thermochemistry.h File Reference

#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.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

Functions
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, gmx_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, gmx_bool linear, const rvec theta, real sigma_r)
	Compute entropy due to rotational motion. More...
double	calcVibrationalInternalEnergy (gmx::ArrayRef< const real > eigval, real temperature, gmx_bool linear, real scale_factor)
	Compute internal energy due to vibrational motion. More...
double	calcSchlitterEntropy (gmx::ArrayRef< const real > eigval, real temperature, gmx_bool linear)
	Compute entropy using Schlitter formula. More...
double	calcQuasiHarmonicEntropy (gmx::ArrayRef< const real > eigval, real temperature, gmx_bool linear, real scale_factor)
	Compute entropy using Quasi-Harmonic formula. More...

Function Documentation

double calcQuasiHarmonicEntropy	(	gmx::ArrayRef< const real >	eigval,
		real	temperature,
		gmx_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,
		gmx_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,
		gmx_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,
		gmx_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,
		gmx_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)