CLUSTER_NATOMS

This is part of the adjmat module | |

It is only available if you configure PLUMED with ./configure –enable-modules=adjmat . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |

Gives the number of atoms in the connected component

As discussed in the section of the manual on Exploiting contact matrices a useful tool for developing complex collective variables is the notion of the so called adjacency matrix. An adjacency matrix is an \(N \times N\) matrix in which the \(i\)th, \(j\)th element tells you whether or not the \(i\)th and \(j\)th atoms/molecules from a set of \(N\) atoms/molecules are adjacent or not. When analyzing these matrix we can treat them as a graph and find connected components using some clustering algorithm. This action is used in tandem with this form of analysis to output the number of atoms that are connected together in a particular connected component. It is important to note that the quantity that is output by this action cannot be differentiated. As such it cannot be used as a collective variable in a biased simulation.

- Examples

The following input uses PLUMED to calculate a adjacency matrix that connects a pair of atoms if they both have a coordination number that is greater than 2.0 and if they are within 6.0 nm of each other. Depth first search clustering is used to find the connected components in this matrix and then the number of atoms in the largest cluster is found. This quantity is then output to a file called colvar

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

# Calculate coordination numbersc1:COORDINATIONNUMBERSPECIES=1-512this keyword is used for colvars such as coordination number.SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} # Select coordination numbers that are more than 2.0This keyword is used if you want to employ an alternative to the continuous switching function defined above.cf:MFILTER_MOREDATA=compulsory keywordThe multicolvar that calculates the set of base quantities that we are interested inc1SWITCH={RATIONAL D_0=2.0 R_0=0.1}This keyword is used if you want to employ an alternative to the continuous switching function defined above.LOWMEM# Build a contact matrix( default=off ) lower the memory requirementsmat:CONTACT_MATRIXATOMS=The list of atoms for which you would like to calculate the contact matrix.cfSWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} # Find largest clusterThis keyword is used if you want to employ an alternative to the continuous switching function defined above.dfs:DFSCLUSTERINGMATRIX=compulsory keywordthe action that calculates the adjacency matrix vessel we would like to analyzematclust1:CLUSTER_PROPERTIESCLUSTERS=compulsory keywordthe label of the action that does the clusteringdfsCLUSTER=1compulsory keyword ( default=1 )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.nat:CLUSTER_NATOMSCLUSTERS=compulsory keywordthe label of the action that does the clusteringdfsCLUSTER=1 PRINTcompulsory keyword ( default=1 )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.ARG=the input for this action is the scalar output from one or more other actions.natFILE=COLVARthe name of the file on which to output these quantities

- Glossary of keywords and components

- Compulsory keywords

CLUSTERS | the label of the action that does the clustering |

CLUSTER | ( default=1 ) 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. |

- Options

NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |

NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |

SERIAL | ( default=off ) do the calculation in serial. Do not use MPI |

LOWMEM | ( default=off ) lower the memory requirements |

TIMINGS | ( default=off ) output information on the timings of the various parts of the calculation |