input parameters for the polarizable continuum model – the pcm data group More...

#include <pcm.h>

Inheritance diagram for madness::PCMParameters:

Collaboration diagram for madness::PCMParameters:

Public Member Functions
	PCMParameters ()

	PCMParameters (World &world, const commandlineparser &parser)

double	area () const

std::string	cavity_type () const

double	correction () const

double	epsilon () const

std::string	get_tag () const override

double	min_radius () const

double	probe_radius () const

std::string	radii_set () const

bool	reader_own () const
	whether PCMSolver should read its own input file instead of our parameters

std::string	restart_name () const

bool	scaling () const

void	set_derived_values (const CalculationParameters &cparam)
	adopt the solvent named by the dft group's `pcm_data`, derive from it, validate

std::string	solvent () const

std::string	solver_type () const

Public Member Functions inherited from madness::QCCalculationParametersBase
virtual std::set< std::string >	case_sensitive_keys () const
	keys whose string values must NOT be case-folded

virtual std::set< std::string >	case_sensitive_keys () const
	keys whose string values must NOT be case-folded

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 const std::map< std::string, std::pair< double, double > > &	solvent_data ()
	the solvents PCMSolver tabulates

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)

Static Public Attributes
static constexpr std::size_t	max_solvent_name_length = 15
	longest solvent name PCMInput::solvent (char[16]) can hold with its NUL

static constexpr char const *	tag = "pcm"

Private Attributes
bool	reader_own_ = false

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

Detailed Description

input parameters for the polarizable continuum model – the pcm data group

Declared outside MADNESS_HAS_PCM on purpose: ParameterManager and madqc hold and print this group whether or not PCMSolver was compiled in, and only the conversion to PCMSolver's PCMInput needs the library.

The group refines pcm_data of the dft group, which stays the on/off switch: pcm_data <solvent> on its own is a complete specification, and the solvent it names arrives here as a derived value that an explicit solvent in this group overrides.

Only the thirteen PCMInput fields that PCMSolver's host-struct reader actually consults are exposed. patch_level, coarsity, min_distance, der_order and equation_type are accepted by the struct but never read by Input::reader(const PCMInput&), and upstream documents no keyword for them.

Constructor & Destructor Documentation

◆ PCMParameters() [1/2]

madness::PCMParameters::PCMParameters ( )

◆ PCMParameters() [2/2]

madness::PCMParameters::PCMParameters	(	World &	world,
		const commandlineparser &	parser
	)

inline

References madness::QCCalculationParametersBase::read_input_and_commandline_options(), and tag.

Member Function Documentation

◆ area()

double madness::PCMParameters::area ( ) const

inline

◆ cavity_type()

std::string madness::PCMParameters::cavity_type ( ) const

inline

◆ correction()

double madness::PCMParameters::correction ( ) const

inline

Referenced by set_derived_values().

◆ epsilon()

double madness::PCMParameters::epsilon ( ) const

inline

◆ get_tag()

std::string madness::PCMParameters::get_tag ( ) const

inlineoverridevirtual

Implements madness::QCCalculationParametersBase.

References tag.

◆ min_radius()

double madness::PCMParameters::min_radius ( ) const

inline

◆ probe_radius()

double madness::PCMParameters::probe_radius ( ) const

inline

◆ radii_set()

std::string madness::PCMParameters::radii_set ( ) const

inline

◆ reader_own()

bool madness::PCMParameters::reader_own ( ) const

inline

whether PCMSolver should read its own input file instead of our parameters

Set from pcm_data pcmsolver_reader_own in the dft group; not a key of this group, because in that mode none of the keys below are consulted.

References reader_own_.

◆ restart_name()

std::string madness::PCMParameters::restart_name ( ) const

inline

Referenced by set_derived_values().

◆ scaling()

bool madness::PCMParameters::scaling ( ) const

inline

◆ set_derived_values()

void madness::PCMParameters::set_derived_values ( const CalculationParameters & cparam )

adopt the solvent named by the dft group's pcm_data, derive from it, validate

The solvent is set as a derived value, so an explicit solvent in the pcm group wins; epsilon and probe_radius are then derived from the solvent in turn, and only stand as given for solvent explicit. Validation that allowed_values cannot express – buffer capacities and cross-key consistency – happens here, as OEP_Parameters does for its density thresholds.

References correction(), MADNESS_CHECK, MADNESS_EXCEPTION, max_solvent_name_length, madness::CalculationParameters::pcm_data(), madness::print(), reader_own_, restart_name(), solvent(), solvent_data(), and solver_type().

Referenced by madness::SCF::SCF().

◆ solvent()

std::string madness::PCMParameters::solvent ( ) const

inline

Referenced by set_derived_values().

◆ solvent_data()

const std::map< std::string, std::pair< double, double > > & madness::PCMParameters::solvent_data ( )

static

the solvents PCMSolver tabulates

Maps the canonical name to {static permittivity, probe radius / Angstrom}; values from PCMSolver's src/utils/Solvent.cpp. Two uses: deriving epsilon and probe_radius from solvent, and spelling out the solvent explicit equivalent for the names that do not fit PCMInput::solvent.

Referenced by set_derived_values().

◆ solver_type()

std::string madness::PCMParameters::solver_type ( ) const

inline

Referenced by set_derived_values().

Member Data Documentation

◆ max_solvent_name_length

constexpr std::size_t madness::PCMParameters::max_solvent_name_length = 15

staticconstexpr

longest solvent name PCMInput::solvent (char[16]) can hold with its NUL

Referenced by set_derived_values().

◆ reader_own_

bool madness::PCMParameters::reader_own_ = false

private

Referenced by reader_own(), and set_derived_values().

◆ tag

constexpr char const* madness::PCMParameters::tag = "pcm"

staticconstexpr

Referenced by PCMParameters(), and get_tag().

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

pcm.h
pcm.cc

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PCMParameters() [1/2]

◆ PCMParameters() [2/2]

Member Function Documentation

◆ area()

◆ cavity_type()

◆ correction()

◆ epsilon()

◆ get_tag()

◆ min_radius()

◆ probe_radius()

◆ radii_set()

◆ reader_own()

◆ restart_name()

◆ scaling()

◆ set_derived_values()

◆ solvent()

◆ solvent_data()

◆ solver_type()

Member Data Documentation

◆ max_solvent_name_length

◆ reader_own_

◆ tag