stormm::topology::CondensedExclusions Struct Reference

Unguarded struct to condense the atom exclusion lists read from an Amber topology. This will transform the list of exclusion counts into an capped prefix sum (an exclusive prefix sum in indices 0...N-1, or an inclusive prefix sum in indices 1...N). Any atoms with no actual exclusions will be listed as having zero exclusions, and blank atoms will be removed from the excluded atoms list. More...

#include <atomgraph_refinement.h>

Public Member Functions
	CondensedExclusions ()
	The constructor simply allocates memory, if dimensions are available.
	CondensedExclusions (int natom_in, int total_exclusions_in)

Public Attributes
int	total_exclusions
std::vector< int >	atom_excl_bounds
std::vector< int >	atom_excl_list

Detailed Description

Unguarded struct to condense the atom exclusion lists read from an Amber topology. This will transform the list of exclusion counts into an capped prefix sum (an exclusive prefix sum in indices 0...N-1, or an inclusive prefix sum in indices 1...N). Any atoms with no actual exclusions will be listed as having zero exclusions, and blank atoms will be removed from the excluded atoms list.

Constructor & Destructor Documentation

CondensedExclusions()

stormm::topology::CondensedExclusions::CondensedExclusions

(

)

The constructor simply allocates memory, if dimensions are available.

Overloaded:

• Create an empty object
• Create an object with pre-allocated memory for each virtual site

Parameters

natom_in
total_exclusions_in

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The documentation for this struct was generated from the following files:

• src/Topology/atomgraph_refinement.h
• src/Topology/atomgraph_refinement.cpp