Project ID: plumID:21.044
Source: 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 onv2.8
tested onmaster
# From NaCl Crystallisation Pathways; Aaron R. Finney and Matteo Salvalaglio
# Plumed driver file to post-process MD and well-tempered metadynamics simulations


# Fixed atom at the centre of the simulation box p:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.,2.,2
# DEfine the ion groups gna:
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
=6151-6520 gcl:
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
=6521-6890 gions:
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
=6151-6890
# Measure coordination in the biased sphere cn0:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=gna
SPECIESB
this keyword is used for colvars such as the coordination number
=gcl
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0} cn1:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=gcl
SPECIESB
this keyword is used for colvars such as the coordination number
=gna
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
sphere0:
INSPHERE
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. More details
ATOM
the atom whose vicinity we are interested in examining
=p
DATA
The multicolvar that calculates the set of base quantities that we are interested in
=cn0
RADIUS
the switching function that tells us the extent of the spherical region of interest
={TANH R_0=1.5}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0} sphere1:
INSPHERE
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. More details
ATOM
the atom whose vicinity we are interested in examining
=p
DATA
The multicolvar that calculates the set of base quantities that we are interested in
=cn1
RADIUS
the switching function that tells us the extent of the spherical region of interest
={TANH R_0=1.5}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0}
ncrysts:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=sphere0.morethan,sphere1.morethan
POWERS
the powers to which you are raising each of the arguments in your function
=1,1
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO vcrysts:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=ncrysts
POWERS
the powers to which you are raising each of the arguments in your function
=0.333
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# Measure coordination throughout the box cn2:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=gna
SPECIESB
this keyword is used for colvars such as the coordination number
=gcl
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0} cn3:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=gcl
SPECIESB
this keyword is used for colvars such as the coordination number
=gna
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0}
ncrysta:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=cn2.morethan,cn3.morethan
POWERS
the powers to which you are raising each of the arguments in your function
=1,1
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO vcrysta:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=ncrysta
POWERS
the powers to which you are raising each of the arguments in your function
=0.333
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# Measure coordination of crystalline ions in the biased sphere q60s:
Q6
Calculate sixth order Steinhardt parameters. More details
SPECIESA
this keyword is used for colvars such as the coordination number
=gna
SPECIESB
this keyword is used for colvars such as the coordination number
=gcl
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
LOWMEM
lower the memory requirements
q61s:
Q6
Calculate sixth order Steinhardt parameters. More details
SPECIESA
this keyword is used for colvars such as the coordination number
=gcl
SPECIESB
this keyword is used for colvars such as the coordination number
=gna
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
LOWMEM
lower the memory requirements

lq60s:
LOCAL_Q6
Calculate the local degree of order around an atoms by taking the average dot product between the $q_6 $ vector on the central atom and the $q_6 $ vector on the atoms in the first coordination sphere. More details
SPECIES
this keyword is used for colvars such as coordination number
=q60s
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
LOWMEM
lower the memory requirements
lq61s:
LOCAL_Q6
Calculate the local degree of order around an atoms by taking the average dot product between the $q_6 $ vector on the central atom and the $q_6 $ vector on the atoms in the first coordination sphere. More details
SPECIES
this keyword is used for colvars such as coordination number
=q61s
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
LOWMEM
lower the memory requirements

flq60s:
MFILTER_MORE
This action can be used to filter the distribution of colvar values in a ef mcolv More details
DATA
The multicolvar that calculates the set of base quantities that we are interested in
=lq60s
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={GAUSSIAN R_0=0.55 D_MAX=0.56} flq61s:
MFILTER_MORE
This action can be used to filter the distribution of colvar values in a ef mcolv More details
DATA
The multicolvar that calculates the set of base quantities that we are interested in
=lq61s
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={GAUSSIAN R_0=0.55 D_MAX=0.56}
cn4:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=flq60s
SPECIESB
this keyword is used for colvars such as the coordination number
=flq61s
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0} cn5:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=flq61s
SPECIESB
this keyword is used for colvars such as the coordination number
=flq60s
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
sphere2:
INSPHERE
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. More details
ATOM
the atom whose vicinity we are interested in examining
=p
DATA
The multicolvar that calculates the set of base quantities that we are interested in
=cn4
RADIUS
the switching function that tells us the extent of the spherical region of interest
={TANH R_0=1.5}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0} sphere3:
INSPHERE
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. More details
ATOM
the atom whose vicinity we are interested in examining
=p
DATA
The multicolvar that calculates the set of base quantities that we are interested in
=cn5
RADIUS
the switching function that tells us the extent of the spherical region of interest
={TANH R_0=1.5}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0}
qncrysts:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=sphere2.morethan,sphere3.morethan
POWERS
the powers to which you are raising each of the arguments in your function
=1,1
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO qvcrysts:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=qncrysts
POWERS
the powers to which you are raising each of the arguments in your function
=0.333
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# Measure coordination of crystalline ions in the box cn6:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=flq60s
SPECIESB
this keyword is used for colvars such as the coordination number
=flq61s
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0} cn7:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=flq61s
SPECIESB
this keyword is used for colvars such as the coordination number
=flq60s
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.38 D_MAX=1.0}
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=5.0}
qncrysta:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=cn6.morethan,cn7.morethan
POWERS
the powers to which you are raising each of the arguments in your function
=1,1
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO qvcrysta:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=qncrysta
POWERS
the powers to which you are raising each of the arguments in your function
=0.333
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# Print
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=ncrysts,vcrysts,qncrysts,qvcrysts,ncrysta,vcrysta,qncrysta,qvcrysta
FILE
the name of the file on which to output these quantities
=q6-sphere-and-all.dat
# histograms for the rxn coordinate variables histcv1:
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
ARG
the input for this action is the scalar output from one or more other actions
=vcrysta
GRID_MIN
the lower bounds for the grid
=-1
GRID_MAX
the upper bounds for the grid
=10
GRID_BIN
the number of bins for the grid
=200
BANDWIDTH
the bandwidths for kernel density estimation
=0.01 histcv2:
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
ARG
the input for this action is the scalar output from one or more other actions
=qvcrysta
GRID_MIN
the lower bounds for the grid
=-1
GRID_MAX
the upper bounds for the grid
=10
GRID_BIN
the number of bins for the grid
=200
BANDWIDTH
the bandwidths for kernel density estimation
=0.01
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the action that creates the grid you would like to output
=histcv1
FILE
the file on which to write the grid
=histn.dat
FMT
the format that should be used to output real numbers
=%8.4f
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the action that creates the grid you would like to output
=histcv2
FILE
the file on which to write the grid
=histnq6.dat
FMT
the format that should be used to output real numbers
=%8.4f
# Get the Na-Cl coordination number cnint:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIES
this keyword is used for colvars such as coordination number
=gions
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.355 D_MAX=0.36}
MEAN
take the mean of these variables
HIGHEST
this flag allows you to recover the highest of these variables

# Report the mean and highest coordination numbers
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
FILE
the name of the file on which to output these quantities
=cn-regions.dat
# DFS on ion clusters built according to simple cut-off criterion mat:
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
ATOMS
The list of atoms for which you would like to calculate the contact matrix
=cnint
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.355 D_MAX=0.36} dfs:
DFSCLUSTERING
Find the connected components of the matrix using the depth first search clustering algorithm. More details
MATRIX
the action that calculates the adjacency matrix vessel we would like to analyze
=mat
# Cluster size distribution and number of ion clusters/monomers nhist:
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. More details
CLUSTERS
the label of the action that does the clustering
=dfs
HISTOGRAM
calculate how many of the values fall in each of the bins of a histogram
={GAUSSIAN LOWER=-1.5 UPPER=499.5 NBINS=501 NORM} nclust1:
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. More details
CLUSTERS
the label of the action that does the clustering
=dfs
MORE_THAN
calculate the number of variables more than a certain target value
={GAUSSIAN D_0=0.95 R_0=0.01 D_MAX=0.96} nclust2:
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. More details
CLUSTERS
the label of the action that does the clustering
=dfs
MORE_THAN
calculate the number of variables more than a certain target value
={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.96} nfree:
CLUSTER_DISTRIBUTION
Calculate functions of the distribution of properties in your connected components. More details
CLUSTERS
the label of the action that does the clustering
=dfs
LESS_THAN
calculate the number of variables less than a certain target value
={GAUSSIAN D_0=0.55 R_0=0.01 D_MAX=0.96}
# Largest cluster at the interface clust0nat:
CLUSTER_NATOMS
Gives the number of atoms in the connected component More details
CLUSTERS
the label of the action that does the clustering
=dfs
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 clust1nat:
CLUSTER_NATOMS
Gives the number of atoms in the connected component More details
CLUSTERS
the label of the action that does the clustering
=dfs
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
=2 clust2nat:
CLUSTER_NATOMS
Gives the number of atoms in the connected component More details
CLUSTERS
the label of the action that does the clustering
=dfs
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
=3
# Report the cluster information
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=nfree.*,nclust1.*,nclust2.*,clust0nat.*,clust1nat.*,clust2nat
FILE
the name of the file on which to output these quantities
=cluster.dat
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=nhist
FILE
the name of the file on which to output these quantities
=csd.dat