Shortcut: SMAC
| Module | symfunc |
|---|---|
| Description | Usage |
| Calculate the SMAC order parameter for a set of molecules |   |
| output value | type |
| the value of the smac parameter for each of the input molecules | vector |
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 |
|---|---|---|---|
| lessthan | scalar | LESS_THAN | the number of colvars that have a value less than a threshold |
| morethan | scalar | MORE_THAN | the number of colvars that have a value more than a threshold |
| altmin | scalar | ALT_MIN | the minimum value of the cv |
| min | scalar | MIN | the minimum colvar |
| max | scalar | MAX | the maximum colvar |
| between | scalar | BETWEEN | the number of colvars that have a value that lies in a particular interval |
| highest | scalar | HIGHEST | the largest of the colvars |
| lowest | scalar | LOWEST | the smallest of the colvars |
| sum | scalar | SUM | the sum of the colvars |
| mean | scalar | MEAN | the mean of the colvars |
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:
- F. Giberti, M. Salvalaglio, M. Mazzotti, M. Parrinello, Insight into the nucleation of urea crystals from the melt. Chemical Engineering Science. 121, 51–59 (2015)
- G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017)
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| SPECIES | optional | not used | |
| SPECIESA | optional | not used | |
| SPECIESB | optional | not used | |
| SWITCH | optional | not used | This keyword is used if you want to employ an alternative to the continuous swiching function defined above. Options for this keyword are explained in the documentation for LESS_THAN. |
| KERNEL | optional | not used | The kernels used in the function of the angle |
| SWITCH_COORD | optional | not used | This keyword is used to define the coordination switching function. Options for this keyword are explained in the documentation for LESS_THAN. |
| LESS_THAN | optional | not used | calculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN. |
| MORE_THAN | optional | not used | calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN. |
| ALT_MIN | optional | not used | calculate the minimum value |
| MIN | optional | not used | calculate the minimum value |
| MAX | optional | not used | calculate the maximum value |
| BETWEEN | optional | not used | calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN. |
| HIGHEST | optional | false | this flag allows you to recover the highest of these variables |
| HISTOGRAM | optional | not used | calculate a discretized histogram of the distribution of values |
| LOWEST | optional | false | this flag allows you to recover the lowest of these variables |
| SUM | optional | false | calculate the sum of all the quantities |
| MEAN | optional | false | calculate the mean of all the quantities |