CLUSTER_DISTRIBUTION

This is part of the clusters module | |

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

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

This collective variable was developed for looking at nucleation phenomena, where you are interested in using studying the behavior of atoms in small aggregates or nuclei. In these sorts of problems you might be interested in the distribution of the sizes of the clusters in your system. A detailed description of this CV can be found in [107].

- Examples

The input provided below 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. As discussed in [107] an input similar to this one was used to analyze the formation of a polycrystal of GeTe from amorphous GeTe.

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

q6:Q6SPECIES=1-300this keyword is used for colvars such as coordination number.SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}the switching function that it used in the construction of the contact matrixLOWMEM( default=off ) this flag does nothing and is present only to ensure back-compatibilitylq6:LOCAL_Q6SPECIES=q6SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}This keyword is used if you want to employ an alternative to the continuous swiching function defined above.LOWMEM( default=off ) this flag does nothing and is present only to ensure back-compatibilityflq6:MFILTER_MOREDATA=compulsory keywordthe vector you wish to transformlq6SWITCH={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}compulsory keywordthe switching function that transformcc:COORDINATIONNUMBERSPECIES=this keyword is used for colvars such as coordination number.flq6SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}the switching function that it used in the construction of the contact matrixfcc:MFILTER_MOREDATA=compulsory keywordthe vector you wish to transformccSWITCH={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}compulsory keywordthe switching function that transformmat:CONTACT_MATRIXATOMS=the atoms for which you would like to calculate the adjacency matrix.fccSWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}specify the switching function to use between two sets of indistinguishable atoms.dfs:DFSCLUSTERINGMATRIX=the input matrix (can use ARG instead)matnclust:CLUSTER_DISTRIBUTIONCLUSTERS=compulsory keywordthe label of the action that does the clusteringdfsTRANSFORM={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}could not find this keywordMORE_THAN={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27} PRINTcalculate the number of variables that are more than a certain target value.ARG=compulsory keywordthe labels of the values that you would like to print to the filenclust.*FILE=colvarthe name of the file on which to output these quantities

- Glossary of keywords and components

- Description of components

Quantity | Keyword | Description |

lessthan | LESS_THAN | the number of colvars that have a value less than a threshold |

morethan | MORE_THAN | the number of colvars that have a value more than a threshold |

altmin | ALT_MIN | the minimum value of the cv |

min | MIN | the minimum colvar |

max | MAX | the maximum colvar |

between | BETWEEN | the number of colvars that have a value that lies in a particular interval |

highest | HIGHEST | the largest of the colvars |

lowest | LOWEST | the smallest of the colvars |

sum | SUM | the sum of the colvars |

mean | MEAN | the mean of the colvars |

- Compulsory keywords

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

- Options

HIGHEST | ( default=off ) this flag allows you to recover the highest of these variables. |

LOWEST | ( default=off ) this flag allows you to recover the lowest of these variables. |

SUM | ( default=off ) calculate the sum of all the quantities. |

MEAN | ( default=off ) calculate the mean of all the quantities. |

WEIGHTS | use the vector of values calculated by this action as weights rather than giving each atom a unit weight |

LESS_THAN | calculate the number of variables that are less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3... |

MORE_THAN | calculate the number of variables that are more than a certain target value. This quantity is calculated using \(\sum_i 1 - \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. MORE_THAN1, MORE_THAN2, MORE_THAN3... |

ALT_MIN | calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = -\frac{1}{\beta} \log \sum_i \exp\left( -\beta s_i \right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)). |

MIN | calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) } \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)) |

MAX | calculate the maximum value. To make this quantity continuous the maximum is calculated using \( \textrm{max} = \beta \log \sum_i \exp\left( \frac{s_i}{\beta}\right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)) |

BETWEEN | calculate the number of values that are within a certain range. These quantities are calculated using kernel density estimation as described on histogrambead.. You can use multiple instances of this keyword i.e. BETWEEN1, BETWEEN2, BETWEEN3... |

HISTOGRAM | calculate a discretized histogram of the distribution of values. This shortcut allows you to calculates NBIN quantites like BETWEEN. |