PLUMED-NEST-TEST-SITE

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

### 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: 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=1-388

### Coordination number distribution 
The GROUP action with label grp calculates somethingcn: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=grp SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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
The COORDINATIONNUMBER action with label cn calculates the following quantities:
 Quantity   
 Description  
cn.mean
the mean of the colvars
cn.value
the coordination numbers of the specified atomsncm1: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=grp SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=6.4 D_MAX=7.0} MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=3.0}
The COORDINATIONNUMBER action with label ncm1 calculates the following quantities:
 Quantity   
 Description  
ncm1.morethan
the number of colvars that have a value more than a threshold
ncm1.value
the coordination numbers of the specified atomsncl: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ncm1.morethan POWERS the powers to which you are raising each of the arguments in your function=1 PERIODICif 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
The COMBINE action with label ncl calculates the following quantities:
 Quantity   
 Description  
ncl.value
a linear compbinationncm2: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=grp SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=6.4 D_MAX=7.0} MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=6.0}
The COORDINATIONNUMBER action with label ncm2 calculates the following quantities:
 Quantity   
 Description  
ncm2.morethan
the number of colvars that have a value more than a threshold
ncm2.value
the coordination numbers of the specified atomsncs: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ncm2.morethan POWERS the powers to which you are raising each of the arguments in your function=1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

### Calculate q4
# 3. Global Q4
The COMBINE action with label ncs calculates the following quantities:
 Quantity   
 Description  
ncs.value
a linear compbinationq4: Q4Calculate fourth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=grp SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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
The Q4 action with label q4 calculates the following quantities:
 Quantity   
 Description  
q4.mean
the mean of the colvars
q4.value
the norms of the vectors of spherical harmonic coefficientslq4: LOCAL_Q4Calculate 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 SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q4 SWITCHThis 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
The LOCAL_Q4 action with label lq4 calculates the following quantities:
 Quantity   
 Description  
lq4.value
the values of the local steinhardt parameters for the input atoms
lq4.mean
the mean of the colvarsflq4: MFILTER_LESSApply a switching function to the input vector. More details DATAthe vector you wish to transform=lq4 SWITCHthe switching function that transform={GAUSSIAN R_0=0.3 D_MAX=0.31}
The MFILTER_LESS action with label flq4 calculates the following quantities:
 Quantity   
 Description  
flq4.value
a vector that has the same dimension as the input vector with elements equal to one if the corresponding component of the vector is less than a tolerance and zero otherwisecnq4: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=flq4 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=6.4 D_MAX=7.0} MEAN calculate the mean of all the quantities MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=6.0}
# 5. Number of local q4>5 particles
The COORDINATIONNUMBER action with label cnq4 calculates the following quantities:
 Quantity   
 Description  
cnq4.morethan
the number of colvars that have a value more than a threshold
cnq4.mean
the mean of the colvars
cnq4.value
the coordination numbers of the specified atomsncnq4: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cnq4.morethan, POWERS the powers to which you are raising each of the arguments in your function=1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 
# 6. Local average q4
The COMBINE action with label ncnq4 calculates the following quantities:
 Quantity   
 Description  
ncnq4.value
a linear compbinationlaq4: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=q4 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL RATIONAL R_0=6.4 D_MAX=7.0} MEAN calculate the mean of all the quantities


### Calculate q6
# 7. Global Q6
The LOCAL_AVERAGE action with label laq4 calculates the following quantities:
 Quantity   
 Description  
laq4.mean
the mean of the colvars
laq4.value
the values of the local averagesq6: Q6Calculate sixth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=grp SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6.mean
the mean of the colvars
q6.value
the norms of the vectors of spherical harmonic coefficientslq6: LOCAL_Q6Calculate 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 SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q6 SWITCHThis 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
The LOCAL_Q6 action with label lq6 calculates the following quantities:
 Quantity   
 Description  
lq6.value
the values of the local steinhardt parameters for the input atoms
lq6.mean
the mean of the colvarsflq6: MFILTER_MOREApply one minus a switching function to the input vector. More details DATAthe vector you wish to transform=lq6 SWITCHthe switching function that transform={GAUSSIAN R_0=0.69 D_MAX=0.70}
The MFILTER_MORE action with label flq6 calculates the following quantities:
 Quantity   
 Description  cnq6: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=flq6 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=6.4 D_MAX=7.0} MEAN calculate the mean of all the quantities MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=6.0}
# 9. Number of local q6>5 particles
The COORDINATIONNUMBER action with label cnq6 calculates the following quantities:
 Quantity   
 Description  
cnq6.morethan
the number of colvars that have a value more than a threshold
cnq6.mean
the mean of the colvars
cnq6.value
the coordination numbers of the specified atomsncnq6: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cnq6.morethan, POWERS the powers to which you are raising each of the arguments in your function=1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# 10. Local average q6
The COMBINE action with label ncnq6 calculates the following quantities:
 Quantity   
 Description  
ncnq6.value
a linear compbinationlaq6: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=q6 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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
The LOCAL_AVERAGE action with label laq6 calculates the following quantities:
 Quantity   
 Description  
laq6.mean
the mean of the colvars
laq6.value
the values of the local averagesmat: 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=cn SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=6.4 D_MAX=7.0}
The CONTACT_MATRIX action with label mat calculates the following quantities:
 Quantity   
 Description  
mat.value
a matrix containing the weights for the bonds between each pair of atomsdfs: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=mat
# 12. Number of particles in the largest cluster
The DFSCLUSTERING action with label dfs calculates the following quantities:
 Quantity   
 Description  
dfs.value
vector with length that is equal to the number of rows in the input matrixclust1nat: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe 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
The CLUSTER_NATOMS action with label clust1nat calculates the following quantities:
 Quantity   
 Description  
clust1nat.value
the number of atoms in the clusterPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cn.mean,ncl.*,ncs.*,q4.mean,lq4.mean,ncnq4,laq4.mean,q6.mean,lq6.mean,ncnq6,laq6.mean,clust1nat FILEthe name of the file on which to output these quantities=CVscreening.dat