#include <gromacs/gmxpreprocess/gpp_atomtype.h>

Description

Storage of all atom types used during preprocessing of a simulation input.

Public Member Functions
	PreprocessingAtomTypes (PreprocessingAtomTypes &&old) noexcept
	Move constructor.

PreprocessingAtomTypes &	operator= (PreprocessingAtomTypes &&old) noexcept
	Move assignment constructor.

std::optional< int >	atomTypeFromName (const std::string &str) const
	Get atom type index for atom type name if present in the database, or empty optional. More...

size_t	size () const
	Get number of defined atom types.

std::optional< const std::string >	atomNameFromAtomType (int nt) const
	Get name of atom from internal atom type number. More...

std::optional< real >	atomMassFromAtomType (int nt) const
	Get normal mass of atom from internal atom type number. More...

std::optional< real >	atomChargeFromAtomType (int nt) const
	Get normal charge of atom from internal atom type number. More...

std::optional< ParticleType >	atomParticleTypeFromAtomType (int nt) const
	Get particle type for atom type `nt`. More...

std::optional< int >	bondAtomTypeFromAtomType (int nt) const
	Get bond atom parameter of atom from internal atom type number. More...

std::optional< int >	atomNumberFromAtomType (int nt) const
	Get atomic number of atom from internal atom type number. More...

std::optional< real >	atomNonBondedParamFromAtomType (int nt, int param) const
	Get the value of `param` of type `nt`. More...

bool	isSet (int nt) const
	If a value is within the range of the current types or not. More...

std::optional< int >	setType (int nt, const t_atom &a, const std::string &name, const InteractionOfType &nb, int bondAtomType, int atomNumber)
	Set the values of an existing atom type `nt`. More...

int	addType (const t_atom &a, const std::string &name, const InteractionOfType &nb, int bondAtomType, int atomNumber)
	Add a unique type to the database. More...

void	renumberTypes (gmx::ArrayRef< InteractionsOfType > plist, gmx_mtop_t mtop, int wallAtomType, bool verbose)
	Renumber existing atom type entries. More...

Member Function Documentation

int PreprocessingAtomTypes::addType	(	const t_atom &	a,
		const std::string &	name,
		const InteractionOfType &	nb,
		int	bondAtomType,
		int	atomNumber
	)

Add a unique type to the database.

Parameters

[in]	a	Atom information.
[in]	name	Atom name.
[in]	nb	Nonbonded parameters.
[in]	bondAtomType	What kind of bonded interactions are there.
[in]	atomNumber	Atomic number of the entry.

Returns: Index to the type in the database. If the type shares a name with an existing type, return the index of that type.

std::optional< real > PreprocessingAtomTypes::atomChargeFromAtomType ( int nt ) const

Get normal charge of atom from internal atom type number.

Parameters

[in] nt Internal number of atom type.

Returns: The optional charge for the atom.

std::optional< real > PreprocessingAtomTypes::atomMassFromAtomType ( int nt ) const

Get normal mass of atom from internal atom type number.

Parameters

[in] nt Internal number of atom type.

Returns: The optional mass for the atom.

std::optional< const std::string > PreprocessingAtomTypes::atomNameFromAtomType ( int nt ) const

Get name of atom from internal atom type number.

Parameters

[in] nt Internal number of atom type.

Returns: The optional type name.

std::optional< real > PreprocessingAtomTypes::atomNonBondedParamFromAtomType	(	int	nt,
		int	param
	)		const

Get the value of param of type nt.

Parameters

[in]	param	The parameter value to find.
[in]	nt	The number of the type.

Returns: The optional value of the parameter.

std::optional< int > PreprocessingAtomTypes::atomNumberFromAtomType ( int nt ) const

Get atomic number of atom from internal atom type number.

Parameters

[in] nt Internal number of atom type.

Returns: The optional atomic number type.

std::optional< ParticleType > PreprocessingAtomTypes::atomParticleTypeFromAtomType ( int nt ) const

Get particle type for atom type nt.

Parameters

[in] nt Internal number of atom type.

Returns: The optional particle type.

std::optional< int > PreprocessingAtomTypes::atomTypeFromName ( const std::string & str ) const

Get atom type index for atom type name if present in the database, or empty optional.

Todo:: The code should be changed to instead use a gmx::compat version of std::optional to return an iterator to the element being searched, or an empty optional construct if the entry has not been found.

Parameters

[in] str Input string to search type for.

Returns: Optional atomtype as integer.

std::optional< int > PreprocessingAtomTypes::bondAtomTypeFromAtomType ( int nt ) const

Get bond atom parameter of atom from internal atom type number.

Parameters

[in] nt Internal number of atom type.

Returns: The optional bond atom parameter.

bool PreprocessingAtomTypes::isSet ( int nt ) const

If a value is within the range of the current types or not.

Parameters

[in] nt Value to check.

Returns: True if value is in range.

void PreprocessingAtomTypes::renumberTypes	(	gmx::ArrayRef< InteractionsOfType >	plist,
		gmx_mtop_t *	mtop,
		int *	wallAtomType,
		bool	verbose
	)

Renumber existing atom type entries.

Parameters

[in]	plist	List of parameters.
[in]	mtop	Global topology.
[in,out]	wallAtomType	Atom types of wall atoms, which may also be renumbered
[in]	verbose	If we want to print additional info.

std::optional< int > PreprocessingAtomTypes::setType	(	int	nt,
		const t_atom &	a,
		const std::string &	name,
		const InteractionOfType &	nb,
		int	bondAtomType,
		int	atomNumber
	)

Set the values of an existing atom type nt.

Parameters

[in]	nt	Type that should be set.
[in]	a	Atom information.
[in]	name	Atom name.
[in]	nb	Nonbonded parameters.
[in]	bondAtomType	What kind of bonded interactions are there.
[in]	atomNumber	Atomic number of the entry.

Returns: Optional number of the type set.

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

src/gromacs/gmxpreprocess/gpp_atomtype.h
src/gromacs/gmxpreprocess/gpp_atomtype.cpp

Description

Public Member Functions

Member Function Documentation