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 SPECIESAthis keyword is used for colvars such as the coordination number=sodintl SPECIESBthis keyword is used for colvars such as the coordination number=chl SWITCHthe 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
cnintr: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=sodintr SPECIESBthis keyword is used for colvars such as the coordination number=chl SWITCHthe 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
cnblkr: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=sodblkr SPECIESBthis keyword is used for colvars such as the coordination number=chl SWITCHthe 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
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 SWITCHspecify the switching function to use between two sets of indistinguishable atoms={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={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 SWITCHspecify the switching function to use between two sets of indistinguishable atoms={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={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 SWITCHspecify the switching function to use between two sets of indistinguishable atoms={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={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