| This is part of the symfunc module |
| It is only available if you configure PLUMED with ./configure –enable-modules=symfunc . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |
Calculate the local crystalinity symmetry function
- Examples
- Glossary of keywords and components
- Description of components
| Quantity | Keyword | Description |
| lessthan | LESS_THAN | the number of colvars that have a value less than a threshold |
| morethan | MORE_THAN | the number of colvars that have a value more than a threshold |
| altmin | ALT_MIN | the minimum value of the cv |
| min | MIN | the minimum colvar |
| max | MAX | the maximum colvar |
| between | BETWEEN | the number of colvars that have a value that lies in a particular interval |
| highest | HIGHEST | the largest of the colvars |
| lowest | LOWEST | the smallest of the colvars |
| sum | SUM | the sum of the colvars |
| mean | MEAN | the mean of the colvars |
- The atoms involved can be specified using
| SPECIES | this keyword is used for colvars such as coordination number. In that context it specifies that plumed should calculate one coordination number for each of the atoms specified. Each of these coordination numbers specifies how many of the other specified atoms are within a certain cutoff of the central atom. You can specify the atoms here as another multicolvar action or using a MultiColvarFilter or ActionVolume action. When you do so the quantity is calculated for those atoms specified in the previous multicolvar. This is useful if you would like to calculate the Steinhardt parameter for those atoms that have a coordination number more than four for example |
- Or alternatively by using
| SPECIESA | this keyword is used for colvars such as the coordination number. In that context it species that plumed should calculate one coordination number for each of the atoms specified in SPECIESA. Each of these cooordination numbers specifies how many of the atoms specifies using SPECIESB is within the specified cutoff. As with the species keyword the input can also be specified using the label of another multicolvar |
| SPECIESB | this keyword is used for colvars such as the coordination number. It must appear with SPECIESA. For a full explanation see the documentation for that keyword |
- Compulsory keywords
| NN | ( default=6 ) The n parameter of the switching function |
| MM | ( default=0 ) The m parameter of the switching function; 0 implies 2*NN |
| D_0 | ( default=0.0 ) The d_0 parameter of the switching function |
| R_0 | The r_0 parameter of the switching function |
- Options
| HIGHEST | ( default=off ) this flag allows you to recover the highest of these variables. |
| LOWEST | ( default=off ) this flag allows you to recover the lowest of these variables. |
| SUM | ( default=off ) calculate the sum of all the quantities. |
| MEAN | ( default=off ) calculate the mean of all the quantities.
|
| SWITCH | the switching function that it used in the construction of the contact matrix |
| LESS_THAN | calculate the number of variables that are less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3... |
| MORE_THAN | calculate the number of variables that are more than a certain target value. This quantity is calculated using \(\sum_i 1 - \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. MORE_THAN1, MORE_THAN2, MORE_THAN3... |
| ALT_MIN | calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = -\frac{1}{\beta} \log \sum_i \exp\left( -\beta s_i \right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)). |
| MIN | calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) } \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)) |
| MAX | calculate the maximum value. To make this quantity continuous the maximum is calculated using \( \textrm{max} = \beta \log \sum_i \exp\left( \frac{s_i}{\beta}\right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)) |
| BETWEEN | calculate the number of values that are within a certain range. These quantities are calculated using kernel density estimation as described on histogrambead.. You can use multiple instances of this keyword i.e. BETWEEN1, BETWEEN2, BETWEEN3... |
| HISTOGRAM | calculate a discretized histogram of the distribution of values. This shortcut allows you to calculates NBIN quantites like BETWEEN. |
| GVECTOR | the coefficients of the linear combinations to compute for the CV. You can use multiple instances of this keyword i.e. GVECTOR1, GVECTOR2, GVECTOR3... |
1.8.17