Project ID: plumID:21.011
Source: NaCl_at_graphite-cmumd/clusters.plmd
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
tested onv2.9
tested onmaster
# 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 
wat: 
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
sod: 
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
=43320-43737:1
chl: 
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
=43738-44155:1
slt: 
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
=43320-44155:1
sln: 
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
=9153-44155:1 

# Set a virtual atom at the origin and in the 'bulk'
p0: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,7.403535
p1: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,11.403535

# Identify cations at the interface and in the bulk
denssod: 
DENSITY
Depreciated command that is bascially equivalant to GROUP. More details
 
SPECIES
the atoms in the group
=43320-43737
sodint: 
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. 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)
=1.4 
ZUPPER
 the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=2.0 
SIGMA
the width of the function to be used for kernel density estimation
=0.01
sodblk: 
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. 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

# Get the Na-Cl coordination number distribution at the interface and in the bulk
cnint: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=sodint 
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

cnblk: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=sodblk 
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


# Report the mean and highest coordination numbers in the different regions

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cnint.*,cnblk 
FILE
the name of the file on which to output these quantities
=cn-regions.dat

# DFS on ion clusters at the interface
mat0: 
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 (basically equivalent to GROUP)
=cnint 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={GAUSSIAN D_0=0.355 R_0=0.01}
dfs0: 
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)
=mat0
# Number of ion clusters at the interface
nclust0: 
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. More details
 
CLUSTERS
the label of the action that does the clustering
=dfs0 
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}
# Largest cluster at the interface
clust0nat: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest More details
 
CLUSTERS
the label of the action that does the clustering
=dfs0 
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

# 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 (basically equivalent to GROUP)
=cnblk 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.355 D_MAX=0.356}
dfs1: 
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
nclust1: 
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. 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}
# Largest cluster in the bulk
clust1nat: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest 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

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=nclust0.*,clust0nat.*,nclust1.*,clust1nat 
FILE
the name of the file on which to output these quantities
=cluster.dat