Collaboration diagram for mpqc::Molecule:

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Documentation

Molecule is a class which contains a vector of AtomBasedClusterables.

Molecule is a recursively-clustered collection of atoms.

Public Member Functions
	Molecule ()=default

	Molecule (const Molecule &)=default

	Molecule (Molecule &&)=default

Molecule &	operator= (Molecule &&)=default

Molecule &	operator= (const Molecule &)=default

	Molecule (const KeyVal &kv)
	The KeyVal constructor. More...

	Molecule (std::istream &file_stream, bool sort_input=true, Vector3d const &sort_origin=Vector3d::Zero(), std::array< Vector3d, 3 > frame={ {Vector3d{1, 0, 0}, Vector3d{0, 1, 0}, Vector3d{0, 0, 1}}})
	Constructs Molecule from an XYZ-format stream. More...

	Molecule (std::vector< AtomBasedClusterable > c, bool sort_input=true)
	Constructor to build Molecule from a vector of clusterables. More...

	Molecule (const std::vector< Atom > &atoms)

virtual	~Molecule ()=default

virtual void	in_units_of (const std::string &units)
	Reinterprets coordinates of atoms as having different units. More...

void	sort_from_point (Vector3d const &point)
	A function to sort the clusters from a given point. More...

void	set_mass (double mass)
	Function to set the mass of the Molecule. More...

int64_t	total_atomic_number () const

double	mass () const
	Mass of the Molecule. More...

std::vector< AtomBasedClusterable >::const_iterator	begin () const
	Iterator to the first clusterable in the Molecule. More...

std::vector< AtomBasedClusterable >::const_iterator	end () const
	Iterator to one past the final clusterable in the Molecule. More...

int64_t	nclusters () const
	Number of clusters in the Molecule. More...

std::vector< AtomBasedClusterable > const &	clusterables () const
	Vector containing the Clusterable that make up the Molecule. More...

int64_t	core_electrons () const
	Computes the number of core electrons in the Molecule. More...

double	nuclear_repulsion_energy () const

std::vector< Atom >	atoms () const
	A vector of all atoms in the Molecule. More...

size_t	natoms () const

Vector3d const &	com () const
	Center of mass of the Molecule. More...

Public Member Functions inherited from mpqc::DescribedClass
	DescribedClass ()=default

virtual	~DescribedClass ()

std::string	class_key () const

Public Member Functions inherited from mpqc::enable_shared_from_this< DescribedClass >
virtual	~enable_shared_from_this ()=default

std::shared_ptr< DescribedClass >	shared_from_this ()
	returns the pointer to this object More...

std::shared_ptr< std::add_const_t< DescribedClass > >	shared_from_this () const
	returns the pointer to this object More...

Public Member Functions inherited from mpqc::detail::virt_base_of_enable_shared_from_this
virtual	~virt_base_of_enable_shared_from_this ()=default

bool	shared_from_this_possible () const

template<typename Target , typename = std::enable_if_t<!std::is_const_v<Target>>>
std::shared_ptr< Target >	cast_shared_from_this_to ()
	returns the pointer to this cast to a particular type More...

template<typename Target >
std::shared_ptr< std::add_const_t< Target > >	cast_shared_from_this_to () const
	returns the pointer to this cast to a particular type More...

Public Member Functions inherited from mpqc::utility::Observable< Molecule >
std::shared_ptr< void *const >	register_message (Observer *observer, std::function< void()> message) const

Public Member Functions inherited from mpqc::enable_shared_from_this< Molecule >
virtual	~enable_shared_from_this ()=default

std::shared_ptr< Molecule >	shared_from_this ()
	returns the pointer to this object More...

std::shared_ptr< std::add_const_t< Molecule > >	shared_from_this () const
	returns the pointer to this object More...

Static Public Member Functions
static std::vector< AtomBasedClusterable >	read_xyz (std::istream &file, const std::array< Vector3d, 3 > &frame={ {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}}})
	Reads atoms from an XYZ file. More...

Static Public Member Functions inherited from mpqc::DescribedClass
static keyval_ctor_wrapper_type	type_to_keyval_ctor (const std::string &type_name)

template<typename T >
static void	register_keyval_ctor ()

template<typename T >
static bool	is_registered ()

template<typename T >
static std::string	class_key ()

static const keyval_ctor_registry_type &	keyval_ctor_registry ()
	returns const ref to the keyval ctor registry More...

Friends
class	MolecularCoordinates
	the only way to mutate coordinates is via MolecularCoordinates More...

Additional Inherited Members
Public Types inherited from mpqc::DescribedClass
typedef std::shared_ptr< DescribedClass >(*	keyval_ctor_wrapper_type) (const KeyVal &)

Public Types inherited from mpqc::utility::Observable< Molecule >
typedef std::map< void *, std::function< void()> >	messages_type

Protected Member Functions inherited from mpqc::utility::Observable< Molecule >
void	message ()

Constructor & Destructor Documentation

◆ Molecule() [1/7]

mpqc::Molecule::Molecule ( )

default

◆ Molecule() [2/7]

mpqc::Molecule::Molecule ( const Molecule & )

default

◆ Molecule() [3/7]

mpqc::Molecule::Molecule ( Molecule && )

default

◆ Molecule() [4/7]

mpqc::Molecule::Molecule ( const KeyVal & kv )

explicit

The KeyVal constructor.

Parameters

kv	the KeyVal object. The following keywords will be queried in `kv` :

Keyword	Type	Default	Description
`file_name`	string	none	This gives the name of a XYZ file, from which the nuclear coordinates will be read (the XYZ format is described here). Only rank 0 in the current madness::World will read the file.
`atoms`	array	none	Will query this if `file_name` not given. Each element of the array must specify an Atom object (see the KeyVal ctor of Atom for more info).
`units`	string	angstrom	If `atoms` given, will use this to determine the units in which the coordinates are given. Valid choices are `"angstrom"` and `"bohr"` See UnitFactory for more information.
`sort_input`	boolean	true	If true, sort atoms in the order of increasing distance from the center of mass
`n_cluster`	int	0	If nonzero, divide the Molecule into `n_cluster` clusters
`attach_hydrogen`	boolean	true	use attach_hydrogen_kmeans when clustering
`"$:world"`	pointer	the value returned by mpqc::get_default_world()	the default madness::World object to use

example input 1:

"molecule": {
  "file_name": "water20.xyz",
  "n_cluster": 20
}

example input 2:

"molecule": {
  "atoms" : [
    { "element" : "O", "xyz" : [0.0,  0.0, 0.0] },
    { "element" : "H", "xyz" : [0.0,  1.0, 1.0] },
    { "element" : "H", "xyz" : [0.0, -1.0, 1.0] }
  ]
  "n_cluster": 1
}

◆ Molecule() [5/7]

mpqc::Molecule::Molecule	(	std::istream &	file_stream,
		bool	sort_input = `true`,
		Vector3d const &	sort_origin = `Vector3d::Zero()`,
		std::array< Vector3d, 3 >	frame = `{ {Vector3d{1, 0, 0}, Vector3d{0, 1, 0}, Vector3d{0, 0, 1}}}`
	)

Constructs Molecule from an XYZ-format stream.

Parameters

file_stream	the XYZ-format stream
sort_input	if true, will resort atoms in the order of increasing distance from the point given by `sort_origin@param` sort_origin the reference point to use for sorting the atoms
frame	coordinate frame basis (in Angstroms) used to compute atomic coordinates.

Note: This is a non-clustering ctor, i.e. produces a Molecule consisting of 1 cluster.

◆ Molecule() [6/7]

mpqc::Molecule::Molecule	(	std::vector< AtomBasedClusterable >	c,
		bool	sort_input = `true`
	)

Constructor to build Molecule from a vector of clusterables.

This constructor takes a vector of AtomBasedClusterables and uses it to initialize the Molecule's Clusterables. If sort_input is true the Clusterables are sorted based on distance from the center of mass.

◆ Molecule() [7/7]

mpqc::Molecule::Molecule ( const std::vector< Atom > & atoms )

explicit

Constructs a Molecule from a sequence of Atom objects atoms

Parameters

[in] atoms a sequence of atoms

Note: does not resort atoms, use Molecule::sort_from_point if needed

◆ ~Molecule()

virtual mpqc::Molecule::~Molecule ( )

virtualdefault

Member Function Documentation

◆ atoms()

std::vector< Atom > mpqc::Molecule::atoms ( ) const

A vector of all atoms in the Molecule.

This function will loop over the clusterables and extract their atoms in the depth-first order.

Note: Returns copies of the atoms, not a reference to the atoms stored in the Clusterables of the Molecule.

◆ begin()

std::vector<AtomBasedClusterable>::const_iterator mpqc::Molecule::begin ( ) const

inline

Iterator to the first clusterable in the Molecule.

◆ clusterables()

std::vector<AtomBasedClusterable> const& mpqc::Molecule::clusterables ( ) const

inline

Vector containing the Clusterable that make up the Molecule.

◆ com()

Vector3d const& mpqc::Molecule::com ( ) const

inline

Center of mass of the Molecule.

Necessary to satisfy the AtomBasedClusterable interface so Molecules are also clusterable.

◆ core_electrons()

int64_t mpqc::Molecule::core_electrons ( ) const

Computes the number of core electrons in the Molecule.

◆ end()

std::vector<AtomBasedClusterable>::const_iterator mpqc::Molecule::end ( ) const

inline

Iterator to one past the final clusterable in the Molecule.

◆ in_units_of()

void mpqc::Molecule::in_units_of ( const std::string & units )

virtual

Reinterprets coordinates of atoms as having different units.

Converts current coordinates of atoms to atomic units assuming that they are currently given in units

Parameters

[in] units the units that the current Atom objects use; see UnitsFactory::make_unit

Reimplemented in mpqc::UnitCell.

◆ mass()

double mpqc::Molecule::mass ( ) const

inline

Mass of the Molecule.

◆ natoms()

size_t mpqc::Molecule::natoms ( ) const

Returns: the number of atoms returned by atoms()

◆ nclusters()

int64_t mpqc::Molecule::nclusters ( ) const

inline

Number of clusters in the Molecule.

◆ nuclear_repulsion_energy()

double mpqc::Molecule::nuclear_repulsion_energy ( ) const

Returns: the nuclear repulsion energy of the Molecule.

◆ operator=() [1/2]

Molecule& mpqc::Molecule::operator= ( const Molecule & )

default

◆ operator=() [2/2]

Molecule& mpqc::Molecule::operator= ( Molecule && )

default

◆ read_xyz()

std::vector< AtomBasedClusterable > mpqc::Molecule::read_xyz	(	std::istream &	file,
		const std::array< Vector3d, 3 > &	frame = `{ {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}}}`
	)

static

Reads atoms from an XYZ file.

Parameters

file	the XYZ-format stream
frame	coordinate frame basis (in Angstroms) used to compute atomic coordinates.

Returns: the vector of Atom objects opaqued as AtomBasedClusterable objects

◆ set_mass()

void mpqc::Molecule::set_mass ( double mass )

inline

Function to set the mass of the Molecule.

◆ sort_from_point()

void mpqc::Molecule::sort_from_point ( Vector3d const & point )

A function to sort the clusters from a given point.

◆ total_atomic_number()

int64_t mpqc::Molecule::total_atomic_number ( ) const

inline

Returns: the sum of atomic numbers of all atoms

See also: Atom::atomic_number()

Friends And Related Function Documentation

◆ MolecularCoordinates

friend class MolecularCoordinates

friend

the only way to mutate coordinates is via MolecularCoordinates

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

mpqc/chemistry/molecule/molecule.h
mpqc/chemistry/molecule/molecule.cpp

Documentation

Public Member Functions

Static Public Member Functions

Friends

Additional Inherited Members

Constructor & Destructor Documentation

◆ Molecule() [1/7]

◆ Molecule() [2/7]

◆ Molecule() [3/7]

◆ Molecule() [4/7]

◆ Molecule() [5/7]

◆ Molecule() [6/7]

◆ Molecule() [7/7]

◆ ~Molecule()

Member Function Documentation

◆ atoms()

◆ begin()

◆ clusterables()

◆ com()

◆ core_electrons()

◆ end()

◆ in_units_of()

◆ mass()

◆ natoms()

◆ nclusters()

◆ nuclear_repulsion_energy()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ read_xyz()

◆ set_mass()

◆ sort_from_point()

◆ total_atomic_number()

Friends And Related Function Documentation

◆ MolecularCoordinates