PLUMED-NEST-TEST-SITE

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

# 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
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
=43320-43737:1
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
=43738-44155:1
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
=43320-44155:1
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
=9153-44155:1 

# 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. This action has hidden defaults. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,7.403535
The FIXEDATOM action with label p0 calculates somethingp0: 
FIXEDATOM
Add a virtual atom in a fixed position. This action uses the defaults shown here. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,7.403535  
SET_MASS
 mass of the virtual atom
=1 
SET_CHARGE
 charge of the virtual atom
=0
p1: 
FIXEDATOM
Add a virtual atom in a fixed position. This action has hidden defaults. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,11.403535
The FIXEDATOM action with label p1 calculates somethingp1: 
FIXEDATOM
Add a virtual atom in a fixed position. This action uses the defaults shown here. More details
 
AT
coordinates of the virtual atom
=2.696525,2.75872,11.403535  
SET_MASS
 mass of the virtual atom
=1 
SET_CHARGE
 charge of the virtual atom
=0

# Identify cations at the interface and in the bulk
denssod: 
DENSITY
Depreciated command that is bascially equivalant to GROUP. This action is a shortcut. More details
 
SPECIES
the atoms in the group
=43320-43737
# PLUMED interprets the command:
# denssod: DENSITY SPECIES=43320-43737
# as follows (Click the red comment above to revert to the short version of the input):
The DENSITY action with label denssod calculates the following quantities:
 Quantity   
 Description  
denssod.value
indices for the specified group of atomsdenssod: 
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 
# --- End of included input --- 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. This action is a shortcut. 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
# PLUMED interprets the command:
# sodint: AROUND DATA=denssod ATOM=p0 ZLOWER=1.4 ZUPPER=2.0 SIGMA=0.01
# as follows (Click the red comment above to revert to the short version of the input):
The AROUND action with label sodint calculates the following quantities:
 Quantity   
 Description  
sodint.value
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interestsodint_grp: 
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
=denssod 
# --- End of included input --- The GROUP action with label sodint_grp calculates somethingsodblk: 
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. This action is a shortcut. 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
# PLUMED interprets the command:
# sodblk: AROUND DATA=denssod ATOM=p1 ZLOWER=-0.5 ZUPPER=0.5 SIGMA=0.01
# as follows (Click the red comment above to revert to the short version of the input):
The AROUND action with label sodblk calculates the following quantities:
 Quantity   
 Description  
sodblk.value
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interestsodblk_grp: 
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
=denssod 
# --- End of included input --- 
# Get the Na-Cl coordination number distribution at the interface and in the bulk
The GROUP action with label sodblk_grp calculates somethingcnint: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. 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
# PLUMED interprets the command:
# cnint: COORDINATIONNUMBER SPECIESA=sodint SPECIESB=chl SWITCH={RATIONAL R_0=0.355 NN=32 MM=64} MEAN HIGHEST
# as follows (Click the red comment above to revert to the short version of the input):
The COORDINATIONNUMBER action with label cnint calculates the following quantities:
 Quantity   
 Description  
cnint.highest
the largest of the colvars
cnint.mean
the mean of the colvarscnint_grp: 
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
=sodint 
The GROUP action with label cnint_grp calculates somethingcnint_mat: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.355 NN=32 MM=64} 
The CONTACT_MATRIX action with label cnint_mat calculates the following quantities:
 Quantity   
 Description  
cnint_mat.value
a matrix containing the weights for the bonds between each pair of atomscnint_ones: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=418
The ONES action with label cnint_ones calculates the following quantities:
 Quantity   
 Description  
cnint_ones.value
a vector of ones with the required number of elementscnint: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cnint_mat,cnint_ones 
cnint_caverage: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnint 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The MEAN action with label cnint_caverage calculates the following quantities:
 Quantity   
 Description  
cnint_caverage.value
the sumcnint_highest: 
HIGHEST
This function can be used to find the highest colvar by magnitude in a set. More details
 
ARG
the input to this function
=cnint 
The HIGHEST action with label cnint_highest calculates the following quantities:
 Quantity   
 Description  
cnint_highest.value
the lowest of the input valuescnint_mean: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnint 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- The MEAN action with label cnint_mean calculates the following quantities:
 Quantity   
 Description  
cnint_mean.value
the sumcnblk: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. 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
# PLUMED interprets the command:
# cnblk: COORDINATIONNUMBER SPECIESA=sodblk SPECIESB=chl SWITCH={RATIONAL R_0=0.355 NN=32 MM=64} MEAN HIGHEST
# as follows (Click the red comment above to revert to the short version of the input):
The COORDINATIONNUMBER action with label cnblk calculates the following quantities:
 Quantity   
 Description  
cnblk.highest
the largest of the colvars
cnblk.mean
the mean of the colvarscnblk_grp: 
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
=sodblk 
The GROUP action with label cnblk_grp calculates somethingcnblk_mat: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.355 NN=32 MM=64} 
The CONTACT_MATRIX action with label cnblk_mat calculates the following quantities:
 Quantity   
 Description  
cnblk_mat.value
a matrix containing the weights for the bonds between each pair of atomscnblk_ones: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=418
The ONES action with label cnblk_ones calculates the following quantities:
 Quantity   
 Description  
cnblk_ones.value
a vector of ones with the required number of elementscnblk: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cnblk_mat,cnblk_ones 
cnblk_caverage: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnblk 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The MEAN action with label cnblk_caverage calculates the following quantities:
 Quantity   
 Description  
cnblk_caverage.value
the sumcnblk_highest: 
HIGHEST
This function can be used to find the highest colvar by magnitude in a set. More details
 
ARG
the input to this function
=cnblk 
The HIGHEST action with label cnblk_highest calculates the following quantities:
 Quantity   
 Description  
cnblk_highest.value
the lowest of the input valuescnblk_mean: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=cnblk 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
# Report the mean and highest coordination numbers in the different regions
The MEAN action with label cnblk_mean calculates the following quantities:
 Quantity   
 Description  
cnblk_mean.value
the sum
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
The PRINT action with label  calculates somethingmat0: 
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
=cnint 
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 mat0 calculates the following quantities:
 Quantity   
 Description  
mat0.value
a matrix containing the weights for the bonds between each pair of atomsdfs0: 
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
The DFSCLUSTERING action with label dfs0 calculates the following quantities:
 Quantity   
 Description  
dfs0.value
vector with length that is equal to the number of rows in the input matrixnclust0: 
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. This action is a shortcut. 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}
# PLUMED interprets the command:
# nclust0: CLUSTER_DISTRIBUTION CLUSTERS=dfs0 MORE_THAN={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_DISTRIBUTION action with label nclust0 calculates the following quantities:
 Quantity   
 Description  
nclust0.morethan
the number of colvars that have a value more than a thresholdnclust0_mt: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the input to this function
=nclust0 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99} 
The MORE_THAN action with label nclust0_mt calculates the following quantities:
 Quantity   
 Description  
nclust0_mt.value
a function that is one if the if the input is more than a thresholdnclust0_morethan: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=nclust0_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- # Largest cluster at the interface
The SUM action with label nclust0_morethan calculates the following quantities:
 Quantity   
 Description  
nclust0_morethan.value
the sumclust0nat: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest This action is a shortcut. 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
# PLUMED interprets the command:
# clust0nat: CLUSTER_NATOMS CLUSTERS=dfs0 CLUSTER=1
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_NATOMS action with label clust0nat calculates the following quantities:
 Quantity   
 Description  
clust0nat.value
the number of atoms in the clusterclust0nat_weights: 
CLUSTER_WEIGHTS
Setup a vector that has one for all the atoms that form part of the cluster of interest and that has zero for all other atoms. 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
The CLUSTER_WEIGHTS action with label clust0nat_weights calculates the following quantities:
 Quantity   
 Description  
clust0nat_weights.value
vector with elements that are one if the atom of interest is part of the required cluster and zero otherwiseclust0nat: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=clust0nat_weights 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
# 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
=cnblk 
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 the following quantities:
 Quantity   
 Description  
mat1.value
a matrix containing the weights for the bonds between each pair of atomsdfs1: 
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. This action is a shortcut. 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}
# PLUMED interprets the command:
# nclust1: CLUSTER_DISTRIBUTION CLUSTERS=dfs1 MORE_THAN={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99}
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_DISTRIBUTION action with label nclust1 calculates the following quantities:
 Quantity   
 Description  
nclust1.morethan
the number of colvars that have a value more than a thresholdnclust1_mt: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the input to this function
=nclust1 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.99} 
The MORE_THAN action with label nclust1_mt calculates the following quantities:
 Quantity   
 Description  
nclust1_mt.value
a function that is one if the if the input is more than a thresholdnclust1_morethan: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=nclust1_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- # Largest cluster in the bulk
The SUM action with label nclust1_morethan calculates the following quantities:
 Quantity   
 Description  
nclust1_morethan.value
the sumclust1nat: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest This action is a shortcut. 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
# PLUMED interprets the command:
# clust1nat: CLUSTER_NATOMS CLUSTERS=dfs1 CLUSTER=1
# as follows (Click the red comment above to revert to the short version of the input):
The CLUSTER_NATOMS action with label clust1nat calculates the following quantities:
 Quantity   
 Description  
clust1nat.value
the number of atoms in the clusterclust1nat_weights: 
CLUSTER_WEIGHTS
Setup a vector that has one for all the atoms that form part of the cluster of interest and that has zero for all other atoms. 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_WEIGHTS action with label clust1nat_weights calculates the following quantities:
 Quantity   
 Description  
clust1nat_weights.value
vector with elements that are one if the atom of interest is part of the required cluster and zero otherwiseclust1nat: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=clust1nat_weights 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
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