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
tested onv2.10
tested onmaster
# 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: 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=1-9152:1 
wat: 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=9153-43319:3,44156-46621:3,47458-49827:3,50664-53117:3
sod: 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=43320-43737,46622-47039,49828-50245,53118-53535
chl: 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=43738-44155,47040-47457,50246-50663,53536-53953
slt: 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=43320-43737,46622-47039,49828-50245,53118-53535,43738-44155,47040-47457,50246-50663,53536-53953
sln: 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=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'
p0: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.696525,2.75872,9.438535
p1: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.696525,2.75872,13.5# Identify cations at the interface and in the bulk
denssod: DENSITYDepreciated command that is bascially equivalant to GROUP. More details SPECIESthe atoms in the group=43320-43737,46622-47039,49828-50245,53118-53535
sodintl: AROUNDThis 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 DATAthe label of an action that calculates multicolvars=denssod ATOMan 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 SIGMAthe width of the function to be used for kernel density estimation=0.01
sodintr: AROUNDThis 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 DATAthe label of an action that calculates multicolvars=denssod ATOMan 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 SIGMAthe width of the function to be used for kernel density estimation=0.01
sodblkr: AROUNDThis 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 DATAthe label of an action that calculates multicolvars=denssod ATOMan 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 SIGMAthe 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
cnintl: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=sodintl SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=chl SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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
cnintr: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=sodintr SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=chl SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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
cnblkr: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=sodblkr SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=chl SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cnintl.*,cnintr.*,cnblkr.* FILEthe name of the file on which to output these quantities=cn-regions.dat

# DFS on ion clusters at the +ve surface interface (left)
mat0l: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details ATOMSthe atoms for which you would like to calculate the adjacency matrix=cnintl 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.={GAUSSIAN D_0=0.355 R_0=0.01}
dfs0l: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=mat0l
# Number of ion clusters at the interface
nclust0l: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details CLUSTERSthe label of the action that does the clustering=dfs0l MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# Largest cluster at the interface
clust0natl: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe 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)
mat0r: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details ATOMSthe atoms for which you would like to calculate the adjacency matrix=cnintr 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.={GAUSSIAN D_0=0.355 R_0=0.01}
dfs0r: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=mat0r
# Number of ion clusters at the interface
nclust0r: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details CLUSTERSthe label of the action that does the clustering=dfs0r MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# Largest cluster at the interface
clust0natr: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe 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
mat1: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details ATOMSthe atoms for which you would like to calculate the adjacency matrix=cnblkr 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=0.355 D_MAX=0.356}
dfs1: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=mat1
# Number of ion clusters in the bulk
nclust1: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details CLUSTERSthe label of the action that does the clustering=dfs1 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# Largest cluster in the bulk
clust1nat: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe 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

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nclust0l.*,clust0natl.*,nclust0r.*,clust0natr.*,nclust1.*,clust1nat.* FILEthe name of the file on which to output these quantities=cluster.dat