BOPS

	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 BOPS order parameter

Examples

Glossary of keywords and components

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_BOPS	the second file containing the list of kernel parameters. Expecting a normalization factor (height), concentration parameter (kappa), and 3 norm vector pieces of the mean (mu_i, mu_j, mu_k )for a fisher distribution. of the form h*exp(kappa*dot(r_mean,r)), where dot is a standard dot product.
CUTOFF	cutoff for the distance matrix