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 onv2.10
tested onmaster
# 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
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=43320-43737:1
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=43738-44155:1
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=43320-44155:1
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=9153-44155:1 

# 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=2.696525,2.75872,7.403535
p1: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.696525,2.75872,11.403535

# 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
sodint: 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)=1.4 ZUPPER the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)=2.0 SIGMAthe width of the function to be used for kernel density estimation=0.01
sodblk: 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
cnint: 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=sodint 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
cnblk: 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=sodblk 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=cnint.*,cnblk.* FILEthe name of the file on which to output these quantities=cn-regions.dat

# DFS on ion clusters at the interface
mat0: 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=cnint SWITCHspecify the switching function to use between two sets of indistinguishable atoms={GAUSSIAN D_0=0.355 R_0=0.01}
dfs0: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=mat0
# Number of ion clusters at the interface
nclust0: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details CLUSTERSthe label of the action that does the clustering=dfs0 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
clust0nat: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe 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_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=cnblk 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=nclust0.*,clust0nat.*,nclust1.*,clust1nat.* FILEthe name of the file on which to output these quantities=cluster.dat