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thermochemistry.h File Reference
#include "gromacs/math/units.h"
#include "gromacs/math/vec.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 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]eigvalThe eigenvalues
[in]temperatureTemperature (K)
[in]linearTrue if this is a linear molecule (typically a diatomic molecule).
[in]scale_factorFactor 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]temperatureTemperature (K)
[in]natomNumber of atoms
[in]linearTRUE if this is a linear molecule
[in]thetaThe principal moments of inertia (unit of Energy)
[in]sigma_rSymmetry 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]eigvalThe eigenvalues
[in]temperatureTemperature (K)
[in]linearTrue 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]massMolecular mass (Dalton)
[in]temperatureTemperature (K)
[in]pressurePressure (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]eigvalThe eigenvalues
[in]temperatureTemperature (K)
[in]linearTRUE if this is a linear molecule
[in]scale_factorFactor 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]eigvalThe eigenvalues
[in]temperatureTemperature (K)
[in]linearTRUE if this is a linear molecule
[in]scale_factorFactor 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]eigvalThe eigenvalues
[in]scale_factorFactor to scale frequencies by before computing cv
Returns
The zero point energy (kJ/mol)