| 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. |
Calculate a matrix of distances
- Examples
- Glossary of keywords and components
- Description of components
By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.
Quantity | Description |
.#!value | a matrix containing the weights for the bonds between each pair of atoms |
In addition the following quantities can be calculated by employing the keywords listed below
Quantity | Keyword | Description |
w | COMPONENTS | a matrix containing the weights for the bonds between each pair of atoms |
x | COMPONENTS | the projection of the bond on the x axis |
y | COMPONENTS | the projection of the bond on the y axis |
z | COMPONENTS | the projection of the bond on the z axis |
- The atoms involved can be specified using
- Or alternatively by using
ATOMS | the atoms for which you would like to calculate the adjacency matrix. This is a depracated syntax that is equivalent to GROUP. You are strongly recommened to use GROUP instead of ATOMS. |
- Compulsory keywords
NL_CUTOFF | ( default=0.0 ) The cutoff for the neighbor list. A value of 0 means we are not using a neighbor list |
NL_STRIDE | ( default=1 ) The frequency with which we are updating the atoms in the neighbor list |
CUTOFF | ( default=-1 ) ignore distances that have a value larger than this cutoff |
- Options
SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |
COMPONENTS | ( default=off ) also calculate the components of the vector connecting the atoms in the contact matrix |
NOPBC | ( default=off ) don't use pbc
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