chemmisol Namespace Reference

Namespaces
namespace	solver

Classes
class	AqueousSpecies
class	ChemicalComponent
class	ChemicalSpecies
struct	ChemicalSpeciesReagent
class	ChemicalSystem
struct	ComponentReagent
class	dH
class	EmptyReagents
class	FixedAqueousSpecies
class	FixedChemicalComponent
class	FixedChemicalSpecies
class	FixedMineralSpecies
class	H
class	Homotopy
class	InvalidMineralSpeciesWithUndefinedSitesCount
class	InvalidReaction
class	InvalidSpecies
class	MineralSpecies
class	MissingProducedSpeciesInReaction
class	Newton
class	Reaction
struct	Reagent
class	RegulaFalsi
class	Solvent
class	TooManyProducedSpeciesInReaction

Typedefs
template<typename T , std::size_t N>
using	X = std::array< T, N >
template<typename T , std::size_t N, std::size_t P = N>
using	M = std::array< std::array< T, P >, N >
template<typename T >
using	VecX = std::vector< T >
template<typename T >
using	VecM = std::vector< std::vector< T > >
template<typename X , typename M >
using	AbsoluteNewton = Newton< X, M, abs >

Enumerations
enum	Phase { SOLVENT , AQUEOUS , MINERAL }
enum	Category {   MASS , LENGTH , VOLUME , SURFACE ,   QUANTITY }

Functions
std::ostream &	operator<< (std::ostream &o, const Phase &phase)
el::Logger *	init_logger (const char *logger_id)
void	log_to_file (el::Logger *logger, const std::string &log_file, bool terminal_logging)
template<typename T >
std::list< std::complex< T > >	unit_roots (int n)
template<typename T >
std::list< std::complex< T > >	roots (const std::complex< T > &c, int n)
template<typename T , std::size_t N, std::size_t P>
X< T, N >	operator* (const M< T, N, P > &m, const X< T, P > &x)
template<typename T , std::size_t N>
X< T, N >	operator- (const X< T, N > &x)
template<typename T , std::size_t N>
X< T, N >	operator+ (const X< T, N > &x1, const X< T, N > &x2)
template<typename T , std::size_t N>
X< T, N >	operator* (const T &a, const X< T, N > &x)
template<typename T , std::size_t N, std::size_t P>
M< T, N, P >	operator* (const T &a, const M< T, N, P > &m)
template<typename T , std::size_t N>
double	norm (const X< T, N > &x)
template<typename T , std::size_t N>
double	norm (const X< std::complex< T >, N > &x)
template<typename T , std::size_t N>
X< T, N >	abs (const X< T, N > &x)
template<typename _M >
M< typename _M::value_type::value_type, std::tuple_size< _M >::value, std::tuple_size< typename _M::value_type >::value+1 >	augment (const _M &m, const X< typename _M::value_type::value_type, std::tuple_size< _M >::value > &x)
template<typename T , std::size_t N>
std::ostream &	operator<< (std::ostream &o, const X< T, N > &x)
template<typename T >
VecX< T >	operator* (const VecM< T > &m, const VecX< T > &x)
template<typename T >
VecX< T >	operator- (const VecX< T > &x)
template<typename T >
VecX< T >	operator+ (const VecX< T > &x1, const VecX< T > &x2)
template<typename T >
double	norm (const VecX< T > &x)
template<typename T >
VecX< T >	abs (const VecX< T > &x)
template<typename T >
VecM< T >	augment (const VecM< T > &m, const VecX< T > &x)
template<typename T >
std::ostream &	operator<< (std::ostream &o, const VecX< T > &x)
template<typename T >
double	norm (const T &x)
template<typename T >
T	abs (const T &x)
template<typename T >
T	identity (const T &x)

Variables
el::Logger *	core_logger
constexpr double	pi = 3.141592653589793238462643383279502884
const double	NA

Detailed Description

Main Chemmisol namespace.

Typedef Documentation

X

template<typename T , std::size_t N>

using chemmisol::X = typedef std::array<T, N>

Vector type hosted by a fixed size std::array.

M

template<typename T , std::size_t N, std::size_t P = N>

using chemmisol::M = typedef std::array<std::array<T, P>, N>

Matrix type hosted by a fixed size std::array.

The matrix contains N rows and P columns.

VecX

template<typename T >

using chemmisol::VecX = typedef std::vector<T>

Vector type hosted by a dynamic size std::vector.

VecM

template<typename T >

using chemmisol::VecM = typedef std::vector<std::vector<T> >

Matrix type hosted by a dynamic size std::vector.

AbsoluteNewton

template<typename X , typename M >

using chemmisol::AbsoluteNewton = typedef Newton<X, M, abs>

Implements the absolute Newton-Raphson method, where the absolute value of x_n+1 is taken as the result of each iteration.

This variant is particularly suitable for chemical equilibrium solving, since it guarantees that x_n+1, that represents activity of species, is always positive.

Moreover, the absolute Newton-Raphson method has proven to have a much larger basin of attraction than the classical Newton-Raphson method [1].

[1] K. Meintjes and A. P. Morgan, “A methodology for solving chemical equilibrium systems,” Applied Mathematics and Computation, vol. 22, no. 4, pp. 333–361, Jun. 1987, doi: 10.1016/0096-3003(87)90076-2.

Enumeration Type Documentation

Phase

enum chemmisol::Phase

Possible phases of a chemical species.

Category

enum chemmisol::Category

Describes the category of each unit.

Function Documentation

operator<<() [1/3]

std::ostream & chemmisol::operator<<	(	std::ostream &	o,
		const Phase &	phase
	)

Phases stream output operator.

init_logger()

el::Logger * chemmisol::init_logger

(

const char *

logger_id

)

Initializes and configures a chemmisol logger with the specified ID.

The method is notably used to initialize the chemmisol::core_logger with the CHEM_CORE_LOGID, but can be used to define other loggers with the same configuration ad the chemmisol::core_logger.

Parameters

logger_id

ID of the logger, used in Easylogging++ CLOG() and CVLOG() macros.

Returns

Initialized and configured logger.

log_to_file()

void chemmisol::log_to_file	(	el::Logger *	logger,
		const std::string &	log_file,
		bool	terminal_logging
	)

Configures the specified logger to output to the specified log file. Logging to std::cout can also be disabled thanks to the terminal_logging argument.

Any Easylogging++ logger can be configured this way, including the chemmisol::core_logger or any logger initialized with init_logger().

Parameters

logger	Logger to output to a file.
log_file	Full path to the log file.
terminal_logging	Set to false to disable std::cout logging.

operator*() [1/2]

template<typename T , std::size_t N, std::size_t P>

X< T, N > chemmisol::operator*	(	const M< T, N, P > &	m,
		const X< T, P > &	x
	)

Computes m*x as a matrix multiplication.

Parameters

m	Matrix of size N*P.
x	Vector of size P.

Returns

Vector of size N.

operator-() [1/2]

template<typename T , std::size_t N>

X< T, N > chemmisol::operator-

(

const X< T, N > &

x

)

Computes -x = [-x_0, ..., -x_N-1].

Parameters

x	Vector of size N.

Returns

Vector of size N.

operator+() [1/2]

template<typename T , std::size_t N>

X< T, N > chemmisol::operator+	(	const X< T, N > &	x1,
		const X< T, N > &	x2
	)

Computes x1+x2 = [x1_0+x2_0, ..., x1_N-1 + x2_N-1].

Parameters

x1	Vector of size N.
x2	Vector of size N.

Returns

Vector of size N.

norm() [1/3]

template<typename T , std::size_t N>

double chemmisol::norm

(

const X< T, N > &

x

)

Computes the euclidean norm of the vector.

abs() [1/3]

template<typename T , std::size_t N>

X< T, N > chemmisol::abs

(

const X< T, N > &

x

)

Computes the absolute value the vector.

augment() [1/2]

template<typename _M >

M< typename _M::value_type::value_type, std::tuple_size< _M >::value, std::tuple_size< typename _M::value_type >::value+1 > chemmisol::augment	(	const _M &	m,
		const X< typename _M::value_type::value_type, std::tuple_size< _M >::value > &	x
	)

Implements the augment operation used by the Gaussian elimination algortihm for fixed size matrices and vectors.

Returns a new matrix corresponding to the concatenation of m and x, where x represents the last column of the new matrix.

Parameters

m	Matrix of size N*P.
x	Vector of size N.

Returns

Matrix of size N*(P+1).

Template Parameters

_M	Fixed size matrix type.

operator<<() [2/3]

template<typename T , std::size_t N>

std::ostream & chemmisol::operator<<	(	std::ostream &	o,
		const X< T, N > &	x
	)

Fixed size vector stream output operator.

The vector is serialized as "[x0, ..., xn]".

operator*() [2/2]

template<typename T >

VecX< T > chemmisol::operator*	(	const VecM< T > &	m,
		const VecX< T > &	x
	)

Computes m*x as a matrix multiplication.

Parameters

m	Matrix of size N*P.
x	Vector of size P.

Returns

Vector of size N.

operator-() [2/2]

template<typename T >

VecX< T > chemmisol::operator-

(

const VecX< T > &

x

)

Computes -x = [-x_0, ..., -x_N-1].

Parameters

x	Vector of size N.

Returns

Vector of size N.

operator+() [2/2]

template<typename T >

VecX< T > chemmisol::operator+	(	const VecX< T > &	x1,
		const VecX< T > &	x2
	)

Computes x1+x2 = [x1_0+x2_0, ..., x1_N-1 + x2_N-1].

The behavior is unspecified if x1 and x2 are not the same size.

Parameters

x1	Vector of size N.
x2	Vector of size N.

Returns

Vector of size N.

norm() [2/3]

template<typename T >

double chemmisol::norm

(

const VecX< T > &

x

)

Computes the euclidean norm of the vector.

abs() [2/3]

template<typename T >

VecX< T > chemmisol::abs

(

const VecX< T > &

x

)

Computes the absolute value the vector.

augment() [2/2]

template<typename T >

VecM< T > chemmisol::augment	(	const VecM< T > &	m,
		const VecX< T > &	x
	)

Implements the augment operation used by the Gaussian elimination algortihm for dynamic size matrices and vectors.

Returns a new matrix corresponding to the concatenation of m and x, where x represents the last column of the new matrix.

The behavior is unspecified if the size of x is not equal to the count of rows in m.

Parameters

m	Matrix of size N*P.
x	Vector of size N.

Returns

Matrix of size N*(P+1).

operator<<() [3/3]

template<typename T >

std::ostream & chemmisol::operator<<	(	std::ostream &	o,
		const VecX< T > &	x
	)

Dynamic size vector stream output operator.

The vector is serialized as "[x0, ..., xn]".

norm() [3/3]

template<typename T >

double chemmisol::norm

(

const T &

x

)

Returns the norm of the scalar value x, i.e. its absolute value.

abs() [3/3]

template<typename T >

T chemmisol::abs

(

const T &

x

)

Returns the absolute value of the scalar value x.

identity()

template<typename T >

T chemmisol::identity

(

const T &

x

)

Identity method, that returns x itself.

Variable Documentation

core_logger

el::Logger* chemmisol::core_logger

extern

Pointer to the Easylogging++ Logger used internally by the chemmisol library.

NA

const double chemmisol::NA

extern

The Avogadro constant.