PLUMED-NEST

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
graThe GROUP action with label gra calculates the following quantities:
 Quantity   
 Type   
 Description  
gra
atoms
indices of atoms specified in GROUP: 
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 
watThe GROUP action with label wat calculates the following quantities:
 Quantity   
 Type   
 Description  
wat
atoms
indices of atoms specified in GROUP: 
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
sodThe GROUP action with label sod calculates the following quantities:
 Quantity   
 Type   
 Description  
sod
atoms
indices of atoms specified in GROUP: 
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
chlThe GROUP action with label chl calculates the following quantities:
 Quantity   
 Type   
 Description  
chl
atoms
indices of atoms specified in GROUP: 
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
sltThe GROUP action with label slt calculates the following quantities:
 Quantity   
 Type   
 Description  
slt
atoms
indices of atoms specified in GROUP: 
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
slnThe GROUP action with label sln calculates the following quantities:
 Quantity   
 Type   
 Description  
sln
atoms
indices of atoms specified in GROUP: 
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'
p0The FIXEDATOM action with label p0 calculates the following quantities:
 Quantity   
 Type   
 Description  
p0
atoms
virtual atom calculated by FIXEDATOM action: 
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
p0: 
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
p1The FIXEDATOM action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1
atoms
virtual atom calculated by FIXEDATOM action: 
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
p1: 
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
denssodThe GROUP action with label denssod calculates the following quantities:
 Quantity   
 Type   
 Description  
denssod
atoms
indices of atoms specified in GROUP: 
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):
denssod: 
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 --- sodintThe AROUND action with label sodint calculates the following quantities:
 Quantity   
 Type   
 Description  
sodint
vector
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest: 
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):
sodint_grpThe GROUP action with label sodint_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
sodint_grp
atoms
indices of atoms specified in GROUP: 
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 --- sodblkThe AROUND action with label sodblk calculates the following quantities:
 Quantity   
 Type   
 Description  
sodblk
vector
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest: 
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):
sodblk_grpThe GROUP action with label sodblk_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
sodblk_grp
atoms
indices of atoms specified in GROUP: 
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
cnintThe COORDINATIONNUMBER action with label cnint calculates the following quantities:
 Quantity   
 Type   
 Description  
cnint
vector
the value calculated by this action
cnint_highest
scalar
the largest of the colvars
cnint_mean
scalar
the mean of the colvars: 
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):
cnint_grpThe GROUP action with label cnint_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cnint_grp
atoms
indices of atoms specified in GROUP: 
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 
cnint_matThe CONTACT_MATRIX action with label cnint_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cnint_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
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} 
cnint_onesThe CONSTANT action with label cnint_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cnint_ones
vector
the constant value that was read from the plumed input: 
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
cnintThe MATRIX_VECTOR_PRODUCT action with label cnint calculates the following quantities:
 Quantity   
 Type   
 Description  
cnint
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
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_caverageThe MEAN action with label cnint_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cnint_caverage
scalar
the mean of all the elements in the input vector: 
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 
cnint_highestThe HIGHEST action with label cnint_highest calculates the following quantities:
 Quantity   
 Type   
 Description  
cnint_highest
scalar
the largest element of the input vector: 
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 
cnint_meanThe MEAN action with label cnint_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
cnint_mean
scalar
the mean of all the elements in the input vector: 
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 --- cnblkThe COORDINATIONNUMBER action with label cnblk calculates the following quantities:
 Quantity   
 Type   
 Description  
cnblk
vector
the value calculated by this action
cnblk_highest
scalar
the largest of the colvars
cnblk_mean
scalar
the mean of the colvars: 
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):
cnblk_grpThe GROUP action with label cnblk_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cnblk_grp
atoms
indices of atoms specified in GROUP: 
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 
cnblk_matThe CONTACT_MATRIX action with label cnblk_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cnblk_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
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} 
cnblk_onesThe CONSTANT action with label cnblk_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cnblk_ones
vector
the constant value that was read from the plumed input: 
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
cnblkThe MATRIX_VECTOR_PRODUCT action with label cnblk calculates the following quantities:
 Quantity   
 Type   
 Description  
cnblk
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
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_caverageThe MEAN action with label cnblk_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cnblk_caverage
scalar
the mean of all the elements in the input vector: 
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 
cnblk_highestThe HIGHEST action with label cnblk_highest calculates the following quantities:
 Quantity   
 Type   
 Description  
cnblk_highest
scalar
the largest element of the input vector: 
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 
cnblk_meanThe MEAN action with label cnblk_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
cnblk_mean
scalar
the mean of all the elements in the input vector: 
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
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 somethingmat0The CONTACT_MATRIX action with label mat0 calculates the following quantities:
 Quantity   
 Type   
 Description  
mat0
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
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}
dfs0The DFSCLUSTERING action with label dfs0 calculates the following quantities:
 Quantity   
 Type   
 Description  
dfs0
vector
vector with length that is equal to the number of rows in the input matrix.  Elements of this vector are equal to the cluster that each node is a part of: 
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
nclust0The CLUSTER_DISTRIBUTION action with label nclust0 calculates the following quantities:
 Quantity   
 Type   
 Description  
nclust0_morethan
scalar
the number of colvars that have a value more than a threshold: 
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):
nclust0_mtThe MORE_THAN action with label nclust0_mt calculates the following quantities:
 Quantity   
 Type   
 Description  
nclust0_mt
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: 
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} 
nclust0_morethanThe SUM action with label nclust0_morethan calculates the following quantities:
 Quantity   
 Type   
 Description  
nclust0_morethan
scalar
the sum of all the elements in the input vector: 
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
clust0natThe CLUSTER_NATOMS action with label clust0nat calculates the following quantities:
 Quantity   
 Type   
 Description  
clust0nat
scalar
the number of atoms in the cluster: 
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):
clust0nat_weightsThe CLUSTER_WEIGHTS action with label clust0nat_weights calculates the following quantities:
 Quantity   
 Type   
 Description  
clust0nat_weights
vector
vector with elements that are one if the atom of interest is part of the required cluster and zero otherwise: 
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
clust0natThe SUM action with label clust0nat calculates the following quantities:
 Quantity   
 Type   
 Description  
clust0nat
scalar
the sum of all the elements in the input vector: 
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
mat1The CONTACT_MATRIX action with label mat1 calculates the following quantities:
 Quantity   
 Type   
 Description  
mat1
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
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}
dfs1The DFSCLUSTERING action with label dfs1 calculates the following quantities:
 Quantity   
 Type   
 Description  
dfs1
vector
vector with length that is equal to the number of rows in the input matrix.  Elements of this vector are equal to the cluster that each node is a part of: 
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
nclust1The CLUSTER_DISTRIBUTION action with label nclust1 calculates the following quantities:
 Quantity   
 Type   
 Description  
nclust1_morethan
scalar
the number of colvars that have a value more than a threshold: 
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):
nclust1_mtThe MORE_THAN action with label nclust1_mt calculates the following quantities:
 Quantity   
 Type   
 Description  
nclust1_mt
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: 
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} 
nclust1_morethanThe SUM action with label nclust1_morethan calculates the following quantities:
 Quantity   
 Type   
 Description  
nclust1_morethan
scalar
the sum of all the elements in the input vector: 
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
clust1natThe CLUSTER_NATOMS action with label clust1nat calculates the following quantities:
 Quantity   
 Type   
 Description  
clust1nat
scalar
the number of atoms in the cluster: 
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):
clust1nat_weightsThe CLUSTER_WEIGHTS action with label clust1nat_weights calculates the following quantities:
 Quantity   
 Type   
 Description  
clust1nat_weights
vector
vector with elements that are one if the atom of interest is part of the required cluster and zero otherwise: 
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
clust1natThe SUM action with label clust1nat calculates the following quantities:
 Quantity   
 Type   
 Description  
clust1nat
scalar
the sum of all the elements in the input vector: 
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