Action: HBPAMM_MATRIX
| Module | pamm |
|---|---|
| Description | Usage |
| Adjacency matrix in which two electronegative atoms are adjacent if they are hydrogen bonded |   |
| 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 |
|---|---|---|
| GROUP | atoms | the atoms for which you would like to calculate the adjacency matrix |
| 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 |
| GROUPC | atoms | a group of atoms that must be summed over when calculating each element of the adjacency 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:
- 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)
- P. Gasparotto, M. Ceriotti, Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond. The Journal of Chemical Physics. 141 (2014)
- P. Gasparotto, R. H. Meißner, M. Ceriotti, Recognizing Local and Global Structural Motifs at the Atomic Scale. Journal of Chemical Theory and Computation. 14, 486–498 (2018)
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| GROUP | input | none | the atoms for which you would like to calculate the adjacency matrix |
| 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 |
| GROUPC | input | none | a group of atoms that must be summed over when calculating each element of the adjacency 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 |
| ORDER | compulsory | dah | the order in which the groups are specified in the input |
| CLUSTERS | compulsory | none | the name of the file that contains the definitions of all the kernels for PAMM |
| REGULARISE | compulsory | 0.001 | don’t allow the denominator to be smaller then this value |
| GAUSS_CUTOFF | compulsory | 6.25 | the cutoff at which to stop evaluating the kernel function is set equal to sqrt(2x)(max(adc)+cov(adc)) |
| 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 |