Heed::MoleculeDef Class Reference

#include <MoleculeDef.h>

Inheritance diagram for Heed::MoleculeDef:

Public Member Functions
const std::string &	name () const
const std::string &	notation () const
const std::vector< long > &	qatom_ps () const
long	qatom_ps (long n) const
long	Z_total () const
double	A_total () const
long	tqatom () const
const std::shared_ptr< VanDerWaals > &	vdw () const
	MoleculeDef ()
	MoleculeDef (const std::string &fname, const std::string &fnotation, long fqatom, const std::vector< std::string > &fatom_not, const std::vector< long > &fqatom_ps, std::shared_ptr< VanDerWaals > fvdw={})
	MoleculeDef (const std::string &fname, const std::string &fnotation, const std::string &fatom_not, long fqatom_ps, std::shared_ptr< VanDerWaals > fvdw={})
	MoleculeDef (const std::string &fname, const std::string &fnotation, const std::string &fatom_not1, long fqatom_ps1, const std::string &fatom_not2, long fqatom_ps2, std::shared_ptr< VanDerWaals > fvdw={})
	MoleculeDef (const std::string &fname, const std::string &fnotation, const std::string &fatom_not1, long fqatom_ps1, const std::string &fatom_not2, long fqatom_ps2, const std::string &fatom_not3, long fqatom_ps3, std::shared_ptr< VanDerWaals > fvdw={})
	~MoleculeDef ()
void	print (std::ostream &file, int l) const
void	verify ()
	Check that there is no molecule with the same name in the container.
MoleculeDef *	copy () const
Public Member Functions inherited from Heed::AtomMixDef
	AtomMixDef ()=default
	Default constructor.
	AtomMixDef (unsigned long fqatom, const std::vector< std::string > &fatom_not, const std::vector< double > &fweight_quan)
	AtomMixDef (unsigned long fqatom, const std::vector< std::string > &fatom_not, const std::vector< long > &fweight_quan)
	AtomMixDef (const std::string &fatom_not)
	AtomMixDef (const std::string &fatom_not1, double fweight_quan1, const std::string &fatom_not2, double fweight_quan2)
	AtomMixDef (const std::string &fatom_not1, double fweight_quan1, const std::string &fatom_not2, double fweight_quan2, const std::string &fatom_not3, double fweight_quan3)
	AtomMixDef (const std::string &fatom_not1, double fweight_quan1, const std::string &fatom_not2, double fweight_quan2, const std::string &fatom_not3, double fweight_quan3, const std::string &fatom_not4, double fweight_quan4)
void	print (std::ostream &file, int l) const
long	qatom () const
const std::vector< AtomDef * > &	atom () const
AtomDef *	atom (long n) const
const std::vector< double > &	weight_quan () const
const std::vector< double > &	weight_mass () const
double	weight_quan (long n) const
double	weight_mass (long n) const
double	Z_mean () const
double	A_mean () const
double	inv_A_mean () const
double	mean_ratio_Z_to_A () const
double	NumberOfElectronsInGram () const

Static Public Member Functions
static void	printall (std::ostream &file)
static std::list< MoleculeDef * > &	get_logbook ()
static const std::list< MoleculeDef * > &	get_const_logbook ()
static MoleculeDef *	get_MoleculeDef (const std::string &fnotation)

Detailed Description

Definition of molecule as a mixture of atoms. Only the basic information: the name, the notation, the mean charge and atomic weight and the parameters of mixture class.

The principle of definitions of matters is the same as for atoms: a dictionary or a database. See details there. But the logbook is different, of course.

1998-2004 I. Smirnov

Definition at line 50 of file MoleculeDef.h.

Constructor & Destructor Documentation

MoleculeDef() [1/5]

Heed::MoleculeDef::MoleculeDef

(

)

Definition at line 62 of file MoleculeDef.cpp.

                         {
  MoleculeDef::get_logbook().push_back(this);
}

Referenced by copy().

MoleculeDef() [2/5]

Heed::MoleculeDef::MoleculeDef	(	const std::string &	fname,
		const std::string &	fnotation,
		long	fqatom,
		const std::vector< std::string > &	fatom_not,
		const std::vector< long > &	fqatom_ps,
		std::shared_ptr< VanDerWaals >	fvdw = {}
	)

Definition at line 66 of file MoleculeDef.cpp.

    : AtomMixDef(fqatom, fatom_not, fqatom_ps),
      nameh(fname),
      notationh(fnotation),
      qatom_psh(fqatom_ps) {
  mfunname("MoleculeDef::MoleculeDef(...)");
  m_vdw = std::move(fvdw);
  for (long n = 0; n < qatom(); n++) {
    Z_totalh += qatom_psh[n] * atom(n)->Z();
    A_totalh += qatom_psh[n] * atom(n)->A();
    tqatomh += qatom_psh[n];
    check_econd11(qatom_psh[n], <= 0, mcerr);
  }
  verify();
  MoleculeDef::get_logbook().push_back(this);
}

MoleculeDef() [3/5]

Heed::MoleculeDef::MoleculeDef	(	const std::string &	fname,
		const std::string &	fnotation,
		const std::string &	fatom_not,
		long	fqatom_ps,
		std::shared_ptr< VanDerWaals >	fvdw = {}
	)

Definition at line 87 of file MoleculeDef.cpp.

    : AtomMixDef(fatom_not),
      nameh(fname),
      notationh(fnotation),
      qatom_psh(1, fqatom_ps),
      tqatomh(fqatom_ps) {
  mfunname("MoleculeDef::MoleculeDef(...)");
  m_vdw = std::move(fvdw);
  Z_totalh = atom(0)->Z() * fqatom_ps;
  A_totalh = atom(0)->A() * fqatom_ps;
  verify();
  MoleculeDef::get_logbook().push_back(this);
}

MoleculeDef() [4/5]

Heed::MoleculeDef::MoleculeDef	(	const std::string &	fname,
		const std::string &	fnotation,
		const std::string &	fatom_not1,
		long	fqatom_ps1,
		const std::string &	fatom_not2,
		long	fqatom_ps2,
		std::shared_ptr< VanDerWaals >	fvdw = {}
	)

Definition at line 104 of file MoleculeDef.cpp.

    : AtomMixDef(fatom_not1, fqatom_ps1, fatom_not2, fqatom_ps2),
      nameh(fname),
      notationh(fnotation),
      qatom_psh(2) {
  mfunname("MoleculeDef::MoleculeDef(...)");
  m_vdw = std::move(fvdw);
  qatom_psh[0] = fqatom_ps1;
  qatom_psh[1] = fqatom_ps2;
  for (long n = 0; n < qatom(); n++) {
    check_econd11(qatom_psh[n], <= 0, mcerr);
    Z_totalh += qatom_psh[n] * atom(n)->Z();
    A_totalh += qatom_psh[n] * atom(n)->A();
    tqatomh += qatom_psh[n];
  }
  verify();
  MoleculeDef::get_logbook().push_back(this);
}

MoleculeDef() [5/5]

Heed::MoleculeDef::MoleculeDef	(	const std::string &	fname,
		const std::string &	fnotation,
		const std::string &	fatom_not1,
		long	fqatom_ps1,
		const std::string &	fatom_not2,
		long	fqatom_ps2,
		const std::string &	fatom_not3,
		long	fqatom_ps3,
		std::shared_ptr< VanDerWaals >	fvdw = {}
	)

Definition at line 127 of file MoleculeDef.cpp.

    : AtomMixDef(fatom_not1, fqatom_ps1, fatom_not2, fqatom_ps2, fatom_not3,
                 fqatom_ps3),
      nameh(fname),
      notationh(fnotation),
      qatom_psh(3) {
  mfunname("MoleculeDef::MoleculeDef(...)");
  m_vdw = std::move(fvdw);
  qatom_psh[0] = fqatom_ps1;
  qatom_psh[1] = fqatom_ps2;
  qatom_psh[2] = fqatom_ps3;
  for (long n = 0; n < qatom(); n++) {
    check_econd11(qatom_psh[n], <= 0, mcerr);
    Z_totalh += qatom_psh[n] * atom(n)->Z();
    A_totalh += qatom_psh[n] * atom(n)->A();
    tqatomh += qatom_psh[n];
  }
  verify();
  MoleculeDef::get_logbook().push_back(this);
}

~MoleculeDef()

Heed::MoleculeDef::~MoleculeDef

(

)

Definition at line 225 of file MoleculeDef.cpp.

{ MoleculeDef::get_logbook().remove(this); }

Member Function Documentation

A_total()

double Heed::MoleculeDef::A_total ( ) const

inline

Definition at line 71 of file MoleculeDef.h.

{ return A_totalh; }

Referenced by Heed::operator<<().

copy()

MoleculeDef * Heed::MoleculeDef::copy ( ) const

inline

Definition at line 106 of file MoleculeDef.h.

{ return new MoleculeDef(*this); }

get_const_logbook()

const std::list< MoleculeDef * > & Heed::MoleculeDef::get_const_logbook ( )

static

Initialize the logbook at the first request and keep it as internal static variable.

Definition at line 180 of file MoleculeDef.cpp.

                                                            {
  return MoleculeDef::get_logbook();
}

get_logbook()

std::list< MoleculeDef * > & Heed::MoleculeDef::get_logbook ( )

static

Definition at line 175 of file MoleculeDef.cpp.

                                                {
  static std::list<MoleculeDef*> logbook;
  return logbook;
}

Referenced by get_const_logbook(), get_MoleculeDef(), MoleculeDef(), printall(), verify(), and ~MoleculeDef().

get_MoleculeDef()

MoleculeDef * Heed::MoleculeDef::get_MoleculeDef ( const std::string &  fnotation )

static

Return the address of the molecule with this name. If there is no molecule with this notation, the function returns NULL but does not terminate the program as that for AtomDef. Be careful.

Definition at line 184 of file MoleculeDef.cpp.

                                                                    {
  for (auto molecule : MoleculeDef::get_logbook()) {
    if (molecule->notation() == fnotation) return molecule;
  }
  return nullptr;
}

Referenced by Heed::GasDef::GasDef().

name()

const std::string & Heed::MoleculeDef::name ( ) const

inline

Definition at line 66 of file MoleculeDef.h.

{ return nameh; }

Referenced by Heed::operator<<().

notation()

const std::string & Heed::MoleculeDef::notation ( ) const

inline

Definition at line 67 of file MoleculeDef.h.

{ return notationh; }

Referenced by Heed::operator<<().

print()

void Heed::MoleculeDef::print	(	std::ostream &	file,
		int	l
	)		const

Definition at line 152 of file MoleculeDef.cpp.

                                                     {
  if (l > 0) file << (*this);
}

printall()

void Heed::MoleculeDef::printall ( std::ostream &  file )

static

Definition at line 156 of file MoleculeDef.cpp.

                                           {
  Ifile << "MoleculeDef::printall:\n";
  for (auto molecule : MoleculeDef::get_logbook()) {
    file << molecule;
  }
}

qatom_ps() [1/2]

const std::vector< long > & Heed::MoleculeDef::qatom_ps ( ) const

inline

Definition at line 68 of file MoleculeDef.h.

{ return qatom_psh; }

Referenced by Heed::operator<<().

qatom_ps() [2/2]

long Heed::MoleculeDef::qatom_ps ( long  n ) const

inline

Definition at line 69 of file MoleculeDef.h.

{ return qatom_psh[n]; }

tqatom()

long Heed::MoleculeDef::tqatom ( ) const

inline

Definition at line 72 of file MoleculeDef.h.

{ return tqatomh; }

Referenced by Heed::operator<<().

vdw()

const std::shared_ptr< VanDerWaals > & Heed::MoleculeDef::vdw ( ) const

inline

Definition at line 73 of file MoleculeDef.h.

{ return m_vdw; }

Referenced by Heed::operator<<().

verify()

void Heed::MoleculeDef::verify

(

)

Check that there is no molecule with the same name in the container.

Definition at line 163 of file MoleculeDef.cpp.

                         {
  mfunnamep("void MoleculeDef::verify()");
  if (nameh == "none" && notationh == "none") return;
  for (auto molecule : MoleculeDef::get_logbook()) {
    if (molecule->nameh != nameh && molecule->notationh != notationh) continue;
    funnw.ehdr(mcerr);
    mcerr << "cannot initialize two molecules with the same name or notation\n";
    mcerr << "name=" << nameh << " notation=" << notationh << '\n';
    spexit(mcerr);
  }
}

Referenced by MoleculeDef().

Z_total()

long Heed::MoleculeDef::Z_total ( ) const

inline

Definition at line 70 of file MoleculeDef.h.

{ return Z_totalh; }

Referenced by Heed::operator<<().

---

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

• MoleculeDef.h
• MoleculeDef.cpp