PreprocessingAtomTypes Class Reference

#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.
int	atomTypeFromName (const std::string &str) const
	Get atom type index for atom type name if present in the database, or NOTSET. More...
size_t	size () const
	Get number of defined atom types.
const char *	atomNameFromAtomType (int nt) const
	Get name of atom from internal atom type number. More...
real	atomMassFromAtomType (int nt) const
	Get normal mass of atom from internal atom type number. More...
real	atomChargeFromAtomType (int nt) const
	Get normal charge of atom from internal atom type number. More...
int	atomParticleTypeFromAtomType (int nt) const
	Get particle type for atom type nt. More...
int	bondAtomTypeFromAtomType (int nt) const
	Get bond atom parameter of atom from internal atom type number. More...
int	atomNumberFromAtomType (int nt) const
	Get atomic number of atom from internal atom type number. More...
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...
void	printTypes (FILE *out)
	Print data to file. More...
int	setType (int nt, t_symtab *tab, 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 (t_symtab *tab, const t_atom &a, const std::string &name, const InteractionOfType &nb, int bondAtomType, int atomNumber)
	Add new atom type to database. More...
void	renumberTypes (gmx::ArrayRef< InteractionsOfType > plist, gmx_mtop_t *mtop, int *wallAtomType, bool verbose)
	Renumber existing atom type entries. More...
void	copyTot_atomtypes (t_atomtypes *atypes) const
	Copy information to other structure. More...

Member Function Documentation

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

Add new atom type to database.

Parameters

[in]	tab	Symbol table.
[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

Number of entries in database.

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 charge for the atom or NOTSET.

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 mass for the atom or NOTSET.

const char * PreprocessingAtomTypes::atomNameFromAtomType

(

int

nt

)

const

Get name of atom from internal atom type number.

Parameters

[in]

nt

Internal number of atom type.

Returns

The type name.

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 value of the parameter or NOTSET.

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 atomic number type or NOTSET.

int PreprocessingAtomTypes::atomParticleTypeFromAtomType

(

int

nt

)

const

Get particle type for atom type nt.

Parameters

[in]

nt

Internal number of atom type.

Returns

The particle type or NOTSET.

int PreprocessingAtomTypes::atomTypeFromName

(

const std::string &

str

)

const

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

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

Atomtype as integer.

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 bond atom parameter or NOTSET.

void PreprocessingAtomTypes::copyTot_atomtypes

(

t_atomtypes *

atypes

)

const

Copy information to other structure.

Parameters

[in,out]

atypes

Other datastructure to copy to.

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::printTypes

(

FILE *

out

)

Print data to file.

Parameters

[in]

out

File pointer.

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.

int PreprocessingAtomTypes::setType	(	int	nt,
		t_symtab *	tab,
		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]	tab	Symbol table.
[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

Number of the type set or NOTSET

---

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

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