gmx::NNPotTopologyPreprocessor Class Reference

#include <gromacs/applied_forces/nnpot/nnpottopologypreprocessor.h>

Inherits QMMMTopologyPreprocessor.

Description

Class responsible for all modifications of the topology during input pre-processing.

Inherits from QMMMTopologyPreprocessor and performs the following modifications for a scheme analoguous to mechanical embedding in QMMM: 1) Split molecules containing NNP input atoms from other molecules in blocks 2) Exclude non-bonded interactions between NNP atoms. 3) Build vector with atomic numbers of all atoms. 4) Make InteractionFunction::ConnectBonds between atoms within NNP region. 5) Remove angles and settles containing 2 or more NNP atoms. 6) Remove dihedrals containing 3 or more NNP atoms.

Public Member Functions
	NNPotTopologyPreprocessor (ArrayRef< const Index > inputIndices)
	Constructor for NNPotTopologyPreprocessor from its parameters. More...
void	preprocess (gmx_mtop_t *mtop, const MDLogger &logger, WarningHandler *wi)
	Process mtop topology containing information about topology modifications. More...

Constructor & Destructor Documentation

gmx::NNPotTopologyPreprocessor::NNPotTopologyPreprocessor

(

ArrayRef< const Index >

inputIndices

)

Constructor for NNPotTopologyPreprocessor from its parameters.

Parameters

[in]

inputIndices

Array with global indices of NN input atoms

Member Function Documentation

void gmx::NNPotTopologyPreprocessor::preprocess	(	gmx_mtop_t *	mtop,
		const MDLogger &	logger,
		WarningHandler *	wi
	)

Process mtop topology containing information about topology modifications.

Parameters

[in,out]	mtop	Topology that needs to be modified
[in]	logger	MDLogger for logging info about modifications
[in]	wi	WarningHandler for handling warnings

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

• src/gromacs/applied_forces/nnpot/nnpottopologypreprocessor.h
• src/gromacs/applied_forces/nnpot/nnpottopologypreprocessor.cpp