Project ID: plumID:22.044
Source: plumed-all-search.dat
Originally used with PLUMED version: 2.7.2
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 onv2.9
tested onmaster
### Plumed driver file to calculate CVs to identify two-step nucleation of colloid crystals
### Dec 2022
### Please cite Aaron R. Finney and Matteo Salvalaglio
##
## The PairEntropy.cpp file should be placed inside src/colvar and PLUMED recompiled to compute this CV.

### Particle group
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
=1-388

### Coordination number distribution 
cn: 
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
=grp 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=6.4 D_MAX=7.0} 
MEAN
 calculate the mean of all the quantities
  
# 1. Number of liquid-like colloids based on coordination
ncm1: 
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
=grp 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=6.4 D_MAX=7.0} 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.0}
ncl: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=ncm1.morethan 
POWERS
 the powers to which you are raising each of the arguments in your function
=1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# 2. Number of solid like particles based on coordinationx
ncm2: 
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
=grp 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=6.4 D_MAX=7.0} 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=6.0}
ncs: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=ncm2.morethan 
POWERS
 the powers to which you are raising each of the arguments in your function
=1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

### Calculate q4
# 3. Global Q4
q4: 
Q4
Calculate fourth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=grp 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=6.4 D_MAX=7.0} 
MEAN
 calculate the mean of all the quantities
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility

# 4. Local Q4
lq4: 
LOCAL_Q4
Calculate the local degree of order around an atoms by taking the average dot product between the $q_4$ vector on the central atom and the $q_4$ vector on the atoms in the first coordination sphere. More details
 SPECIES=q4 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=6.4 D_MAX=7.0} 
MEAN
 calculate the mean of all the quantities
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility

flq4: 
MFILTER_LESS
Basically equivalent to LESS_THAN. More details
 
DATA
the vector you wish to transform
=lq4 
SWITCH
the switching function that transform
={GAUSSIAN R_0=0.3 D_MAX=0.31}
cnq4: 
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
=flq4 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=6.4 D_MAX=7.0} 
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=6.0}
# 5. Number of local q4>5 particles
ncnq4: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=cnq4.morethan 
POWERS
 the powers to which you are raising each of the arguments in your function
=1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# 6. Local average q4
laq4: 
LOCAL_AVERAGE
Calculate averages over spherical regions centered on atoms More details
 
SPECIES
this keyword is used for colvars such as coordination number
=q4 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL RATIONAL R_0=6.4 D_MAX=7.0} 
MEAN
 calculate the mean of all the quantities



### Calculate q6
# 7. Global Q6
q6: 
Q6
Calculate sixth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=grp 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=6.4 D_MAX=7.0} 
MEAN
 calculate the mean of all the quantities
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility

# 8. Local Q6
lq6: 
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=q6 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=6.4 D_MAX=7.0} 
MEAN
 calculate the mean of all the quantities
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility

flq6: 
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=lq6 
SWITCH
the switching function that transform
={GAUSSIAN R_0=0.69 D_MAX=0.70}
cnq6: 
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
=flq6 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=6.4 D_MAX=7.0} 
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=6.0}
# 9. Number of local q6>5 particles
ncnq6: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=cnq6.morethan 
POWERS
 the powers to which you are raising each of the arguments in your function
=1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# 10. Local average q6
laq6: 
LOCAL_AVERAGE
Calculate averages over spherical regions centered on atoms More details
 
SPECIES
this keyword is used for colvars such as coordination number
=q6 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL RATIONAL R_0=6.4 D_MAX=7.0} 
MEAN
 calculate the mean of all the quantities



### S2 Entropy
# 11. S2
#ent: PAIRENTROPY ATOMS=1-388 MAXR=12.0 SIGMA=0.01


### DFS on particle-particle contact matrix
mat: 
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 (basically equivalent to GROUP)
=cn 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=6.4 D_MAX=7.0}
dfs: 
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)
=mat
# 12. Number of particles in the largest cluster
clust1nat: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest 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


### PRINT
#PRINT ARG=cn.mean,ncl.*,ncs.*,q4.mean,lq4.mean,ncnq4,laq4.mean,q6.mean,lq6.mean,ncnq6,laq6.mean,ent,clust1nat FILE=CVscreening.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
=cn.mean,ncl.*,ncs.*,q4.mean,lq4.mean,ncnq4,laq4.mean,q6.mean,lq6.mean,ncnq6,laq6.mean,clust1nat 
FILE
the name of the file on which to output these quantities
=CVscreening.dat