PLUMED-NEST

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. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,9.438535
The FIXEDATOM action with label p0 calculates somethingp1: 
FIXEDATOM
Add a virtual atom in a fixed position. 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 somethingdenssod: 
DENSITY
Depreciated command that is bascially equivalant to GROUP. More details
 
SPECIES
the atoms in the group
=43320-43737,46622-47039,49828-50245,53118-53535
The DENSITY action with label denssod calculates somethingsodintl: 
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)
=-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
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 interestsodintr: 
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)
=1.45 
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
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 interestsodblkr: 
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
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 interestcnintl: 
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
=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
The COORDINATIONNUMBER action with label cnintl calculates somethingcnintr: 
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
=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
The COORDINATIONNUMBER action with label cnintr calculates somethingcnblkr: 
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
=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

# Report the mean and highest coordination numbers in the different regions
The COORDINATIONNUMBER action with label cnblkr calculates something
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 (basically equivalent to GROUP)
=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 somethingdfs0l: 
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. 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}
# Largest cluster at the interface
The CLUSTER_DISTRIBUTION action with label nclust0l calculates somethingclust0natl: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest 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

# DFS on ion clusters at the -ve surface interface (right)
The CLUSTER_NATOMS action with label clust0natl calculates somethingmat0r: 
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)
=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 somethingdfs0r: 
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. 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}
# Largest cluster at the interface
The CLUSTER_DISTRIBUTION action with label nclust0r calculates somethingclust0natr: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest 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


# DFS on ion clusters in the bulk
The CLUSTER_NATOMS action with label clust0natr calculates somethingmat1: 
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)
=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 somethingdfs1: 
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. 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
The CLUSTER_DISTRIBUTION action with label nclust1 calculates somethingclust1nat: 
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

The CLUSTER_NATOMS action with label clust1nat calculates something
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