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gmx::QMMMTopologyPreprocessor Class Reference

#include <gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.h>

Description

Class implementing gmx_mtop_t QMMM modifications during preprocessing 1) Split QM-containing molecules from other molecules in blocks 2) Nullify charges on all virtual sites consisting of QM only atoms 3) Nullifies charges on all QM atoms 4) Excludes LJ interactions between QM atoms 5) Builds vector with atomic numbers of all atoms 6) Makes F_CONNBOND between atoms within QM region 7) Removes angles and settles containing 2 or more QM atoms 8) Removes dihedrals containing 3 or more QM atoms 9) Builds vector containing pairs of bonded QM - MM atoms (Link frontier)

Public Member Functions

 QMMMTopologyPreprocessor (ArrayRef< const Index > qmIndices)
 Constructor for QMMMTopologyPreprocessor from its parameters. More...
 
void preprocess (gmx_mtop_t *mtop)
 Pocesses mtop topology and prepares atomNumbers_ and linkFrontier_ vectors Builds topInfo_ containing information about topology modifications. More...
 
const QMMMTopologyInfotopInfo () const
 Returns data about modifications made via QMMMTopologyInfo.
 
ArrayRef< const int > atomNumbers () const
 Returns view of atomic numbers for all atoms in the processed topology.
 
ArrayRef< const realatomCharges () const
 Returns view of point charges for all atoms in the processed topology.
 
ArrayRef< const LinkFrontierlinkFrontier () const
 Returns view of the whole Link Frontier for the processed topology.
 

Constructor & Destructor Documentation

gmx::QMMMTopologyPreprocessor::QMMMTopologyPreprocessor ( ArrayRef< const Index qmIndices)

Constructor for QMMMTopologyPreprocessor from its parameters.

Parameters
[in]qmIndicesArray with global indicies of QM atoms

Member Function Documentation

void gmx::QMMMTopologyPreprocessor::preprocess ( gmx_mtop_t *  mtop)

Pocesses mtop topology and prepares atomNumbers_ and linkFrontier_ vectors Builds topInfo_ containing information about topology modifications.

Parameters
[in,out]mtopTopology that needs to be modified

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