| This is part of the crystdistrib module |
| It is only available if you configure PLUMED with ./configure –enable-modules=crystdistrib . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |
Calculate the ROPS order parameter
- Examples
- Glossary of keywords and components
- Description of components
Quantity | Description |
.#!value | the values of the ROPS order parameters |
- 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. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
- 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
QUATERNIONS | the label of the action that computes the quaternions that should be used |
KERNELFILE_DOPS | the file containing the list of kernel parameters. We expect h, mu and sigma parameters for a 1D Gaussian kernel of the form h*exp(-(x-mu)^2/2sigma^2) |
KERNELFILE_ROPS | the file containing the list of kernel parameters. We expect the normalization factor (height), concentration parameter (kappa), and 4 quaternion pieces of the mean for a bipolar watson distribution (mu_w,mu_i,mu_j,mu_k)): (h*exp(kappa*dot(q_mean,q))), where dot is the dot product |
CUTOFF | cutoff for the distance matrix |