#include <ConfigIONovelty.hh>

Inheritance diagram for CASM::ConfigIO::Novelty:

Detailed Description

A DatumFormatter class to measure the 'novelty' of a configuration with respect to a population of configurations Larger numbers indicate a more novel configuration, and a very large number (>~100) indicates a configuration that is linearly independent from the population (in terms of its correlations)

The novelty is based on the Mahalanobis distance. Given a population of correlations, indexed by 'i' and basis functions, indexed by 'j', that depend on the DoFs of those configurations, we define a correlation matrix

corr_mat(i,j) = <function 'j' evaluated in configuration 'i'>

and an average correlation, 'avg_corr', which is taken by averaging over the rows of corr_mat

The covariance of the correlations is given as

covar = corr_mat.transpose()*corr_mat/Nconfig - avg_corr.transpose()*avg_corr

The Mahalanobis distance, 'M', for a particular correlation vector, 'C' (which corresponds to a particular correlation) is

M = sqrt( (C-avg_corr) * inv(covar) * (C-avg_corr).transpose() )

We call inv(covar) the 'Gram matrix', which is conventional terminology for scalar products.

We use a slightly different definition for the novelty measure, 'N', which is

N = sqrt( (C-avg_corr) * inv(covar+epsilon*identity) * (C-avg_corr).transpose() / Ncorr )

Which is regularized by adding a small matrix (epsilon*identity, where epsilon is ~1e-5/Ncorr) and divided by Ncorr, in order to get a number that does not depend strongly on the number of basis functions in the basis set

Definition at line 42 of file ConfigIONovelty.hh.

Public Types
enum	FormatterType

typedef DataObject	DataObject

typedef long	difference_type

typedef DataFormatterDictionary < DataObject, BaseDatumFormatter< DataObject > >	DictType

Public Member Functions
	Novelty ()

std::unique_ptr< Novelty >	clone () const

double	evaluate (const Configuration &_config) const override

void	init (const Configuration &_tmplt) const override

std::string	short_header (const Configuration &_config) const override

bool	parse_args (const std::string &args) override

virtual ValueType	operator() (const DataObject &obj) const
	Return requested data from obj, throwing std::runtime_error if not valid. More...

virtual ValueType	evaluate (const DataObject &obj) const =0

virtual void	inject (const DataObject &_data_obj, DataStream &_stream, Index pass_index=0) const override
	Default implementation injects each element, via operator<<. More...

virtual void	print (const DataObject &_data_obj, std::ostream &_stream, Index pass_index=0) const override
	Default implementation prints each element in a column, via operator<<. More...

virtual jsonParser &	to_json (const DataObject &_data_obj, jsonParser &json) const override
	Default implementation calls jsonParser& to_json(const ValueType&, jsonParser&) More...

const std::string &	name () const
	Returns a name for the formatter, which becomes the tag used for parsing. More...

const std::string &	description () const
	Returns a short description of the formatter and its allowed arguments (if any). This description is used to automatically generate help screens. More...

virtual FormatterType	type () const

const DictType &	home () const
	const Access the dictionary containing this formatter, set during DictType::lookup More...

void	set_home (const DictType &home) const
	Set the dictionary containing this formatter, set during DictType::lookup. More...

virtual void	init (const DataObject &_template_obj) const

virtual bool	validate (const DataObject &_data_obj) const
	Returns true if _data_obj has valid values for requested data. More...

virtual std::vector< std::string >	col_header (const DataObject &_template_obj) const
	Returns a header string for each scalar produced by the formatter parsing the entries in the col_header should reproduce the exact query described by the formatter. Ex: "clex(formation_energy)" or "comp(a)", "comp(c)". More...

virtual std::string	long_header (const DataObject &_template_obj) const
	Returns a long expression for each scalar produced by the formatter parsing the long_header should reproduce the exact query described by the formatter Ex: "clex(formation_energy)" or "comp(a) comp(c)". More...

virtual std::string	short_header (const DataObject &_template_obj) const
	Returns a short expression for the formatter parsing the short_header should allow the formatter to be recreated (but the short header does not specify a subset of the elements) Ex: "clex(formation_energy)" or "comp". More...

virtual Index	num_passes (const DataObject &_data_obj) const

Protected Types
typedef multivector< Index > ::X< 2 >	IndexContainer

Protected Member Functions
void	_parse_index_expression (const std::string &_expr)

void	_add_rule (const std::vector< Index > &new_rule) const

const IndexContainer &	_index_rules () const

Private Member Functions
Novelty *	_clone () const override
	Clone. More...

Private Attributes
std::string	m_selection
	specifies which selection to use as the population More...

Eigen::MatrixXd	m_gram_mat
	Gram matrix, which defind Mahalanobis scalar product. More...

Eigen::VectorXd	m_avg_corr
	The average correlation vector of the population. More...

DataFormatter< Configuration >	m_format
	Formatter which is used to obtain correlations. More...

Member Typedef Documentation

typedef DataObject CASM::BaseDatumFormatter< DataObject >::DataObject

inherited

Definition at line 313 of file DataFormatter.hh.

typedef DataFormatterDictionary<DataObject, BaseDatumFormatter<DataObject> > CASM::BaseDatumFormatter< DataObject >::DictType

inherited

Definition at line 316 of file DataFormatter.hh.

typedef long CASM::BaseDatumFormatter< DataObject >::difference_type

inherited

Definition at line 315 of file DataFormatter.hh.

typedef multivector<Index>::X<2> CASM::BaseDatumFormatter< DataObject >::IndexContainer

protectedinherited

Definition at line 435 of file DataFormatter.hh.

Member Enumeration Documentation

enum CASM::BaseDatumFormatter::FormatterType

inherited

Definition at line 314 of file DataFormatter.hh.

Constructor & Destructor Documentation

CASM::ConfigIO::Novelty::Novelty ( )

inline

Definition at line 46 of file ConfigIONovelty.hh.

Member Function Documentation

void CASM::BaseDatumFormatter< DataObject >::_add_rule ( const std::vector< Index > & new_rule ) const

inlineprotectedinherited

Definition at line 447 of file DataFormatter.hh.

Novelty* CASM::ConfigIO::Novelty::_clone ( ) const

inlineoverrideprivatevirtual

Clone.

Implements CASM::BaseValueFormatter< ValueType, DataObject >.

Definition at line 76 of file ConfigIONovelty.hh.

const IndexContainer& CASM::BaseDatumFormatter< DataObject >::_index_rules ( ) const

inlineprotectedinherited

Definition at line 451 of file DataFormatter.hh.

void CASM::BaseDatumFormatter< DataObject >::_parse_index_expression ( const std::string & _expr )

protectedinherited

Derived DatumFormatters have some optional functionality for parsing index expressions in order to make it easy to handle ranges such as:

formatter_name(3,4:8)

in which case, DerivedDatumFormatter::parse_args() is called with the string "3,4:8" by dispatching that string to BaseDatumFormatter::_parse_index_expression(), m_index_rules will be populated with {{3,4},{3,5},{3,6},{3,7},{3,8}}

std::unique_ptr<Novelty> CASM::ConfigIO::Novelty::clone ( ) const

inline

Definition at line 52 of file ConfigIONovelty.hh.

virtual std::vector<std::string> CASM::BaseDatumFormatter< DataObject >::col_header ( const DataObject & _template_obj ) const

inlinevirtualinherited

Returns a header string for each scalar produced by the formatter parsing the entries in the col_header should reproduce the exact query described by the formatter. Ex: "clex(formation_energy)" or "comp(a)", "comp(c)".

Default uses col_header

Reimplemented in CASM::Base1DDatumFormatter< Container, DataObject >, and CASM::DatumFormatterAlias< DataObject >.

Definition at line 373 of file DataFormatter.hh.

const std::string& CASM::BaseDatumFormatter< DataObject >::description ( ) const

inlineinherited

Returns a short description of the formatter and its allowed arguments (if any). This description is used to automatically generate help screens.

Definition at line 332 of file DataFormatter.hh.

double CASM::ConfigIO::Novelty::evaluate ( const Configuration & _config ) const

override

Definition at line 80 of file ConfigIONovelty.cc.

template<typename ValueType, typename DataObject>

virtual ValueType CASM::BaseValueFormatter< ValueType, DataObject >::evaluate ( const DataObject & obj ) const

pure virtualinherited

Implemented in CASM::Generic1DDatumFormatter< Container, DataObject >, CASM::GenericDatumFormatter< ValueType, DataObject >, CASM::ConfigIO::ClexHullDist, CASM::ConfigIO::OnClexHull, CASM::ConfigIO::HullDist, and CASM::ConfigIO::OnHull.

const DictType& CASM::BaseDatumFormatter< DataObject >::home ( ) const

inlineinherited

const Access the dictionary containing this formatter, set during DictType::lookup

Definition at line 341 of file DataFormatter.hh.

void CASM::ConfigIO::Novelty::init ( const Configuration & _tmplt ) const

override

Definition at line 12 of file ConfigIONovelty.cc.

virtual void CASM::BaseDatumFormatter< DataObject >::init ( const DataObject & _template_obj ) const

inlinevirtualinherited

Reimplemented in CASM::Base1DDatumFormatter< Container, DataObject >, and CASM::DatumFormatterAlias< DataObject >.

Definition at line 356 of file DataFormatter.hh.

template<typename ValueType, typename DataObject>

virtual void CASM::BaseValueFormatter< ValueType, DataObject >::inject	(	const DataObject &	_data_obj,
		DataStream &	_stream,
		Index	pass_index = `0`
	)		const

inlineoverridevirtualinherited

Default implementation injects each element, via operator<<.

sets DataStream::failbit if validation fails

Implements CASM::BaseDatumFormatter< DataObject >.

Reimplemented in CASM::Base1DDatumFormatter< Container, DataObject >.

Definition at line 747 of file DataFormatterTools.hh.

virtual std::string CASM::BaseDatumFormatter< DataObject >::long_header ( const DataObject & _template_obj ) const

inlinevirtualinherited

Returns a long expression for each scalar produced by the formatter parsing the long_header should reproduce the exact query described by the formatter Ex: "clex(formation_energy)" or "comp(a) comp(c)".

Default uses col_header

Definition at line 382 of file DataFormatter.hh.

const std::string& CASM::BaseDatumFormatter< DataObject >::name ( ) const

inlineinherited

Returns a name for the formatter, which becomes the tag used for parsing.

Definition at line 326 of file DataFormatter.hh.

virtual Index CASM::BaseDatumFormatter< DataObject >::num_passes ( const DataObject & _data_obj ) const

inlinevirtualinherited

If data must be printed on multiple rows, returns number of rows needed to output all data from _data_obj DataFormatter class will subsequently pass over _data_obj multiple times to complete printing (if necessary)

Reimplemented in CASM::DatumFormatterAlias< DataObject >.

Definition at line 406 of file DataFormatter.hh.

template<typename ValueType, typename DataObject>

virtual ValueType CASM::BaseValueFormatter< ValueType, DataObject >::operator() ( const DataObject & obj ) const

inlinevirtualinherited

Return requested data from obj, throwing std::runtime_error if not valid.

Definition at line 729 of file DataFormatterTools.hh.

bool CASM::ConfigIO::Novelty::parse_args ( const std::string & args )

overridevirtual

If DatumFormatter accepts arguments, parse them here. Arguments are assumed to be passed from the command line via: formattername(argument1,argument2,...)

from which DerivedDatumFormatter::parse_args() receives the string "argument1,argument2,..." Returns true if parse is successful, false if not (e.g., takes no arguments, already initialized, malformed input, etc).

Reimplemented from CASM::BaseDatumFormatter< DataObject >.

Definition at line 39 of file ConfigIONovelty.cc.

template<typename ValueType, typename DataObject>

virtual void CASM::BaseValueFormatter< ValueType, DataObject >::print	(	const DataObject &	_data_obj,
		std::ostream &	_stream,
		Index	pass_index = `0`
	)		const

inlineoverridevirtualinherited

Default implementation prints each element in a column, via operator<<.

Prints "unknown" if validation fails

Implements CASM::BaseDatumFormatter< DataObject >.

Reimplemented in CASM::Base1DDatumFormatter< Container, DataObject >.

Definition at line 757 of file DataFormatterTools.hh.

void CASM::BaseDatumFormatter< DataObject >::set_home ( const DictType & home ) const

inlineinherited

Set the dictionary containing this formatter, set during DictType::lookup.

Definition at line 346 of file DataFormatter.hh.

std::string CASM::ConfigIO::Novelty::short_header ( const Configuration & _config ) const

override

Definition at line 51 of file ConfigIONovelty.cc.

virtual std::string CASM::BaseDatumFormatter< DataObject >::short_header ( const DataObject & _template_obj ) const

inlinevirtualinherited

Returns a short expression for the formatter parsing the short_header should allow the formatter to be recreated (but the short header does not specify a subset of the elements) Ex: "clex(formation_energy)" or "comp".

Reimplemented in CASM::DatumFormatterAlias< DataObject >, and CASM::DataFormatterOperator< ValueType, ArgType, DataObject >.

Definition at line 400 of file DataFormatter.hh.

template<typename ValueType, typename DataObject>

virtual jsonParser& CASM::BaseValueFormatter< ValueType, DataObject >::to_json	(	const DataObject &	_data_obj,
		jsonParser &	json
	)		const

inlineoverridevirtualinherited

Default implementation calls jsonParser& to_json(const ValueType&, jsonParser&)

Does nothing if validation fails

Implements CASM::BaseDatumFormatter< DataObject >.

Definition at line 769 of file DataFormatterTools.hh.

virtual FormatterType CASM::BaseDatumFormatter< DataObject >::type ( ) const

inlinevirtualinherited

Reimplemented in CASM::DatumFormatterAlias< DataObject >, and CASM::DataFormatterOperator< ValueType, ArgType, DataObject >.

Definition at line 336 of file DataFormatter.hh.

virtual bool CASM::BaseDatumFormatter< DataObject >::validate ( const DataObject & _data_obj ) const

inlinevirtualinherited

Returns true if _data_obj has valid values for requested data.

Default implementation always returns true

Reimplemented in CASM::Generic1DDatumFormatter< Container, DataObject >, CASM::GenericDatumFormatter< ValueType, DataObject >, CASM::DatumFormatterAlias< DataObject >, and CASM::DataFormatterOperator< ValueType, ArgType, DataObject >.

Definition at line 363 of file DataFormatter.hh.

Member Data Documentation

Eigen::VectorXd CASM::ConfigIO::Novelty::m_avg_corr

mutableprivate

The average correlation vector of the population.

Definition at line 87 of file ConfigIONovelty.hh.

DataFormatter<Configuration> CASM::ConfigIO::Novelty::m_format

mutableprivate

Formatter which is used to obtain correlations.

Definition at line 90 of file ConfigIONovelty.hh.

Eigen::MatrixXd CASM::ConfigIO::Novelty::m_gram_mat

mutableprivate

Gram matrix, which defind Mahalanobis scalar product.

Definition at line 84 of file ConfigIONovelty.hh.

std::string CASM::ConfigIO::Novelty::m_selection

mutableprivate

specifies which selection to use as the population

Definition at line 81 of file ConfigIONovelty.hh.

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

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clex/ConfigIONovelty.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/clex/ConfigIONovelty.cc

Detailed Description

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation