#include <molecule.h>

Inheritance diagram for madness::Molecule::GeometryParameters:

Collaboration diagram for madness::Molecule::GeometryParameters:

Public Member Functions
	GeometryParameters ()

	GeometryParameters (const GeometryParameters &other)=default

	GeometryParameters (World &world, const commandlineparser &parser)

std::set< std::string >	case_sensitive_keys () const override
	source_name is a path (xyz file / input file) – never case-fold it

std::string	core_type () const

double	eprec () const

std::vector< double >	field () const

std::string	get_tag () const override

bool	no_orient () const

bool	psp_calc () const

bool	pure_ae () const

void	set_derived_values (const commandlineparser &parser)

void	set_global_convenience_options (const commandlineparser &parser)

std::string	source_name () const

std::string	source_type () const

double	symtol () const

std::string	units () const

Public Member Functions inherited from madness::QCCalculationParametersBase
bool	file_exists (World &world, std::string filename) const

bool	file_exists (World &world, std::string filename) const

void	from_json (const json &j)

void	from_json (const json &j)

template<typename T >
T	get (const std::string key) const

template<typename T >
T	get (const std::string key) const

ParameterContainerT	get_all_parameters () const

ParameterContainerT	get_all_parameters () const

QCParameter &	get_parameter (const std::string key)

QCParameter &	get_parameter (const std::string key)

hashT	hash () const

hashT	hash () const

bool	is_user_defined (std::string key) const

bool	is_user_defined (std::string key) const

bool	keeps_case (const std::string &key) const

bool	keeps_case (const std::string &key) const

bool	parameter_exists (const std::string &key) const

bool	parameter_exists (const std::string &key) const

void	print (const std::string header="", const std::string footer="") const
	print all parameters

void	print (const std::string header="", const std::string footer="") const
	print all parameters

std::string	print_to_string (const std::list< std::string > precedences={"all"}) const

std::string	print_to_string (const std::list< std::string > precedences={"all"}) const

template<typename... Types>
void	qcparameter_to_json (json &j, const std::pair< std::string, QCParameter > &p, const std::tuple< Types... > &) const

template<typename... Types>
void	qcparameter_to_json (json &j, const std::pair< std::string, QCParameter > &p, const std::tuple< Types... > &) const

template<typename Tuple >
void	qcparameter_to_json_from_tuple (json &j, const std::pair< std::string, QCParameter > &p, const Tuple &) const

template<typename Tuple >
void	qcparameter_to_json_from_tuple (json &j, const std::pair< std::string, QCParameter > &p, const Tuple &) const

void	read_commandline_options (World &world, const commandlineparser &parser, const std::string tag)
	read the parameters from the command line and broadcast

void	read_commandline_options (World &world, const commandlineparser &parser, const std::string tag)

virtual void	read_internal (World &world, std::string &filecontents, std::string tag)
	read the stream, starting from tag

virtual void	read_internal (World &world, std::string &filecontents, std::string tag)
	read the stream, starting from tag

template<typename Archive >
void	serialize (Archive &ar)

template<typename Archive >
void	serialize (Archive &ar)

template<typename T >
void	set_derived_value (const std::string &key, const T &value)

template<typename T >
void	set_derived_value (const std::string &key, const T &value)

template<typename T >
void	set_user_defined_value (const std::string &key, const T &value)

template<typename T >
void	set_user_defined_value (const std::string &key, const T &value)

json	to_json () const
	convert all parameters to a json object

json	to_json () const
	convert all parameters to a json object

void	to_json (json &j) const
	convert all parameters to a json object

void	to_json (json &j) const
	convert all parameters to a json object

json	to_json_if_precedence (const std::string &precedence) const
	convert all parameters to a json object, but only those with a given precedence

json	to_json_if_precedence (const std::string &precedence) const
	convert all parameters to a json object, but only those with a given precedence

template<typename T >
std::string	to_stored_string (const std::string &key, const T &value) const
	stringify `value` for storage, honoring case_sensitive_keys()

template<typename T >
std::string	to_stored_string (const std::string &key, const T &value) const
	stringify `value` for storage, honoring case_sensitive_keys()

template<typename... Types>
bool	try_set_from_json (QCParameter &parameter, const nlohmann::json &value)

template<typename... Types>
bool	try_set_from_json (QCParameter &parameter, const nlohmann::json &value)

Static Public Member Functions
static std::string	absolute_path (const std::string &path)
	make a relative path absolute, relative to the current working directory

static std::string	derive_source_type_from_name (const std::string name, const commandlineparser &parser)

static std::string	input_tag (const commandlineparser &parser)
	name of the data group carrying the geometry in the input file

Static Public Member Functions inherited from madness::QCCalculationParametersBase
static std::string	add_quotes (const std::string arg)

static std::string	add_quotes (const std::string arg)

template<typename T >
static bool	check_type (const std::string key, const QCParameter &parameter)

template<typename T >
static bool	check_type (const std::string key, const QCParameter &parameter)

template<typename T >
static bool	check_type_silent (const QCParameter &parameter)

template<typename T >
static bool	check_type_silent (const QCParameter &parameter)

template<typename T >
static std::enable_if<!std::is_same< T, bool >::value, T >::type	fromstring (const std::string &arg)

template<typename T >
static std::enable_if< std::is_same< T, bool >::value, T >::type	fromstring (const std::string &arg)

template<typename T >
static std::enable_if<!std::is_same< T, bool >::value, T >::type	fromstring (const std::string &arg)

template<typename T >
static std::enable_if< std::is_same< T, bool >::value, T >::type	fromstring (const std::string &arg)

template<typename T >
static std::enable_if< std::is_floating_point< T >::value, void >::type	overwrite_if_inf (std::string &str, const T &arg)

template<typename T >
static std::enable_if<!std::is_floating_point< T >::value, void >::type	overwrite_if_inf (std::string &str, const T &arg)

template<typename T >
static std::enable_if< std::is_floating_point< T >::value, void >::type	overwrite_if_inf (std::string &str, const T &arg)

template<typename T >
static std::enable_if<!std::is_floating_point< T >::value, void >::type	overwrite_if_inf (std::string &str, const T &arg)

template<typename T >
static std::enable_if< std::is_same< T, std::string >::value, T >::type	read_quotes (std::stringstream &ssvalue)

template<typename T >
static std::enable_if<!std::is_same< T, std::string >::value, T >::type	read_quotes (std::stringstream &ssvalue)

template<typename T >
static std::enable_if< std::is_same< T, std::string >::value, T >::type	read_quotes (std::stringstream &ssvalue)

template<typename T >
static std::enable_if<!std::is_same< T, std::string >::value, T >::type	read_quotes (std::stringstream &ssvalue)

static std::string	tostring (const bool &arg)

static std::string	tostring (const bool &arg)

template<typename T >
static std::string	tostring (const T &arg)

template<typename T >
static std::string	tostring (const T &arg)

static std::string	trim_blanks (const std::string arg)

static std::string	trim_blanks (const std::string arg)

static std::string	trim_quotes (const std::string arg)

static std::string	trim_quotes (const std::string arg)

Additional Inherited Members
Public Types inherited from madness::QCCalculationParametersBase
using	all_parameter_types = std::tuple< double, int, unsigned int, long, std::size_t, bool, std::string, std::vector< double >, std::vector< int >, std::vector< std::size_t >, std::vector< std::string >, std::pair< std::string, double > >

using	all_parameter_types = std::tuple< double, int, unsigned int, long, std::size_t, bool, std::string, std::vector< double >, std::vector< int >, std::vector< std::size_t >, std::vector< std::string >, std::pair< std::string, double > >

Protected Types inherited from madness::QCCalculationParametersBase
typedef std::map< std::string, QCParameter >	ParameterContainerT

typedef std::map< std::string, QCParameter >	ParameterContainerT

Protected Member Functions inherited from madness::QCCalculationParametersBase
	QCCalculationParametersBase ()
	ctor for testing

	QCCalculationParametersBase ()
	ctor for testing

	QCCalculationParametersBase (const QCCalculationParametersBase &other)
	copy ctor

	QCCalculationParametersBase (const QCCalculationParametersBase &other)
	copy ctor

virtual	~QCCalculationParametersBase ()
	destructor

virtual	~QCCalculationParametersBase ()
	destructor

const QCParameter &	get_parameter (const std::string &key) const

const QCParameter &	get_parameter (const std::string &key) const

template<typename T >
void	initialize (const std::string &key, const T &value, const std::string comment="", const std::vector< T > allowed_values={})

template<typename T >
void	initialize (const std::string &key, const T &value, const std::string comment="", const std::vector< T > allowed_values={})

void	read_input_and_commandline_options (World &world, const commandlineparser &parser, const std::string tag)

void	read_input_and_commandline_options (World &world, const commandlineparser &parser, const std::string tag)

template<typename Tuple >
bool	try_setting_any (const std::string &key, const std::string &value)
	helper function for try_setting_user_defined_value

template<typename Tuple >
bool	try_setting_any (const std::string &key, const std::string &value)
	helper function for try_setting_user_defined_value

template<typename Tuple , std::size_t... I>
bool	try_setting_any_impl (const std::string &key, const std::string &value, Tuple, std::index_sequence< I... >)
	helper function for try_setting_user_defined_value

template<typename Tuple , std::size_t... I>
bool	try_setting_any_impl (const std::string &key, const std::string &value, Tuple, std::index_sequence< I... >)
	helper function for try_setting_user_defined_value

template<typename T >
bool	try_setting_user_defined_value (const std::string &key, const std::string &val)
	helper function for try_setting_user_defined_value

template<typename T >
bool	try_setting_user_defined_value (const std::string &key, const std::string &val)
	helper function for try_setting_user_defined_value

Protected Attributes inherited from madness::QCCalculationParametersBase
bool	ignore_unknown_keys = true

bool	ignore_unknown_keys_silently = false

ParameterContainerT	parameters

bool	print_debug = false

bool	throw_if_datagroup_not_found = false

Constructor & Destructor Documentation

◆ GeometryParameters() [1/3]

madness::Molecule::GeometryParameters::GeometryParameters ( const GeometryParameters & other )

default

◆ GeometryParameters() [2/3]

madness::Molecule::GeometryParameters::GeometryParameters	(	World &	world,
		const commandlineparser &	parser
	)

inline

References e(), input_tag(), madness::QCCalculationParametersBase::print(), madness::QCCalculationParametersBase::read_commandline_options(), madness::QCCalculationParametersBase::read_input_and_commandline_options(), set_derived_values(), set_global_convenience_options(), and madness::Molecule::tag.

◆ GeometryParameters() [3/3]

madness::Molecule::GeometryParameters::GeometryParameters ( )

inline

References madness::QCCalculationParametersBase::ignore_unknown_keys, madness::QCCalculationParametersBase::ignore_unknown_keys_silently, madness::nonlinear_vector_solver(), and madness::QCCalculationParametersBase::throw_if_datagroup_not_found.

Member Function Documentation

◆ absolute_path()

std::string madness::Molecule::GeometryParameters::absolute_path ( const std::string & path )

static

make a relative path absolute, relative to the current working directory

Returns path unchanged if it is already absolute or cannot be resolved here – the reader then reports the name as given, which is the more useful diagnostic.

References madness::nonlinear_vector_solver().

Referenced by set_derived_values().

◆ case_sensitive_keys()

std::set< std::string > madness::Molecule::GeometryParameters::case_sensitive_keys ( ) const

inlineoverridevirtual

source_name is a path (xyz file / input file) – never case-fold it

Reimplemented from madness::QCCalculationParametersBase.

◆ core_type()

std::string madness::Molecule::GeometryParameters::core_type ( ) const

inline

References madness::nonlinear_vector_solver().

Referenced by madness::Molecule::Molecule(), madness::SCF::derivatives(), madness::Molecule::get_structure(), madness::SCF::initial_guess(), and madness::SCF::make_nuclear_potential().

◆ derive_source_type_from_name()

static std::string madness::Molecule::GeometryParameters::derive_source_type_from_name	(	const std::string	name,
		const commandlineparser &	parser
	)

inlinestatic

References madness::name(), madness::nonlinear_vector_solver(), and madness::commandlineparser::value().

Referenced by set_derived_values().

◆ eprec()

double madness::Molecule::GeometryParameters::eprec ( ) const

inline

References madness::nonlinear_vector_solver().

Referenced by madness::Molecule::get_eprec(), madness::MolecularEnergy::output_calc_info_schema(), madness::Molecule::read(), and madness::Molecule::read_xyz().

◆ field()

std::vector< double > madness::Molecule::GeometryParameters::field ( ) const

inline

References madness::nonlinear_vector_solver().

Referenced by madness::Molecule::Molecule().

◆ get_tag()

std::string madness::Molecule::GeometryParameters::get_tag ( ) const

inlineoverridevirtual

Implements madness::QCCalculationParametersBase.

◆ input_tag()

std::string madness::Molecule::GeometryParameters::input_tag ( const commandlineparser & parser )

static

name of the data group carrying the geometry in the input file

The group is spelled geometry (canonical – the moldft/nemo/cc2 decks) or molecule (alias – the madqc decks and the structure library). Returns whichever the input file contains, preferring the canonical name and falling back to it when the file has neither (or does not exist), so that the missing-data-group diagnostic names the documented spelling.

References madness::f, madness::position_stream_to_word(), madness::Molecule::tag, and madness::commandlineparser::value().

Referenced by GeometryParameters().