Action: COORDINATION
| Module | colvar |
|---|---|
| Description | Usage |
| Calculate coordination numbers. |   |
| output value | type |
| the value of the coordination | scalar |
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 | First list of atoms |
| GROUPB | atoms | Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted) |
Further details and examples
Text from manual goes here
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| GROUPA | input | none | First list of atoms |
| GROUPB | input | none | Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted) |
| 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 |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| SERIAL | optional | false | Perform the calculation in serial - for debug purpose |
| PAIR | optional | false | Pair only 1st element of the 1st group with 1st element in the second, etc |
| NLIST | optional | false | Use a neighbor list to speed up the calculation |
| NL_CUTOFF | optional | not used | The cutoff for the neighbor list |
| NL_STRIDE | optional | not used | The frequency with which we are updating the atoms in the neighbor list |
| SWITCH | optional | not used | This keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN. |