
Description	Usage
Build a matrix with ones in for the N nearest neighbours of an atom
output value	type
a matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise	matrix

Details and examples

Build a matrix with ones in for the N nearest neighbours of an atom

The following input illustrates how to use this action in tandem with DISTANCE_MATRIX to find the six nearest atoms to each of the first 100 atoms in the input file:

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

d1The DISTANCE_MATRIX action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 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=1-100
d1: 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=1-100  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
nThe NEIGHBORS action with label n calculates the following quantities: Quantity    Type    Description  
n matrix a matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action has hidden defaults. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=d1 NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=6
n: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action uses the defaults shown here. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=d1 NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=6  NHIGHEST in each row of the output matrix set the elements that correspond to the n highest elements in each row of the input matrix equal to one=0

Alternatively, if you would like to use a CONTACT_MATRIX to do something similar you would do the following:

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=0.5}
nThe NEIGHBORS action with label n calculates the following quantities: Quantity    Type    Description  
n matrix a matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action has hidden defaults. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=c1 NHIGHEST in each row of the output matrix set the elements that correspond to the n highest elements in each row of the input matrix equal to one=6
n: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action uses the defaults shown here. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=c1 NHIGHEST in each row of the output matrix set the elements that correspond to the n highest elements in each row of the input matrix equal to one=6  NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=0

This command is useful for implementing alternatives to the symmatry functions that are defined by the shortcuts in the module symfunc. For example, suppose that you want to calculate a variant on the TETRAHEDRAL symmetry function. In this variant on the CV the coordination sphere around each central atom is not defined using a switching function. Instad this coordination sphere contains only the four nearest atoms. You can implement this CV by using the following input:

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

d1The DISTANCE_MATRIX action with label d1 calculates the following quantities: Quantity    Type    Description  
d1.w matrix a matrix containing the weights for the bonds between each pair of atoms
d1.x matrix the projection of the bond on the x axis
d1.y matrix the projection of the bond on the y axis
d1.z matrix the projection of the bond on the z axis: 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=1-100 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
d1: 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=1-100 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 CUTOFF ignore distances that have a value larger than this cutoff=-1
nThe NEIGHBORS action with label n calculates the following quantities: Quantity    Type    Description  
n matrix a matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action has hidden defaults. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=d1.w NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=4
n: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action uses the defaults shown here. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=d1.w NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=4  NHIGHEST in each row of the output matrix set the elements that correspond to the n highest elements in each row of the input matrix equal to one=0
fThe CUSTOM action with label f calculates the following quantities: Quantity    Type    Description  
f matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=n,d1.x,d1.y,d1.z,d1.w VARthe names to give each of the arguments in the function=w,x,y,z,r PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=w*(((x+y+z)/r)^3+((x-y-z)/r)^3+((-x+y-z)/r)^3+((-x-y+z)/r)^3)
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 --- ucvThe MATRIX_VECTOR_PRODUCT action with label ucv calculates the following quantities: Quantity    Type    Description  
ucv 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=f,ones
cvThe CUSTOM action with label cv calculates the following quantities: Quantity    Type    Description  
cv 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=ucv PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=x/4

You can even use these ideas with the functionality that is in the volumes module as 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=1-16500
# 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}
# The distance matrix
dmapThe DISTANCE_MATRIX action with label dmap calculates the following quantities: Quantity    Type    Description  
dmap.w matrix a matrix containing the weights for the bonds between each pair of atoms
dmap.x matrix the projection of the bond on the x axis
dmap.y matrix the projection of the bond on the y axis
dmap.z matrix the projection of the bond on the z axis: DISTANCE_MATRIXCalculate a matrix of distances between atoms. This action has hidden defaults. More details COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix GROUPthe atoms for which you would like to calculate the adjacency matrix=ow CUTOFF ignore distances that have a value larger than this cutoff=1.0 MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=sphere
dmap: DISTANCE_MATRIXCalculate a matrix of distances between atoms. This action uses the defaults shown here. More details COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix GROUPthe atoms for which you would like to calculate the adjacency matrix=ow CUTOFF ignore distances that have a value larger than this cutoff=1.0 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
# Find the four nearest neighbors
acv_neighThe NEIGHBORS action with label acv_neigh calculates the following quantities: Quantity    Type    Description  
acv_neigh matrix a matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action has hidden defaults. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=dmap.w NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=4 MASKa vector that is used to used to determine which rows of the neighbors matrix to compute=sphere
acv_neigh: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action uses the defaults shown here. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=dmap.w NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=4 MASKa vector that is used to used to determine which rows of the neighbors matrix to compute=sphere  NHIGHEST in each row of the output matrix set the elements that correspond to the n highest elements in each row of the input matrix equal to one=0
# Compute a function for the atoms that are in the first coordination sphere
acv_g8The GSYMFUNC_THREEBODY action with label acv_g8 calculates the following quantities: Quantity    Type    Description  
acv_g8.g8 vector the function defined by the FUNCTION1 keyword: GSYMFUNC_THREEBODYCalculate functions of the coordinates of the coordinates of all pairs of bonds in the first coordination sphere of an atom More details ...
  WEIGHTthe matrix that contains the weights that should be used for each connection=acv_neigh ARGthree matrices containing the bond vectors of interest=dmap.x,dmap.y,dmap.z
  FUNCTION1the parameters of the function you would like to compute={FUNC=(cos(ajik)+1/3)^2 LABEL=g8}
  MASKa vector that is used to used to determine which symmetry functions should be calculated=sphere
...
# Now compute the value of the function above for those atoms that are in the
# sphere of interest
acvThe CUSTOM action with label acv calculates the following quantities: Quantity    Type    Description  
acv 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=acv_g8.g8,sphere FUNCthe function you wish to evaluate=y*(1-(3*x/8)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And now compute the final average
acv_sumThe SUM action with label acv_sum calculates the following quantities: Quantity    Type    Description  
acv_sum 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=acv PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
acv_normThe SUM action with label acv_norm calculates the following quantities: Quantity    Type    Description  
acv_norm 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
meanThe CUSTOM action with label mean calculates the following quantities: Quantity    Type    Description  
mean scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=acv_sum,acv_norm 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=mean FILEthe name of the file on which to output these quantities=colvar

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
MASK	vector	a vector that is used to used to determine which rows of the neighbors matrix to compute
ARG	matrix	the label of an adjacency/distance matrix that will be used to find the nearest neighbors

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 neighbors matrix to compute
ARG	input	none	the label of an adjacency/distance matrix that will be used to find the nearest neighbors
NLOWEST	compulsory	0	in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one
NHIGHEST	compulsory	0	in each row of the output matrix set the elements that correspond to the n highest elements in each row of the input matrix equal to one

Quantity	Type	Description
d1	matrix	a matrix containing the weights for the bonds between each pair of atoms