Module: adjmat
| Description | Usage |
|---|---|
| methods for calculating adjacency matrices | |
| Authors: Gareth Tribello |   |
Details
An adjacency matrix is an matrix in which the th, th element tells you whether or not the th and th atoms/molecules from a set of atoms/molecules are adjacent or not. There are various ways of defining whether a pair of atoms/molecules are adjacent or not. For example we can say two atoms are adjacent if the distance between them is less than some cutoff. Alternatively, if we have a have a pair of molecules, we might state they are adjacent if their centers of mass are within a certain cutoff and if the two molecules have the same orientation. Two electronegative atoms might be said to be adjacent if there is a hydrogen bond between them. For these reasons then PLUMED contains all the multiple methods for calculating adjacency matrices.
Once you have calculated an adjacency matrix you can use it to calculate symmetry functions by exploting functionalility in the symfunc module. Alternatively, you can find the connected components in the graph representation of the matrix by using the functionality in the clusters module. You can even work with the properties of this graph representation of the matrix directly by exploiting the methods described in the sprint module.
You will get a colossal speedup by specifying the D_MAX keyword in all switching functions that act on distances. D_MAX tells PLUMED that the switching function is strictly zero if the distance is greater than this value. As a result PLUMED knows that it does not need to calculate these zero terms in what are essentially sums with a very large number of terms. In fact when D_MAX is set PLUMED uses linked lists when calculating these coordination numbers, which is what gives you such a dramatic increase in performance.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| BRIDGE | Calculate the number of briding atoms between two groups | MCOLVAR |
| BRIDGE_MATRIX | Calculate the number of atoms that bridge two parts of a structure | MCOLVAR |
| CONTACT_MATRIX | Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. | MATRIX |
| DISTANCE_MATRIX | Calculate a matrix of distances between atoms. | MATRIX |
| HBOND_MATRIX | Adjacency matrix in which two atoms are adjacent if there is a hydrogen bond between them. | MATRIX |
| NEIGHBORS | Build a matrix with ones in for the N nearest neighbours of an atom | MCOLVAR |
| TOPOLOGY_MATRIX | Adjacency matrix in which two atoms are adjacent if they are connected topologically | MATRIX |
| TORSIONS_MATRIX | Calculate the matrix of torsions between two vectors of molecules | MCOLVAR |