src/gromacs/mdtypes/enerdata.h

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  35 #ifndef GMX_MDTYPES_TYPES_ENERDATA_H
  36 #define GMX_MDTYPES_TYPES_ENERDATA_H
  37
  38 #include <array>
  39 #include <utility>
  40 #include <vector>
  41
  42 #include "gromacs/mdtypes/md_enums.h"
  43 #include "gromacs/topology/idef.h"
  44 #include "gromacs/utility/arrayref.h"
  45 #include "gromacs/utility/gmxassert.h"
  46 #include "gromacs/utility/real.h"
  47
  48 struct t_commrec;
  49 struct t_lambda;
  50
  51 // The non-bonded energy terms accumulated for energy group pairs
  52 enum
  53 {
  54     egCOULSR,
  55     egLJSR,
  56     egBHAMSR,
  57     egCOUL14,
  58     egLJ14,
  59     egNR
  60 };
  61
  62 // Struct for accumulating non-bonded energies between energy group pairs
  63 struct gmx_grppairener_t
  64 {
  65     gmx_grppairener_t(int numEnergyGroups) : nener(numEnergyGroups * numEnergyGroups)
  66     {
  67         for (auto& elem : ener)
  68         {
  69             elem.resize(nener);
  70         }
  71     }
  72
  73     int                                 nener; /* The number of energy group pairs */
  74     std::array<std::vector<real>, egNR> ener;  /* Energy terms for each pair of groups */
  75 };
  76
  77 //! Accumulates free-energy foreign lambda energies and dH/dlamba
  78 class ForeignLambdaTerms
  79 {
  80 public:
  81     /*! \brief Constructor
  82      *
  83      * \param[in] numLambdas  The number of foreign lambda values
  84      */
  85     ForeignLambdaTerms(int numLambdas);
  86
  87     //! Returns the number of foreign lambda values
  88     int numLambdas() const { return numLambdas_; }
  89
  90     //! Returns the H(lambdaIndex) - H(lambda_current)
  91     double deltaH(int lambdaIndex) const { return energies_[1 + lambdaIndex] - energies_[0]; }
  92
  93     /*! \brief Returns a list of partial energies, the part which depends on lambda),
  94      * current lambda in entry 0, foreign lambda i in entry 1+i
  95      *
  96      * Note: the potential terms needs to be finalized before calling this method.
  97      */
  98     gmx::ArrayRef<double> energies()
  99     {
 100         GMX_ASSERT(finalizedPotentialContributions_, "Should be finalized");
 101         return energies_;
 102     }
 103
 104     /*! \brief Returns a list of partial energies, the part which depends on lambda),
 105      * current lambda in entry 0, foreign lambda i in entry 1+i
 106      *
 107      * Note: the potential terms needs to be finalized before calling this method.
 108      */
 109     gmx::ArrayRef<const double> energies() const
 110     {
 111         GMX_ASSERT(finalizedPotentialContributions_, "Should be finalized");
 112         return energies_;
 113     }
 114
 115     /*! \brief Adds an energy and dV/dl constribution to lambda list index \p listIndex
 116      *
 117      * This should only be used for terms with non-linear dependence on lambda
 118      * The value passed as listIndex should be 0 for the current lambda
 119      * and 1+i for foreign lambda index i.
 120      */
 121     void accumulate(int listIndex, double energy, double dvdl)
 122     {
 123         GMX_ASSERT(!finalizedPotentialContributions_,
 124                    "Can only accumulate with an unfinalized object");
 125
 126         energies_[listIndex] += energy;
 127         dhdl_[listIndex] += dvdl;
 128     }
 129
 130     /*! \brief Finalizes the potential (non-kinetic) terms
 131      *
 132      * Note: This can be called multiple times during the same force calculations
 133      * without affecting the results.
 134      *
 135      * \param[in] dvdlLinear  List of dV/dlambda contributions of size efptNR with depend linearly on lambda
 136      * \param[in] lambda      Lambda values for the efptNR contribution types
 137      * \param[in] fepvals     Free-energy parameters
 138      */
 139     void finalizePotentialContributions(gmx::ArrayRef<const double> dvdlLinear,
 140                                         gmx::ArrayRef<const real>   lambda,
 141                                         const t_lambda&             fepvals);
 142
 143     /*! \brief Accumulates the kinetic and constraint free-energy contributions
 144      *
 145      * \param[in] energyTerms  List of energy terms, pass \p term in \p gmx_enerdata_t
 146      * \param[in] dhdlMass     The mass dependent contribution to dH/dlambda
 147      * \param[in] lambda       Lambda values for the efptNR contribution types
 148      * \param[in] fepvals      Free-energy parameters
 149      */
 150     void finalizeKineticContributions(gmx::ArrayRef<const real> energyTerms,
 151                                       double                    dhdlMass,
 152                                       gmx::ArrayRef<const real> lambda,
 153                                       const t_lambda&           fepvals);
 154
 155     /*! \brief Returns a pair of lists of deltaH and dH/dlambda
 156      *
 157      * Both lists are of size numLambdas() and are indexed with the lambda index.
 158      *
 159      * Note: should only be called after the object has been finalized by a call to
 160      * accumulateLinearPotentialComponents() (is asserted).
 161      *
 162      * \param[in] cr  Communication record, used to reduce the terms when !=nullptr
 163      */
 164     std::pair<std::vector<double>, std::vector<double>> getTerms(const t_commrec* cr) const;
 165
 166     //! Sets all terms to 0
 167     void zeroAllTerms();
 168
 169 private:
 170     //! As accumulate(), but for kinetic contributions
 171     void accumulateKinetic(int listIndex, double energy, double dhdl);
 172
 173     //! Add a dH/dl contribution that does not depend on lambda to all foreign dH/dl terms
 174     void addConstantDhdl(double dhdl);
 175
 176     //! The number of foreign lambdas
 177     int numLambdas_;
 178     //! Storage for foreign lambda energies
 179     std::vector<double> energies_;
 180     //! Storage for foreign lambda dH/dlambda
 181     std::vector<double> dhdl_;
 182     //! Tells whether all potential energy contributions have been accumulated
 183     bool finalizedPotentialContributions_ = false;
 184 };
 185
 186 //! Struct for accumulating all potential energy terms and some kinetic energy terms
 187 struct gmx_enerdata_t
 188 {
 189     /*! \brief
 190      * Constructor with specific number of energy groups and lambdas.
 191      *
 192      * \param[in] numEnergyGroups Number of energy groups used.
 193      * \param[in] numFepLambdas   Number of free energy lambdas, zero if none.
 194      */
 195     gmx_enerdata_t(int numEnergyGroups, int numFepLambdas);
 196
 197     //! The energies for all different interaction types
 198     real term[F_NRE] = { 0 };
 199     //! Energy group pair non-bonded energies
 200     struct gmx_grppairener_t grpp;
 201     //! Contributions to dV/dlambda with linear dependence on lambda
 202     double dvdl_lin[efptNR] = { 0 };
 203     //! Contributions to dV/dlambda with non-linear dependence on lambda
 204     double dvdl_nonlin[efptNR] = { 0 };
 205     /* The idea is that dvdl terms with linear lambda dependence will be added
 206      * automatically to enerpart_lambda. Terms with non-linear lambda dependence
 207      * should explicitly determine the energies at foreign lambda points
 208      * when n_lambda > 0. */
 209
 210     //! Foreign lambda energies and dH/dl
 211     ForeignLambdaTerms foreignLambdaTerms;
 212
 213     //! Alternate, temporary array for storing foreign lambda energies
 214     real foreign_term[F_NRE] = { 0 };
 215     //! Alternate, temporary  array for storing foreign lambda group pair energies
 216     struct gmx_grppairener_t foreign_grpp;
 217 };
 218
 219 #endif