PLUMED-NEST-TEST-SITE

Project ID: plumID:23.027
Source: ion-structure-driver.dat
Originally used with PLUMED version: 2.5.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

# Plumed driver script to calculate ion coordination numbers and identify ion clusters in the EDL and bulk solution regions of CmuMD simulations 
# Aaron R. Finney and Matteo Salvalaglio
# Properties of aqueous electrolyte solutions at carbon electrodes: 
# effects of concentration and surface charge on solution structure, ion clustering and thermodynamics in the electric double layer
# June 2023

# Define atom groups
gra: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-9152:1 
The GROUP action with label gra calculates somethingwat: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=9153-43319:3,44156-46621:3,47458-49827:3,50664-53117:3
The GROUP action with label wat calculates somethingsod: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=43320-43737,46622-47039,49828-50245,53118-53535
The GROUP action with label sod calculates somethingchl: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=43738-44155,47040-47457,50246-50663,53536-53953
The GROUP action with label chl calculates somethingslt: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=43320-43737,46622-47039,49828-50245,53118-53535,43738-44155,47040-47457,50246-50663,53536-53953
The GROUP action with label slt calculates somethingsln: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=9153-43319:3,44156-46621:3,47458-49827:3,50664-53117:3,43320-43737,46622-47039,49828-50245,53118-53535,43738-44155,47040-47457,50246-50663,53536-53953

# Set a virtual atom at the origin and in the 'bulk'
The GROUP action with label sln calculates somethingp0: 
FIXEDATOM
Add a virtual atom in a fixed position. This action has hidden defaults. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,9.438535
The FIXEDATOM action with label p0 calculates somethingp0: 
FIXEDATOM
Add a virtual atom in a fixed position. This action uses the defaults shown here. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,9.438535  
SET_MASS
 mass of the virtual atom
=1 
SET_CHARGE
 charge of the virtual atom
=0
p1: 
FIXEDATOM
Add a virtual atom in a fixed position. This action has hidden defaults. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,13.5# Identify cations at the interface and in the bulk
The FIXEDATOM action with label p1 calculates somethingp1: 
FIXEDATOM
Add a virtual atom in a fixed position. This action uses the defaults shown here. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,13.5# Identify cations at the interface and in the bulk  SET_MASS=1 SET_CHARGE=0
denssod: 
DENSITY
Depreciated command that is bascially equivalant to GROUP. This action is a shortcut. More details
 
SPECIES
the atoms in the group
=43320-43737,46622-47039,49828-50245,53118-53535
# PLUMED interprets the command:
# denssod: DENSITY SPECIES=43320-43737,46622-47039,49828-50245,53118-53535
# as follows (Click the red comment above to revert to the short version of the input):
The DENSITY action with label denssod calculates the following quantities:
 Quantity   
 Description  
denssod.value
indices for the specified group of atomsdenssod: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=43320-43737,46622-47039,49828-50245,53118-53535 
# --- End of included input --- sodintl: 
AROUND
This 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. This action is a shortcut. More details
 
DATA
the label of an action that calculates multicolvars
=denssod 
ATOM
an alternative to ORIGIN
=p0 
ZLOWER
 the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=-2.45 
ZUPPER
 the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=-1.45 
SIGMA
the width of the function to be used for kernel density estimation
=0.01
# PLUMED interprets the command:
# sodintl: AROUND DATA=denssod ATOM=p0 ZLOWER=-2.45 ZUPPER=-1.45 SIGMA=0.01
# as follows (Click the red comment above to revert to the short version of the input):
The AROUND action with label sodintl calculates the following quantities:
 Quantity   
 Description  
sodintl.value
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interestsodintl_grp: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=denssod 
# --- End of included input --- The GROUP action with label sodintl_grp calculates somethingsodintr: 
AROUND
This 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. This action is a shortcut. More details
 
DATA
the label of an action that calculates multicolvars
=denssod 
ATOM
an alternative to ORIGIN
=p0 
ZLOWER
 the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=1.45 
ZUPPER
 the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=2.45 
SIGMA
the width of the function to be used for kernel density estimation
=0.01
# PLUMED interprets the command:
# sodintr: AROUND DATA=denssod ATOM=p0 ZLOWER=1.45 ZUPPER=2.45 SIGMA=0.01
# as follows (Click the red comment above to revert to the short version of the input):
The AROUND action with label sodintr calculates the following quantities:
 Quantity   
 Description  
sodintr.value
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interestsodintr_grp: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=denssod 
# --- End of included input --- The GROUP action with label sodintr_grp calculates somethingsodblkr: 
AROUND
This 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. This action is a shortcut. More details
 
DATA
the label of an action that calculates multicolvars
=denssod 
ATOM
an alternative to ORIGIN
=p1 
ZLOWER
 the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=-0.5 
ZUPPER
 the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=0.5 
SIGMA
the width of the function to be used for kernel density estimation
=0.01
# PLUMED interprets the command:
# sodblkr: AROUND DATA=denssod ATOM=p1 ZLOWER=-0.5 ZUPPER=0.5 SIGMA=0.01
# as follows (Click the red comment above to revert to the short version of the input):
The AROUND action with label sodblkr calculates the following quantities:
 Quantity   
 Description  
sodblkr.value
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interestsodblkr_grp: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=denssod 
# --- End of included input --- 
# Get the Na-Cl coordination number distribution at the interface and in the bulk
The GROUP action with label sodblkr_grp calculates somethingcnintl: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=sodintl 
SPECIESB
this keyword is used for colvars such as the coordination number
=chl 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.355 NN=32 MM=64} 
MEAN
 calculate the mean of all the quantities
 
HIGHEST
 this flag allows you to recover the highest of these variables
# PLUMED interprets the command:
# cnintl: COORDINATIONNUMBER SPECIESA=sodintl SPECIESB=chl SWITCH={RATIONAL R_0=0.355 NN=32 MM=64} MEAN HIGHEST
# as follows (Click the red comment above to revert to the short version of the input):
The COORDINATIONNUMBER action with label cnintl calculates the following quantities:
 Quantity   
 Description  
cnintl.highest
the largest of the colvars
cnintl.mean
the mean of the colvarscnintl_grp: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=sodintl 
The GROUP action with label cnintl_grp calculates somethingcnintl_mat: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.355 NN=32 MM=64} 
The CONTACT_MATRIX action with label cnintl_mat calculates the following quantities:
 Quantity   
 Description  
cnintl_mat.value
a matrix containing the weights for the bonds between each pair of atomscnintl_ones: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1672
The ONES action with label cnintl_ones calculates the following quantities:
 Quantity   
 Description  
cnintl_ones.value
a vector of ones with the required number of elementscnintl: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cnintl_mat,cnintl_ones 
cnintl_caverage: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnintl 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The MEAN action with label cnintl_caverage calculates the following quantities:
 Quantity   
 Description  
cnintl_caverage.value
the sumcnintl_highest: 
HIGHEST
This function can be used to find the highest colvar by magnitude in a set. More details
 
ARG
the input to this function
=cnintl 
The HIGHEST action with label cnintl_highest calculates the following quantities:
 Quantity   
 Description  
cnintl_highest.value
the lowest of the input valuescnintl_mean: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnintl 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- The MEAN action with label cnintl_mean calculates the following quantities:
 Quantity   
 Description  
cnintl_mean.value
the sumcnintr: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=sodintr 
SPECIESB
this keyword is used for colvars such as the coordination number
=chl 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.355 NN=32 MM=64} 
MEAN
 calculate the mean of all the quantities
 
HIGHEST
 this flag allows you to recover the highest of these variables
# PLUMED interprets the command:
# cnintr: COORDINATIONNUMBER SPECIESA=sodintr SPECIESB=chl SWITCH={RATIONAL R_0=0.355 NN=32 MM=64} MEAN HIGHEST
# as follows (Click the red comment above to revert to the short version of the input):
The COORDINATIONNUMBER action with label cnintr calculates the following quantities:
 Quantity   
 Description  
cnintr.highest
the largest of the colvars
cnintr.mean
the mean of the colvarscnintr_grp: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=sodintr 
The GROUP action with label cnintr_grp calculates somethingcnintr_mat: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.355 NN=32 MM=64} 
The CONTACT_MATRIX action with label cnintr_mat calculates the following quantities:
 Quantity   
 Description  
cnintr_mat.value
a matrix containing the weights for the bonds between each pair of atomscnintr_ones: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1672
The ONES action with label cnintr_ones calculates the following quantities:
 Quantity   
 Description  
cnintr_ones.value
a vector of ones with the required number of elementscnintr: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cnintr_mat,cnintr_ones 
cnintr_caverage: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnintr 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The MEAN action with label cnintr_caverage calculates the following quantities:
 Quantity   
 Description  
cnintr_caverage.value
the sumcnintr_highest: 
HIGHEST
This function can be used to find the highest colvar by magnitude in a set. More details
 
ARG
the input to this function
=cnintr 
The HIGHEST action with label cnintr_highest calculates the following quantities:
 Quantity   
 Description  
cnintr_highest.value
the lowest of the input valuescnintr_mean: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnintr 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- The MEAN action with label cnintr_mean calculates the following quantities:
 Quantity   
 Description  
cnintr_mean.value
the sumcnblkr: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=sodblkr 
SPECIESB
this keyword is used for colvars such as the coordination number
=chl 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.355 NN=32 MM=64} 
MEAN
 calculate the mean of all the quantities
 
HIGHEST
 this flag allows you to recover the highest of these variables
# PLUMED interprets the command:
# cnblkr: COORDINATIONNUMBER SPECIESA=sodblkr SPECIESB=chl SWITCH={RATIONAL R_0=0.355 NN=32 MM=64} MEAN HIGHEST
# as follows (Click the red comment above to revert to the short version of the input):
The COORDINATIONNUMBER action with label cnblkr calculates the following quantities:
 Quantity   
 Description  
cnblkr.highest
the largest of the colvars
cnblkr.mean
the mean of the colvarscnblkr_grp: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=sodblkr 
The GROUP action with label cnblkr_grp calculates somethingcnblkr_mat: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.355 NN=32 MM=64} 
The CONTACT_MATRIX action with label cnblkr_mat calculates the following quantities:
 Quantity   
 Description  
cnblkr_mat.value
a matrix containing the weights for the bonds between each pair of atomscnblkr_ones: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1672
The ONES action with label cnblkr_ones calculates the following quantities:
 Quantity   
 Description  
cnblkr_ones.value
a vector of ones with the required number of elementscnblkr: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cnblkr_mat,cnblkr_ones 
cnblkr_caverage: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnblkr 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The MEAN action with label cnblkr_caverage calculates the following quantities:
 Quantity   
 Description  
cnblkr_caverage.value
the sumcnblkr_highest: 
HIGHEST
This function can be used to find the highest colvar by magnitude in a set. More details
 
ARG
the input to this function
=cnblkr 
The HIGHEST action with label cnblkr_highest calculates the following quantities:
 Quantity   
 Description  
cnblkr_highest.value
the lowest of the input valuescnblkr_mean: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnblkr 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
# Report the mean and highest coordination numbers in the different regions
The MEAN action with label cnblkr_mean calculates the following quantities:
 Quantity   
 Description  
cnblkr_mean.value
the sum
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cnintl.*,cnintr.*,cnblkr 
FILE
the name of the file on which to output these quantities
=cn-regions.dat

# DFS on ion clusters at the +ve surface interface (left)
The PRINT action with label  calculates somethingmat0l: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
ATOMS
the atoms for which you would like to calculate the adjacency matrix
=cnintl 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={GAUSSIAN D_0=0.355 R_0=0.01}
The CONTACT_MATRIX action with label mat0l calculates the following quantities:
 Quantity   
 Description  
mat0l.value
a matrix containing the weights for the bonds between each pair of atomsdfs0l: 
DFSCLUSTERING
Find the connected components of the matrix using the depth first search clustering algorithm. More details
 
MATRIX
the input matrix (can use ARG instead)
=mat0l
# Number of ion clusters at the interface
The DFSCLUSTERING action with label dfs0l calculates the following quantities:
 Quantity   
 Description  
dfs0l.value
vector with length that is equal to the number of rows in the input matrixnclust0l: 
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. This action is a shortcut. More details
 
CLUSTERS
the label of the action that does the clustering
=dfs0l 
MORE_THAN
calculate the number of variables that are more than a certain target value
={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# PLUMED interprets the command:
# nclust0l: CLUSTER_DISTRIBUTION CLUSTERS=dfs0l MORE_THAN={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_DISTRIBUTION action with label nclust0l calculates the following quantities:
 Quantity   
 Description  
nclust0l.morethan
the number of colvars that have a value more than a thresholdnclust0l_mt: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the input to this function
=nclust0l 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99} 
The MORE_THAN action with label nclust0l_mt calculates the following quantities:
 Quantity   
 Description  
nclust0l_mt.value
a function that is one if the if the input is more than a thresholdnclust0l_morethan: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=nclust0l_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- # Largest cluster at the interface
The SUM action with label nclust0l_morethan calculates the following quantities:
 Quantity   
 Description  
nclust0l_morethan.value
the sumclust0natl: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest This action is a shortcut. More details
 
CLUSTERS
the label of the action that does the clustering
=dfs0l 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1
# PLUMED interprets the command:
# clust0natl: CLUSTER_NATOMS CLUSTERS=dfs0l CLUSTER=1
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_NATOMS action with label clust0natl calculates the following quantities:
 Quantity   
 Description  
clust0natl.value
the number of atoms in the clusterclust0natl_weights: 
CLUSTER_WEIGHTS
Setup a vector that has one for all the atoms that form part of the cluster of interest and that has zero for all other atoms. More details
  
CLUSTERS
the label of the action that does the clustering
=dfs0l 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1
The CLUSTER_WEIGHTS action with label clust0natl_weights calculates the following quantities:
 Quantity   
 Description  
clust0natl_weights.value
vector with elements that are one if the atom of interest is part of the required cluster and zero otherwiseclust0natl: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=clust0natl_weights 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
# DFS on ion clusters at the -ve surface interface (right)
mat0r: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
ATOMS
the atoms for which you would like to calculate the adjacency matrix
=cnintr 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={GAUSSIAN D_0=0.355 R_0=0.01}
The CONTACT_MATRIX action with label mat0r calculates the following quantities:
 Quantity   
 Description  
mat0r.value
a matrix containing the weights for the bonds between each pair of atomsdfs0r: 
DFSCLUSTERING
Find the connected components of the matrix using the depth first search clustering algorithm. More details
 
MATRIX
the input matrix (can use ARG instead)
=mat0r
# Number of ion clusters at the interface
The DFSCLUSTERING action with label dfs0r calculates the following quantities:
 Quantity   
 Description  
dfs0r.value
vector with length that is equal to the number of rows in the input matrixnclust0r: 
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. This action is a shortcut. More details
 
CLUSTERS
the label of the action that does the clustering
=dfs0r 
MORE_THAN
calculate the number of variables that are more than a certain target value
={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# PLUMED interprets the command:
# nclust0r: CLUSTER_DISTRIBUTION CLUSTERS=dfs0r MORE_THAN={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_DISTRIBUTION action with label nclust0r calculates the following quantities:
 Quantity   
 Description  
nclust0r.morethan
the number of colvars that have a value more than a thresholdnclust0r_mt: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the input to this function
=nclust0r 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99} 
The MORE_THAN action with label nclust0r_mt calculates the following quantities:
 Quantity   
 Description  
nclust0r_mt.value
a function that is one if the if the input is more than a thresholdnclust0r_morethan: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=nclust0r_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- # Largest cluster at the interface
The SUM action with label nclust0r_morethan calculates the following quantities:
 Quantity   
 Description  
nclust0r_morethan.value
the sumclust0natr: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest This action is a shortcut. More details
 
CLUSTERS
the label of the action that does the clustering
=dfs0r 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1
# PLUMED interprets the command:
# clust0natr: CLUSTER_NATOMS CLUSTERS=dfs0r CLUSTER=1
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_NATOMS action with label clust0natr calculates the following quantities:
 Quantity   
 Description  
clust0natr.value
the number of atoms in the clusterclust0natr_weights: 
CLUSTER_WEIGHTS
Setup a vector that has one for all the atoms that form part of the cluster of interest and that has zero for all other atoms. More details
  
CLUSTERS
the label of the action that does the clustering
=dfs0r 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1
The CLUSTER_WEIGHTS action with label clust0natr_weights calculates the following quantities:
 Quantity   
 Description  
clust0natr_weights.value
vector with elements that are one if the atom of interest is part of the required cluster and zero otherwiseclust0natr: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=clust0natr_weights 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 

# DFS on ion clusters in the bulk
mat1: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
ATOMS
the atoms for which you would like to calculate the adjacency matrix
=cnblkr 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.355 D_MAX=0.356}
The CONTACT_MATRIX action with label mat1 calculates the following quantities:
 Quantity   
 Description  
mat1.value
a matrix containing the weights for the bonds between each pair of atomsdfs1: 
DFSCLUSTERING
Find the connected components of the matrix using the depth first search clustering algorithm. More details
 
MATRIX
the input matrix (can use ARG instead)
=mat1
# Number of ion clusters in the bulk
The DFSCLUSTERING action with label dfs1 calculates the following quantities:
 Quantity   
 Description  
dfs1.value
vector with length that is equal to the number of rows in the input matrixnclust1: 
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. This action is a shortcut. More details
 
CLUSTERS
the label of the action that does the clustering
=dfs1 
MORE_THAN
calculate the number of variables that are more than a certain target value
={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# PLUMED interprets the command:
# nclust1: CLUSTER_DISTRIBUTION CLUSTERS=dfs1 MORE_THAN={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_DISTRIBUTION action with label nclust1 calculates the following quantities:
 Quantity   
 Description  
nclust1.morethan
the number of colvars that have a value more than a thresholdnclust1_mt: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the input to this function
=nclust1 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99} 
The MORE_THAN action with label nclust1_mt calculates the following quantities:
 Quantity   
 Description  
nclust1_mt.value
a function that is one if the if the input is more than a thresholdnclust1_morethan: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=nclust1_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- # Largest cluster in the bulk
The SUM action with label nclust1_morethan calculates the following quantities:
 Quantity   
 Description  
nclust1_morethan.value
the sumclust1nat: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest This action is a shortcut. More details
 
CLUSTERS
the label of the action that does the clustering
=dfs1 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1
# PLUMED interprets the command:
# clust1nat: CLUSTER_NATOMS CLUSTERS=dfs1 CLUSTER=1
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_NATOMS action with label clust1nat calculates the following quantities:
 Quantity   
 Description  
clust1nat.value
the number of atoms in the clusterclust1nat_weights: 
CLUSTER_WEIGHTS
Setup a vector that has one for all the atoms that form part of the cluster of interest and that has zero for all other atoms. More details
  
CLUSTERS
the label of the action that does the clustering
=dfs1 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1
The CLUSTER_WEIGHTS action with label clust1nat_weights calculates the following quantities:
 Quantity   
 Description  
clust1nat_weights.value
vector with elements that are one if the atom of interest is part of the required cluster and zero otherwiseclust1nat: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=clust1nat_weights 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=nclust0l.*,clust0natl.*,nclust0r.*,clust0natr.*,nclust1.*,clust1nat 
FILE
the name of the file on which to output these quantities
=cluster.dat