src/gromacs/gmxana/thermochemistry.h

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  35 /*! \internal \file
  36  * \brief
  37  * Code for computing entropy and heat capacity from eigenvalues
  38  *
  39  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  40  */
  41 #ifndef GMXANA_THERMOCHEMISTRY_H
  42 #define GMXANA_THERMOCHEMISTRY_H
  43
  44 #include "gromacs/math/units.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/utility/basedefinitions.h"
  47
  48 namespace gmx
  49 {
  50 template<typename>
  51 class ArrayRef;
  52 }
  53
  54 /*! \brief Compute zero point energy from an array of eigenvalues.
  55  *
  56  * This routine first converts the eigenvalues from a normal mode
  57  * analysis to frequencies and then computes the zero point energy.
  58  *
  59  * \param[in] eigval       The eigenvalues
  60  * \param[in] scale_factor Factor to scale frequencies by before computing cv
  61  * \return The zero point energy (kJ/mol)
  62  */
  63 double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor);
  64
  65 /*! \brief Compute heat capacity due to vibrational motion
  66  *
  67  * \param[in] eigval       The eigenvalues
  68  * \param[in] temperature  Temperature (K)
  69  * \param[in] linear       TRUE if this is a linear molecule
  70  * \param[in] scale_factor Factor to scale frequencies by before computing cv
  71  * \return The heat capacity at constant volume (J/mol K)
  72  */
  73 double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval,
  74                                    real                      temperature,
  75                                    gmx_bool                  linear,
  76                                    real                      scale_factor);
  77
  78 /*! \brief Compute entropy due to translational motion
  79  *
  80  * Following the equations in J. W. Ochterski,
  81  * Thermochemistry in Gaussian, Gaussian, Inc., 2000
  82  * Pitssburg PA
  83  *
  84  * \param[in] mass         Molecular mass (Dalton)
  85  * \param[in] temperature  Temperature (K)
  86  * \param[in] pressure     Pressure (bar) at which to compute
  87  * \returns The translational entropy (J/mol K)
  88  */
  89 double calcTranslationalEntropy(real mass, real temperature, real pressure);
  90
  91 /*! \brief Compute entropy due to rotational motion
  92  *
  93  * Following the equations in J. W. Ochterski,
  94  * Thermochemistry in Gaussian, Gaussian, Inc., 2000
  95  * Pitssburg PA
  96  *
  97  * \param[in] temperature  Temperature (K)
  98  * \param[in] natom        Number of atoms
  99  * \param[in] linear       TRUE if this is a linear molecule
 100  * \param[in] theta        The principal moments of inertia (unit of Energy)
 101  * \param[in] sigma_r      Symmetry factor, should be >= 1
 102  * \returns The rotational entropy (J/mol K)
 103  */
 104 double calcRotationalEntropy(real temperature, int natom, gmx_bool linear, const rvec theta, real sigma_r);
 105
 106 /*! \brief Compute internal energy due to vibrational motion
 107  *
 108  * \param[in] eigval       The eigenvalues
 109  * \param[in] temperature  Temperature (K)
 110  * \param[in] linear       TRUE if this is a linear molecule
 111  * \param[in] scale_factor Factor to scale frequencies by before computing E
 112  * \return The internal energy (J/mol K)
 113  */
 114 double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval,
 115                                      real                      temperature,
 116                                      gmx_bool                  linear,
 117                                      real                      scale_factor);
 118
 119 /*! \brief Compute entropy using Schlitter formula
 120  *
 121  * Computes entropy for a molecule / molecular system using the
 122  * algorithm due to Schlitter (Chem. Phys. Lett. 215 (1993)
 123  * 617-621).
 124  * The input should be eigenvalues from a covariance analysis,
 125  * the units of the eigenvalues are those of energy.
 126  *
 127  * \param[in] eigval       The eigenvalues
 128  * \param[in] temperature  Temperature (K)
 129  * \param[in] linear       True if this is a linear molecule (typically a diatomic molecule).
 130  * \return the entropy (J/mol K)
 131  */
 132 double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear);
 133
 134 /*! \brief Compute entropy using Quasi-Harmonic formula
 135  *
 136  * Computes entropy for a molecule / molecular system using the
 137  * Quasi-harmonic algorithm (Macromolecules 1984, 17, 1370).
 138  * The input should be eigenvalues from a normal mode analysis.
 139  * In both cases the units of the eigenvalues are those of energy.
 140  *
 141  * \param[in] eigval       The eigenvalues
 142  * \param[in] temperature  Temperature (K)
 143  * \param[in] linear       True if this is a linear molecule (typically a diatomic molecule).
 144  * \param[in] scale_factor Factor to scale frequencies by before computing S0
 145  * \return the entropy (J/mol K)
 146  */
 147 double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor);
 148
 149 #endif