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PLUMED manual

Shortcut: CLUSTER_DISTRIBUTION

Shortcut: CLUSTER_DISTRIBUTION

Module	clusters
Description	Usage
Calculate functions of the distribution of properties in your connected components.

Details and examples

Calculate functions of the distribution of properties in your connected components.

This action allows you to calculate the number of atoms in each of the connected components that were detected when you performed DFSCLUSTERING on one of the adjacency matrices computed using the admat. The following example illustrates how you can use this to compute the number of atoms in each of the identified clusters:

Click on the labels of the actions for more information on what each action computes

cmThe CONTACT_MATRIX action with label cm calculates the following quantities: Quantity    Type    Description  
cm matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-100 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.={CUBIC D_0=0.45  D_MAX=0.55}
dfsThe DFSCLUSTERING action with label dfs calculates the following quantities: Quantity    Type    Description  
dfs 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: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details ARGthe input matrix=cm
clustThe CLUSTER_DISTRIBUTION action with label clust calculates the following quantities: Quantity    Type    Description  
clust vector a vector containing the sum of a atomic-cv that is calculated for each of the identified clusters: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details CLUSTERSthe label of the action that does the clustering=dfs
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=clust FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1

The output from the CLUSTER_DISTRIBUTION action here is a vector with 100 elements. The first element of this vector is the number of atoms in the largest connected component, the second element of the vector is the number of atoms in the second largest connected component and so on (many elements of the vector will be zero).

As illustrated in the inputs below there are multiple shortcuts that allow you to probe the distribution of cluster sizes. For example, the following input calculates how many clusters with more than 10 atoms are present.

Click on the labels of the actions for more information on what each action computes

cmThe CONTACT_MATRIX action with label cm calculates the following quantities: Quantity    Type    Description  
cm matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-100 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.={CUBIC D_0=0.45  D_MAX=0.55}
dfsThe DFSCLUSTERING action with label dfs calculates the following quantities: Quantity    Type    Description  
dfs 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: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details ARGthe input matrix=cm
clustThe CLUSTER_DISTRIBUTION action with label clust calculates the following quantities: Quantity    Type    Description  
clust_morethan scalar the number of colvars that have a value more than a threshold: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. This action is a shortcut. More details CLUSTERSthe label of the action that does the clustering=dfs 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 D_0=10 R_0=0.0001}
# PLUMED interprets the command:
# clust: CLUSTER_DISTRIBUTION CLUSTERS=dfs MORE_THAN={RATIONAL D_0=10 R_0=0.0001}
# as follows (Click the red comment above to revert to the short version of the input):
clust_mtThe MORE_THAN action with label clust_mt calculates the following quantities: Quantity    Type    Description  
clust_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_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=clust SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL D_0=10 R_0=0.0001}
clust_morethanThe SUM action with label clust_morethan calculates the following quantities: Quantity    Type    Description  
clust_morethan scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=clust_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=clust.morethan FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1

By a similar logic you can compute the number of clusters that were identified as follows:

Click on the labels of the actions for more information on what each action computes

cmThe CONTACT_MATRIX action with label cm calculates the following quantities: Quantity    Type    Description  
cm matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-100 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.={CUBIC D_0=0.45  D_MAX=0.55}
dfsThe DFSCLUSTERING action with label dfs calculates the following quantities: Quantity    Type    Description  
dfs 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: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details ARGthe input matrix=cm
clustThe CLUSTER_DISTRIBUTION action with label clust calculates the following quantities: Quantity    Type    Description  
clust_lessthan scalar the number of colvars that have a value less than a threshold: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. This action is a shortcut. More details CLUSTERSthe label of the action that does the clustering=dfs LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.0001}
# PLUMED interprets the command:
# clust: CLUSTER_DISTRIBUTION CLUSTERS=dfs LESS_THAN={RATIONAL R_0=0.0001}
# as follows (Click the red comment above to revert to the short version of the input):
clust_ltThe LESS_THAN action with label clust_lt calculates the following quantities: Quantity    Type    Description  
clust_lt vector the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=clust SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.0001}
clust_lessthanThe SUM action with label clust_lessthan calculates the following quantities: Quantity    Type    Description  
clust_lessthan scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=clust_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ncThe CUSTOM action with label nc calculates the following quantities: Quantity    Type    Description  
nc scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=clust.lessthan FUNCthe function you wish to evaluate=100-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nc FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1

This input calculates the number of zeros in the vector output by the CLUSTER_DISTRIBUTION action. If we subtract the number of non-zero elements from the size of the vector we then get the number of clusters.

Lastly, you can calculate the number of clusters that are within a certain range or a set of ranges using the BETWEEN and HISGTOGRAM keywords as indicated below:

Click on the labels of the actions for more information on what each action computes

cmThe CONTACT_MATRIX action with label cm calculates the following quantities: Quantity    Type    Description  
cm matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-100 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.={CUBIC D_0=0.45  D_MAX=0.55}
dfsThe DFSCLUSTERING action with label dfs calculates the following quantities: Quantity    Type    Description  
dfs 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: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details ARGthe input matrix=cm
clustThe CLUSTER_DISTRIBUTION action with label clust calculates the following quantities: Quantity    Type    Description  
clust_between scalar the number of colvars that have a value that lies in a particular interval
clust_between-1 scalar the number of colvars that have a value that lies in a particular interval
clust_between-2 scalar the number of colvars that have a value that lies in a particular interval
clust_between-3 scalar the number of colvars that have a value that lies in a particular interval
clust_between-4 scalar the number of colvars that have a value that lies in a particular interval: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. This action is a shortcut. More details ...
   CLUSTERSthe label of the action that does the clustering=dfs
   BETWEENcalculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=5 UPPER=6 SMEAR=0.5}
   HISTOGRAMcalculate a discretized histogram of the distribution of values={GAUSSIAN LOWER=6 UPPER=10 NBINS=4 SMEAR=0.5}
...
# PLUMED interprets the command:
# clust: CLUSTER_DISTRIBUTION ...
#    CLUSTERS=dfs
#    BETWEEN={GAUSSIAN LOWER=5 UPPER=6 SMEAR=0.5}
#    HISTOGRAM={GAUSSIAN LOWER=6 UPPER=10 NBINS=4 SMEAR=0.5}
# ...
# as follows (Click the red comment above to revert to the short version of the input):
clust_btThe BETWEEN action with label clust_bt calculates the following quantities: Quantity    Type    Description  
clust_bt vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=clust SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=5 UPPER=6 SMEAR=0.5}
clust_betweenThe SUM action with label clust_between calculates the following quantities: Quantity    Type    Description  
clust_between scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=clust_bt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
clust_bt1The BETWEEN action with label clust_bt1 calculates the following quantities: Quantity    Type    Description  
clust_bt1 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=clust SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=6 UPPER=7 SMEAR=0.5}
clust_between-1The SUM action with label clust_between-1 calculates the following quantities: Quantity    Type    Description  
clust_between-1 scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=clust_bt1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
clust_bt2The BETWEEN action with label clust_bt2 calculates the following quantities: Quantity    Type    Description  
clust_bt2 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=clust SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=7 UPPER=8 SMEAR=0.5}
clust_between-2The SUM action with label clust_between-2 calculates the following quantities: Quantity    Type    Description  
clust_between-2 scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=clust_bt2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
clust_bt3The BETWEEN action with label clust_bt3 calculates the following quantities: Quantity    Type    Description  
clust_bt3 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=clust SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=8 UPPER=9 SMEAR=0.5}
clust_between-3The SUM action with label clust_between-3 calculates the following quantities: Quantity    Type    Description  
clust_between-3 scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=clust_bt3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
clust_bt4The BETWEEN action with label clust_bt4 calculates the following quantities: Quantity    Type    Description  
clust_bt4 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=clust SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=9 UPPER=10 SMEAR=0.5}
clust_between-4The SUM action with label clust_between-4 calculates the following quantities: Quantity    Type    Description  
clust_between-4 scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=clust_bt4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=clust.* FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1

This input will output 5 quantities:

clust.between tells you the number of connected components that contain between 5 and 6 atoms.
clust.between-1 tells you the number of connected components that contain between 6 and 7 atoms.
clust.between-2 tells you the number of connected components that contain between 7 and 8 atoms.
clust.between-3 tells you the number of connected components that contain between 8 and 9 atoms.
clust.between-4 tells you the number of connected components that contain between 9 and 10 atoms.

If you expand the inputs above you can find more details on how these quantities are calculated.

The input provided below shows just how this can be used to perform quite complicated calculations. The input calculates the local q6 Steinhardt parameter on each atom. The coordination number that atoms with a high value for the local q6 Steinhardt parameter have with other atoms that have a high value for the local q6 Steinhardt parameter is then computed. A contact matrix is then computed that measures whether atoms atoms $i$ and $j$ have a high value for this coordination number and if they are within 3.6 nm of each other. The connected components of this matrix are then found using a depth first clustering algorithm on the corresponding graph. The number of components in this graph that contain more than 27 atoms is then computed. An input similar to this one was used to analyze the formation of a polycrystal of GeTe from amorphous GeTe in the paper cited below

Click on the labels of the actions for more information on what each action computes

q6The Q6 action with label q6 calculates the following quantities: Quantity    Type    Description  
q6 vector the norms of the vectors of spherical harmonic coefficients: Q6Calculate sixth order Steinhardt parameters. This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-300 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.={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}
# PLUMED interprets the command:
# q6: Q6 SPECIES=1-300 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}
# as follows (Click the red comment above to revert to the short version of the input):
q6_grpThe GROUP action with label q6_grp calculates the following quantities: Quantity    Type    Description  
q6_grp atoms indices of atoms specified in GROUP: 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=1-300
q6_matThe CONTACT_MATRIX action with label q6_mat calculates the following quantities: Quantity    Type    Description  
q6_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q6_mat.x matrix the projection of the bond on the x axis
q6_mat.y matrix the projection of the bond on the y axis
q6_mat.z matrix the projection of the bond on the z axis: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-300 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.={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
q6_shThe SPHERICAL_HARMONIC action with label q6_sh calculates the following quantities: Quantity    Type    Description  
q6_sh.rm-n6 matrix the real parts of the spherical harmonic values with the m value given  This is the n6th of these quantities
q6_sh.rm-n5 matrix the real parts of the spherical harmonic values with the m value given  This is the n5th of these quantities
q6_sh.rm-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q6_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q6_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q6_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q6_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q6_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q6_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q6_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q6_sh.rm-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q6_sh.rm-p5 matrix the real parts of the spherical harmonic values with the m value given  This is the p5th of these quantities
q6_sh.rm-p6 matrix the real parts of the spherical harmonic values with the m value given  This is the p6th of these quantities
q6_sh.im-n6 matrix the real parts of the spherical harmonic values with the m value given  This is the n6th of these quantities
q6_sh.im-n5 matrix the real parts of the spherical harmonic values with the m value given  This is the n5th of these quantities
q6_sh.im-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q6_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q6_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q6_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q6_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q6_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q6_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q6_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q6_sh.im-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q6_sh.im-p5 matrix the real parts of the spherical harmonic values with the m value given  This is the p5th of these quantities
q6_sh.im-p6 matrix the real parts of the spherical harmonic values with the m value given  This is the p6th of these quantities: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q6_mat.x,q6_mat.y,q6_mat.z,q6_mat.w Lthe value of the angular momentum=6
q6_denom_onesThe CONSTANT action with label q6_denom_ones calculates the following quantities: Quantity    Type    Description  
q6_denom_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=300
q6_denomThe MATRIX_VECTOR_PRODUCT action with label q6_denom calculates the following quantities: Quantity    Type    Description  
q6_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q6_mat.w,q6_denom_ones
q6_spThe MATRIX_VECTOR_PRODUCT action with label q6_sp calculates the following quantities: Quantity    Type    Description  
q6_sp.rm-n6 vector the product of the matrix q6_sh.rm-n6 and the vector q6_denom_ones
q6_sp.rm-n5 vector the product of the matrix q6_sh.rm-n5 and the vector q6_denom_ones
q6_sp.rm-n4 vector the product of the matrix q6_sh.rm-n4 and the vector q6_denom_ones
q6_sp.rm-n3 vector the product of the matrix q6_sh.rm-n3 and the vector q6_denom_ones
q6_sp.rm-n2 vector the product of the matrix q6_sh.rm-n2 and the vector q6_denom_ones
q6_sp.rm-n1 vector the product of the matrix q6_sh.rm-n1 and the vector q6_denom_ones
q6_sp.rm-0 vector the product of the matrix q6_sh.rm-0 and the vector q6_denom_ones
q6_sp.rm-p1 vector the product of the matrix q6_sh.rm-p1 and the vector q6_denom_ones
q6_sp.rm-p2 vector the product of the matrix q6_sh.rm-p2 and the vector q6_denom_ones
q6_sp.rm-p3 vector the product of the matrix q6_sh.rm-p3 and the vector q6_denom_ones
q6_sp.rm-p4 vector the product of the matrix q6_sh.rm-p4 and the vector q6_denom_ones
q6_sp.rm-p5 vector the product of the matrix q6_sh.rm-p5 and the vector q6_denom_ones
q6_sp.rm-p6 vector the product of the matrix q6_sh.rm-p6 and the vector q6_denom_ones
q6_sp.im-n6 vector the product of the matrix q6_sh.im-n6 and the vector q6_denom_ones
q6_sp.im-n5 vector the product of the matrix q6_sh.im-n5 and the vector q6_denom_ones
q6_sp.im-n4 vector the product of the matrix q6_sh.im-n4 and the vector q6_denom_ones
q6_sp.im-n3 vector the product of the matrix q6_sh.im-n3 and the vector q6_denom_ones
q6_sp.im-n2 vector the product of the matrix q6_sh.im-n2 and the vector q6_denom_ones
q6_sp.im-n1 vector the product of the matrix q6_sh.im-n1 and the vector q6_denom_ones
q6_sp.im-0 vector the product of the matrix q6_sh.im-0 and the vector q6_denom_ones
q6_sp.im-p1 vector the product of the matrix q6_sh.im-p1 and the vector q6_denom_ones
q6_sp.im-p2 vector the product of the matrix q6_sh.im-p2 and the vector q6_denom_ones
q6_sp.im-p3 vector the product of the matrix q6_sh.im-p3 and the vector q6_denom_ones
q6_sp.im-p4 vector the product of the matrix q6_sh.im-p4 and the vector q6_denom_ones
q6_sp.im-p5 vector the product of the matrix q6_sh.im-p5 and the vector q6_denom_ones
q6_sp.im-p6 vector the product of the matrix q6_sh.im-p6 and the vector q6_denom_ones: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q6_sh.*,q6_denom_ones
q6_norm2The COMBINE action with label q6_norm2 calculates the following quantities: Quantity    Type    Description  
q6_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q6_sp.rm-n6,q6_sp.im-n6,q6_sp.rm-n5,q6_sp.im-n5,q6_sp.rm-n4,q6_sp.im-n4,q6_sp.rm-n3,q6_sp.im-n3,q6_sp.rm-n2,q6_sp.im-n2,q6_sp.rm-n1,q6_sp.im-n1,q6_sp.rm-0,q6_sp.im-0,q6_sp.rm-p1,q6_sp.im-p1,q6_sp.rm-p2,q6_sp.im-p2,q6_sp.rm-p3,q6_sp.im-p3,q6_sp.rm-p4,q6_sp.im-p4,q6_sp.rm-p5,q6_sp.im-p5,q6_sp.rm-p6,q6_sp.im-p6
q6_normThe CUSTOM action with label q6_norm calculates the following quantities: Quantity    Type    Description  
q6_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q6_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6The CUSTOM action with label q6 calculates the following quantities: Quantity    Type    Description  
q6 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q6_norm,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- lq6The LOCAL_Q6 action with label lq6 calculates the following quantities: Quantity    Type    Description  
lq6 vector the values of the local steinhardt parameters for the input atoms: 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. This action is a shortcut. 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={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}
# PLUMED interprets the command:
# lq6: LOCAL_Q6 SPECIES=q6 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}
# as follows (Click the red comment above to revert to the short version of the input):
lq6_uvecThe CONSTANT action with label lq6_uvec calculates the following quantities: Quantity    Type    Description  
lq6_uvec vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=26
lq6_grpThe GROUP action with label lq6_grp calculates the following quantities: Quantity    Type    Description  
lq6_grp atoms indices of atoms specified in GROUP: 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=q6
lq6_nmatThe OUTER_PRODUCT action with label lq6_nmat calculates the following quantities: Quantity    Type    Description  
lq6_nmat matrix a matrix containing the outer product of the two input vectors that was obtained using the function that was input: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=q6_norm,lq6_uvec
lq6_uvecsThe VSTACK action with label lq6_uvecs calculates the following quantities: Quantity    Type    Description  
lq6_uvecs matrix a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=q6_sp.rm-n6,q6_sp.im-n6,q6_sp.rm-n5,q6_sp.im-n5,q6_sp.rm-n4,q6_sp.im-n4,q6_sp.rm-n3,q6_sp.im-n3,q6_sp.rm-n2,q6_sp.im-n2,q6_sp.rm-n1,q6_sp.im-n1,q6_sp.rm-0,q6_sp.im-0,q6_sp.rm-p1,q6_sp.im-p1,q6_sp.rm-p2,q6_sp.im-p2,q6_sp.rm-p3,q6_sp.im-p3,q6_sp.rm-p4,q6_sp.im-p4,q6_sp.rm-p5,q6_sp.im-p5,q6_sp.rm-p6,q6_sp.im-p6
lq6_vecsThe CUSTOM action with label lq6_vecs calculates the following quantities: Quantity    Type    Description  
lq6_vecs matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=lq6_uvecs,lq6_nmat FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq6_vecsTThe TRANSPOSE action with label lq6_vecsT calculates the following quantities: Quantity    Type    Description  
lq6_vecsT matrix the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=lq6_vecs
lq6_cmapThe CONTACT_MATRIX action with label lq6_cmap calculates the following quantities: Quantity    Type    Description  
lq6_cmap matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=q6 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.={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}
lq6_dpmatThe MATRIX_PRODUCT action with label lq6_dpmat calculates the following quantities: Quantity    Type    Description  
lq6_dpmat matrix the product of the two input matrices: MATRIX_PRODUCTCalculate the product of two matrices More details ARGthe label of the two matrices from which the product is calculated=lq6_vecs,lq6_vecsT MASKa matrix that is used to used to determine which elements of the output matrix to compute=lq6_cmap
lq6_prodThe CUSTOM action with label lq6_prod calculates the following quantities: Quantity    Type    Description  
lq6_prod matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=lq6_cmap,lq6_dpmat FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq6_onesThe CONSTANT action with label lq6_ones calculates the following quantities: Quantity    Type    Description  
lq6_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=300
lq6The MATRIX_VECTOR_PRODUCT action with label lq6 calculates the following quantities: Quantity    Type    Description  
lq6 vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=lq6_prod,lq6_ones
lq6_denomThe MATRIX_VECTOR_PRODUCT action with label lq6_denom calculates the following quantities: Quantity    Type    Description  
lq6_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=lq6_cmap,lq6_ones
lq6_avThe CUSTOM action with label lq6_av calculates the following quantities: Quantity    Type    Description  
lq6_av vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=lq6,lq6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- flq6The MORE_THAN action with label flq6 calculates the following quantities: Quantity    Type    Description  
flq6 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_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=lq6 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}
ccThe COORDINATIONNUMBER action with label cc calculates the following quantities: Quantity    Type    Description  
cc vector the coordination numbers of the specified atoms: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-300 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.={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
# PLUMED interprets the command:
# cc: COORDINATIONNUMBER SPECIES=1-300 SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
# as follows (Click the red comment above to revert to the short version of the input):
cc_grpThe GROUP action with label cc_grp calculates the following quantities: Quantity    Type    Description  
cc_grp atoms indices of atoms specified in GROUP: 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=1-300
cc_matThe CONTACT_MATRIX action with label cc_mat calculates the following quantities: Quantity    Type    Description  
cc_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-300 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.={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
cc_onesThe CONSTANT action with label cc_ones calculates the following quantities: Quantity    Type    Description  
cc_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=300
ccThe MATRIX_VECTOR_PRODUCT action with label cc calculates the following quantities: Quantity    Type    Description  
cc vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=cc_mat,cc_ones
# --- End of included input --- fccThe MORE_THAN action with label fcc calculates the following quantities: Quantity    Type    Description  
fcc 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_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=cc SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}
matThe CONTACT_MATRIX action with label mat calculates the following quantities: Quantity    Type    Description  
mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-300 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.={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
dfsThe DFSCLUSTERING action with label dfs calculates the following quantities: Quantity    Type    Description  
dfs 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: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details ARGthe input matrix=mat
nclustThe CLUSTER_DISTRIBUTION action with label nclust calculates the following quantities: Quantity    Type    Description  
nclust_morethan scalar the number of colvars that have a value more than a threshold: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. This action is a shortcut. More details ...
   CLUSTERSthe label of the action that does the clustering=dfs WEIGHTSuse the vector of values calculated by this action as weights rather than giving each atom a unit weight=fcc
   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.={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}
...
# PLUMED interprets the command:
# nclust: CLUSTER_DISTRIBUTION ...
#    CLUSTERS=dfs WEIGHTS=fcc
#    MORE_THAN={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}
# ...
# as follows (Click the red comment above to revert to the short version of the input):
nclust_mtThe MORE_THAN action with label nclust_mt calculates the following quantities: Quantity    Type    Description  
nclust_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_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=nclust SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}
nclust_morethanThe SUM action with label nclust_morethan calculates the following quantities: Quantity    Type    Description  
nclust_morethan scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=nclust_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nclust.* FILEthe name of the file on which to output these quantities=colvar

Notice how the WEIGHTS keyword is used here in the input to CLUSTER_DISTRIBUTION. By using this keyword here we ensure that the size of each cluster is the sum of the components of the vector fcc that are part of the connected component. The size of each cluster that is output is thus the number of atoms in that cluster that have a COORDINATIONNUMBER that is greater than 4.

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Keyword	Description
lessthan	scalar	LESS_THAN	the number of colvars that have a value less than a threshold
morethan	scalar	MORE_THAN	the number of colvars that have a value more than a threshold
altmin	scalar	ALT_MIN	the minimum value of the cv
min	scalar	MIN	the minimum colvar
max	scalar	MAX	the maximum colvar
between	scalar	BETWEEN	the number of colvars that have a value that lies in a particular interval
highest	scalar	HIGHEST	the largest of the colvars
lowest	scalar	LOWEST	the smallest of the colvars
sum	scalar	SUM	the sum of the colvars
mean	scalar	MEAN	the mean of the colvars

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
CLUSTERS	compulsory	none	the label of the action that does the clustering
WEIGHTS	optional	not used	use the vector of values calculated by this action as weights rather than giving each atom a unit weight

deprecated keywords

The keywords in the following table can still be used with this action but have been deprecated

Keyword	Description
LESS_THAN	calculate the number of variables that are less than a certain target value
MORE_THAN	calculate the number of variables that are more than a certain target value
BETWEEN	calculate the number of values that are within a certain range
HISTOGRAM	calculate a discretized histogram of the distribution of values