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 properties of the distribution of some quantities that are part of a connected component
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 degree the atoms in a nucleus have adopted their crystalline structure or (in the case of heterogeneous nucleation of a solute from a solvent) you might be interested in how many atoms are present in the largest cluster [107].
The input below calculates the coordination numbers of atoms 1-100 and then computes the an adjacency matrix whose elements measures whether atoms \(i\) and \(j\) are within 0.55 nm of each other. The action labelled dfs then treats the elements of this matrix as zero or ones and thus thinks of the matrix as defining a graph. This dfs action then finds the largest connected component in this graph. The sum of the coordination numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar file. The way this input can be used is described in detail in [107].
lq: COORDINATIONNUMBERSPECIES=1-100this keyword is used for colvars such as coordination number.SWITCH={CUBIC D_0=0.45 D_MAX=0.55}the switching function that it used in the construction of the contact matrixLOWMEMcm: CONTACT_MATRIX( default=off ) this flag does nothing and is present only to ensure back-compatibilityATOMS=lqthe atoms for which you would like to calculate the adjacency matrix (basically equivalent to GROUP)SWITCH={CUBIC D_0=0.45 D_MAX=0.55} dfs: DFSCLUSTERINGspecify the switching function to use between two sets of indistinguishable atoms.MATRIX=cm clust1: CLUSTER_PROPERTIESthe input matrix (can use ARG instead)CLUSTERS=dfscompulsory keyword the label of the action that does the clusteringCLUSTER=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.SUMPRINT( default=off ) calculate the sum of all the quantities.ARG=clust1.*the input for this action is the scalar output from one or more other actions.FILE=colvarthe name of the file on which to output these quantities
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 |
ARG | calculate the sum of the arguments calculated by this action for the cluster |
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. |
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. |
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. |