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/arrayref.h"
  47 #include "gromacs/utility/basedefinitions.h"
  48
  49 /*! \brief Compute zero point energy from an array of eigenvalues.
  50  *
  51  * This routine first converts the eigenvalues from a normal mode
  52  * analysis to frequencies and then computes the zero point energy.
  53  *
  54  * \param[in] eigval       The eigenvalues
  55  * \param[in] scale_factor Factor to scale frequencies by before computing cv
  56  * \return The zero point energy (kJ/mol)
  57  */
  58 double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval,
  59                            real                      scale_factor);
  60
  61 /*! \brief Compute heat capacity due to vibrational motion
  62  *
  63  * \param[in] eigval       The eigenvalues
  64  * \param[in] temperature  Temperature (K)
  65  * \param[in] linear       TRUE if this is a linear molecule
  66  * \param[in] scale_factor Factor to scale frequencies by before computing cv
  67  * \return The heat capacity at constant volume (J/mol K)
  68  */
  69 double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval,
  70                                    real                      temperature,
  71                                    gmx_bool                  linear,
  72                                    real                      scale_factor);
  73
  74 /*! \brief Compute entropy due to translational motion
  75  *
  76  * Following the equations in J. W. Ochterski,
  77  * Thermochemistry in Gaussian, Gaussian, Inc., 2000
  78  * Pitssburg PA
  79  *
  80  * \param[in] mass         Molecular mass (Dalton)
  81  * \param[in] temperature  Temperature (K)
  82  * \param[in] pressure     Pressure (bar) at which to compute
  83  * \returns The translational entropy (J/mol K)
  84  */
  85 double calcTranslationalEntropy(real mass,
  86                                 real temperature,
  87                                 real pressure);
  88
  89 /*! \brief Compute entropy due to rotational motion
  90  *
  91  * Following the equations in J. W. Ochterski,
  92  * Thermochemistry in Gaussian, Gaussian, Inc., 2000
  93  * Pitssburg PA
  94  *
  95  * \param[in] temperature  Temperature (K)
  96  * \param[in] natom        Number of atoms
  97  * \param[in] linear       TRUE if this is a linear molecule
  98  * \param[in] theta        The principal moments of inertia (unit of Energy)
  99  * \param[in] sigma_r      Symmetry factor, should be >= 1
 100  * \returns The rotational entropy (J/mol K)
 101  */
 102 double calcRotationalEntropy(real       temperature,
 103                              int        natom,
 104                              gmx_bool   linear,
 105                              const rvec theta,
 106                              real       sigma_r);
 107
 108 /*! \brief Compute internal energy due to vibrational motion
 109  *
 110  * \param[in] eigval       The eigenvalues
 111  * \param[in] temperature  Temperature (K)
 112  * \param[in] linear       TRUE if this is a linear molecule
 113  * \param[in] scale_factor Factor to scale frequencies by before computing E
 114  * \return The internal energy (J/mol K)
 115  */
 116 double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval,
 117                                      real                      temperature,
 118                                      gmx_bool                  linear,
 119                                      real                      scale_factor);
 120
 121 /*! \brief Compute entropy using Schlitter formula
 122  *
 123  * Computes entropy for a molecule / molecular system using the
 124  * algorithm due to Schlitter (Chem. Phys. Lett. 215 (1993)
 125  * 617-621).
 126  * The input should be eigenvalues from a covariance analysis,
 127  * the units of the eigenvalues are those of energy.
 128  *
 129  * \param[in] eigval       The eigenvalues
 130  * \param[in] temperature  Temperature (K)
 131  * \param[in] linear       True if this is a linear molecule (typically a diatomic molecule).
 132  * \return the entropy (J/mol K)
 133  */
 134 double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval,
 135                             real                      temperature,
 136                             gmx_bool                  linear);
 137
 138 /*! \brief Compute entropy using Quasi-Harmonic formula
 139  *
 140  * Computes entropy for a molecule / molecular system using the
 141  * Quasi-harmonic algorithm (Macromolecules 1984, 17, 1370).
 142  * The input should be eigenvalues from a normal mode analysis.
 143  * In both cases the units of the eigenvalues are those of energy.
 144  *
 145  * \param[in] eigval       The eigenvalues
 146  * \param[in] temperature  Temperature (K)
 147  * \param[in] linear       True if this is a linear molecule (typically a diatomic molecule).
 148  * \param[in] scale_factor Factor to scale frequencies by before computing S0
 149  * \return the entropy (J/mol K)
 150  */
 151 double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval,
 152                                 real                      temperature,
 153                                 gmx_bool                  linear,
 154                                 real                      scale_factor);
 155
 156 #endif