src/gromacs/gmxpreprocess/grompp_impl.h

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  38
  39 #ifndef GMX_GMXPREPROCESS_GROMPP_IMPL_H
  40 #define GMX_GMXPREPROCESS_GROMPP_IMPL_H
  41
  42 #include <string>
  43
  44 #include "gromacs/gmxpreprocess/notset.h"
  45 #include "gromacs/topology/atoms.h"
  46 #include "gromacs/topology/block.h"
  47 #include "gromacs/topology/idef.h"
  48 #include "gromacs/utility/basedefinitions.h"
  49 #include "gromacs/utility/exceptions.h"
  50 #include "gromacs/utility/listoflists.h"
  51 #include "gromacs/utility/real.h"
  52
  53 namespace gmx
  54 {
  55 template<typename>
  56 class ArrayRef;
  57 }
  58
  59 /*! \libinternal \brief
  60  * Describes an interaction of a given type, plus its parameters.
  61  */
  62 class InteractionOfType
  63 {
  64 public:
  65     //! Constructor that initializes vectors.
  66     InteractionOfType(gmx::ArrayRef<const int>  atoms,
  67                       gmx::ArrayRef<const real> params,
  68                       const std::string&        name = "");
  69     /*!@{*/
  70     //! Access the individual elements set for the parameter.
  71     const int& ai() const;
  72     const int& aj() const;
  73     const int& ak() const;
  74     const int& al() const;
  75     const int& am() const;
  76
  77     const real& c0() const;
  78     const real& c1() const;
  79     const real& c2() const;
  80
  81     const std::string& interactionTypeName() const;
  82     /*!@}*/
  83
  84     /*! \brief Renumbers atom Ids.
  85      *
  86      *  Enforces that ai() is less than the opposite terminal atom index,
  87      *  with the number depending on the interaction type.
  88      */
  89     void sortAtomIds();
  90
  91     //! Set single force field parameter.
  92     void setForceParameter(int pos, real value);
  93
  94     //! View on all atoms numbers that are actually set.
  95     gmx::ArrayRef<int> atoms() { return atoms_; }
  96     //! Const view on all atoms numbers that are actually set.
  97     gmx::ArrayRef<const int> atoms() const { return atoms_; }
  98     //! View on all of the force field parameters
  99     gmx::ArrayRef<const real> forceParam() const { return forceParam_; }
 100     //! View on all of the force field parameters
 101     gmx::ArrayRef<real> forceParam() { return forceParam_; }
 102
 103 private:
 104     //! Return if we have a bond parameter, means two atoms right now.
 105     bool isBond() const { return atoms_.size() == 2; }
 106     //! Return if we have an angle parameter, means three atoms right now.
 107     bool isAngle() const { return atoms_.size() == 3; }
 108     //! Return if we have a dihedral parameter, means four atoms right now.
 109     bool isDihedral() const { return atoms_.size() == 4; }
 110     //! Return if we have a cmap parameter, means five atoms right now.
 111     bool isCmap() const { return atoms_.size() == 5; }
 112     //! Enforce that atom id ai() is less than aj().
 113     void sortBondAtomIds();
 114     //! Enforce that atom id ai() is less than ak(). Does not change aj().
 115     void sortAngleAtomIds();
 116     /*! \brief Enforce order of atoms in dihedral.
 117      *
 118      * Changes atom order if needed to enforce that ai() is less than al().
 119      * If ai() and al() are swapped, aj() and ak() are swapped as well,
 120      * independent of their previous order.
 121      */
 122     void sortDihedralAtomIds();
 123     //! The atom list (eg. bonds: particle, i = atoms[0] (ai), j = atoms[1] (aj))
 124     std::vector<int> atoms_;
 125     //! Force parameters (eg. b0 = forceParam[0])
 126     std::array<real, MAXFORCEPARAM> forceParam_;
 127     //! Used with forcefields whose .rtp files name the interaction types (e.g. GROMOS), rather than look them up from the atom names.
 128     std::string interactionTypeName_;
 129 };
 130
 131 /*! \libinternal \brief
 132  * A set of interactions of a given type
 133  * (found in the enumeration in ifunc.h), complete with
 134  * atom indices and force field function parameters.
 135  *
 136  * This is used for containing the data obtained from the
 137  * lists of interactions of a given type in a [moleculetype]
 138  * topology file definition.
 139  */
 140 struct InteractionsOfType
 141 { // NOLINT (clang-analyzer-optin.performance.Padding)
 142     //! The different parameters in the system.
 143     std::vector<InteractionOfType> interactionTypes;
 144     //! CMAP grid spacing.
 145     int cmakeGridSpacing = -1;
 146     //! Number of cmap angles.
 147     int cmapAngles = -1;
 148     //! CMAP grid data.
 149     std::vector<real> cmap;
 150     //! The five atomtypes followed by a number that identifies the type.
 151     std::vector<int> cmapAtomTypes;
 152
 153     //! Number of parameters.
 154     size_t size() const { return interactionTypes.size(); }
 155     //! Elements in cmap grid data.
 156     int ncmap() const { return cmap.size(); }
 157     //! Number of elements in cmapAtomTypes.
 158     int nct() const { return cmapAtomTypes.size(); }
 159 };
 160
 161 struct t_excls
 162 {
 163     int  nr; /* The number of exclusions             */
 164     int* e;  /* The excluded atoms                   */
 165 };
 166
 167
 168 /*! \libinternal \brief
 169  * Holds the molecule information during preprocessing.
 170  */
 171 struct MoleculeInformation
 172 {
 173     //! Name of the molecule.
 174     char** name = nullptr;
 175     //! Number of exclusions per atom.
 176     int nrexcl = 0;
 177     //! Have exclusions been generated?.
 178     bool excl_set = false;
 179     //! Has the mol been processed.
 180     bool bProcessed = false;
 181     //! Atoms in the moelcule.
 182     t_atoms atoms;
 183     //! Molecules separated in datastructure.
 184     t_block mols;
 185     //! Exclusions in the molecule.
 186     gmx::ListOfLists<int> excls;
 187     //! Interactions of a defined type.
 188     std::array<InteractionsOfType, F_NRE> interactions;
 189
 190     /*! \brief
 191      * Initializer.
 192      *
 193      * This should be removed as soon as the underlying datastructures
 194      * have been cleaned up to use proper initialization and can be copy
 195      * constructed.
 196      */
 197     void initMolInfo();
 198
 199     /*! \brief
 200      * Partial clean up function.
 201      *
 202      * Should be removed once this datastructure actually owns all its own memory and
 203      * elements of it are not stolen by other structures and properly copy constructed
 204      * or moved.
 205      * Cleans up the mols and plist datastructures but not cgs and excls.
 206      */
 207     void partialCleanUp();
 208
 209     /*! \brief
 210      * Full clean up function.
 211      *
 212      * Should be removed once the destructor can always do this.
 213      */
 214     void fullCleanUp();
 215 };
 216
 217 struct t_mols
 218 {
 219     std::string name;
 220     int         nr;
 221 };
 222
 223 bool is_int(double x);
 224 /* Returns TRUE when x is integer */
 225
 226 #endif