Action: CONTACT_MATRIX
| Module | adjmat |
|---|---|
| Description | Usage |
| Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. |   |
| output value | type |
| a matrix containing the weights for the bonds between each pair of atoms | matrix |
Output components
This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action’s label followed by a dot and the name of the value required from the list below.
| Name | Type | Keyword | Description |
|---|---|---|---|
| w | matrix | COMPONENTS | a matrix containing the weights for the bonds between each pair of atoms |
| x | matrix | COMPONENTS | the projection of the bond on the x axis |
| y | matrix | COMPONENTS | the projection of the bond on the y axis |
| z | matrix | COMPONENTS | the projection of the bond on the z axis |
Input
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| GROUPA | atoms | when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB |
| GROUPB | atoms | when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA |
| ATOMS | atoms | the atoms for which you would like to calculate the adjacency matrix |
| GROUP | atoms | the group of atoms for which you are calculating the NxN contact matrix |
Further details and examples
Text from manual goes here
References
More information about how this action can be used is available in the following articles:
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| GROUPA | input | none | when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB |
| GROUPB | input | none | when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA |
| ATOMS | input | none | the atoms for which you would like to calculate the adjacency matrix |
| GROUP | input | none | the group of atoms for which you are calculating the NxN contact matrix |
| NL_CUTOFF | compulsory | 0.0 | The cutoff for the neighbor list |
| NL_STRIDE | compulsory | 1 | The frequency with which we are updating the atoms in the neighbor list |
| NN | compulsory | 6 | The n parameter of the switching function |
| MM | compulsory | 0 | The m parameter of the switching function; 0 implies 2*NN |
| D_0 | compulsory | 0.0 | The d_0 parameter of the switching function |
| R_0 | compulsory | none | The r_0 parameter of the switching function |
| SERIAL | optional | false | do the calculation in serial |
| COMPONENTS | optional | false | also calculate the components of the vectors connecting the atoms in the contact matrix |
| NOPBC | optional | false | don’t use pbc |
| SWITCH | optional | not used | the input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN. |