thermochemistry.h File Reference

#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/real.h"

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Description

Code for computing entropy and heat capacity from eigenvalues.

Author

David van der Spoel david.nosp@m..van.nosp@m.dersp.nosp@m.oel@.nosp@m.icm.u.nosp@m.u.se

Classes
class	gmx::ArrayRef< typename >
	STL-like interface to a C array of T (or part of a std container of T). More...

Functions
double	eigenvalueToFrequency (double eigval)
	Convert eigenvalues which are input (such as from the Hessian) into the corresponding frequencies. More...
double	calcZeroPointEnergy (gmx::ArrayRef< const real > eigval, real scale_factor)
	Compute zero point energy from an array of eigenvalues. More...
double	calcVibrationalHeatCapacity (gmx::ArrayRef< const real > eigval, real temperature, bool linear, real scale_factor)
	Compute heat capacity due to vibrational motion. More...
double	calcTranslationalEntropy (real mass, real temperature, real pressure)
	Compute entropy due to translational motion. More...
double	calcRotationalEntropy (real temperature, int natom, bool linear, const rvec theta, real sigma_r)
	Compute entropy due to rotational motion. More...
double	calcVibrationalInternalEnergy (gmx::ArrayRef< const real > eigval, real temperature, bool linear, real scale_factor)
	Compute internal energy due to vibrational motion. More...
double	calcSchlitterEntropy (gmx::ArrayRef< const real > eigval, real temperature, bool linear)
	Compute entropy using Schlitter formula. More...
double	calcQuasiHarmonicEntropy (gmx::ArrayRef< const real > eigval, real temperature, bool linear, real scale_factor)
	Compute entropy using Quasi-Harmonic formula. More...

Function Documentation

double calcQuasiHarmonicEntropy	(	gmx::ArrayRef< const real >	eigval,
		real	temperature,
		bool	linear,
		real	scale_factor
	)

Compute entropy using Quasi-Harmonic formula.

Computes entropy for a molecule / molecular system using the Quasi-harmonic algorithm (Macromolecules 1984, 17, 1370). The input should be eigenvalues from a normal mode analysis. In both cases the units of the eigenvalues are those of energy.

Parameters

[in]	eigval	The eigenvalues
[in]	temperature	Temperature (K)
[in]	linear	True if this is a linear molecule (typically a diatomic molecule).
[in]	scale_factor	Factor to scale frequencies by before computing S0

Returns

the entropy (J/mol K)

double calcRotationalEntropy	(	real	temperature,
		int	natom,
		bool	linear,
		const rvec	theta,
		real	sigma_r
	)

Compute entropy due to rotational motion.

Following the equations in J. W. Ochterski, Thermochemistry in Gaussian, Gaussian, Inc., 2000 Pitssburg PA

Parameters

[in]	temperature	Temperature (K)
[in]	natom	Number of atoms
[in]	linear	TRUE if this is a linear molecule
[in]	theta	The principal moments of inertia (unit of Energy)
[in]	sigma_r	Symmetry factor, should be >= 1

Returns

The rotational entropy (J/mol K)

double calcSchlitterEntropy	(	gmx::ArrayRef< const real >	eigval,
		real	temperature,
		bool	linear
	)

Compute entropy using Schlitter formula.

Computes entropy for a molecule / molecular system using the algorithm due to Schlitter (Chem. Phys. Lett. 215 (1993) 617-621). The input should be eigenvalues from a covariance analysis, the units of the eigenvalues are those of energy.

Parameters

[in]	eigval	The eigenvalues
[in]	temperature	Temperature (K)
[in]	linear	True if this is a linear molecule (typically a diatomic molecule).

Returns

the entropy (J/mol K)

double calcTranslationalEntropy	(	real	mass,
		real	temperature,
		real	pressure
	)

Compute entropy due to translational motion.

Following the equations in J. W. Ochterski, Thermochemistry in Gaussian, Gaussian, Inc., 2000 Pitssburg PA

Parameters

[in]	mass	Molecular mass (Dalton)
[in]	temperature	Temperature (K)
[in]	pressure	Pressure (bar) at which to compute

Returns

The translational entropy (J/mol K)

double calcVibrationalHeatCapacity	(	gmx::ArrayRef< const real >	eigval,
		real	temperature,
		bool	linear,
		real	scale_factor
	)

Compute heat capacity due to vibrational motion.

Parameters

[in]	eigval	The eigenvalues
[in]	temperature	Temperature (K)
[in]	linear	TRUE if this is a linear molecule
[in]	scale_factor	Factor to scale frequencies by before computing cv

Returns

The heat capacity at constant volume (J/mol K)

double calcVibrationalInternalEnergy	(	gmx::ArrayRef< const real >	eigval,
		real	temperature,
		bool	linear,
		real	scale_factor
	)

Compute internal energy due to vibrational motion.

Parameters

[in]	eigval	The eigenvalues
[in]	temperature	Temperature (K)
[in]	linear	TRUE if this is a linear molecule
[in]	scale_factor	Factor to scale frequencies by before computing E

Returns

The internal energy (J/mol K)

double calcZeroPointEnergy	(	gmx::ArrayRef< const real >	eigval,
		real	scale_factor
	)

Compute zero point energy from an array of eigenvalues.

This routine first converts the eigenvalues from a normal mode analysis to frequencies and then computes the zero point energy.

Parameters

[in]	eigval	The eigenvalues
[in]	scale_factor	Factor to scale frequencies by before computing cv

Returns

The zero point energy (kJ/mol)

double eigenvalueToFrequency

(

double

eigval

)

Convert eigenvalues which are input (such as from the Hessian) into the corresponding frequencies.

This routine performs a unit scaling from GROMACS units into SI units, and extracts then computes the set of corresponding harmonic frequencies.

Parameters

[in]

eigval

A single eigenvalue, Units are kJ/(mol*nm*nm*amu)

Returns

The corresponding harmonics frequency (rads/sec)