src/gromacs/gmxpreprocess/gpp_atomtype.h

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  37 /*! \libinternal \file
  38  * \brief
  39  * Declares PreprocessingAtomType.
  40  *
  41  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  42  * \author Paul Bauer <paul.bauer.q@gmail.com>
  43  * \inlibraryapi
  44  * \ingroup module_preprocessing
  45  */
  46 #ifndef GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
  47 #define GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
  48
  49 #include <cstdio>
  50
  51 #include <string>
  52
  53 #include "gromacs/utility/classhelpers.h"
  54 #include "gromacs/utility/real.h"
  55
  56 struct gmx_mtop_t;
  57 struct t_atom;
  58 struct t_atomtypes;
  59 class InteractionOfType;
  60 struct InteractionsOfType;
  61 struct t_symtab;
  62
  63 namespace gmx
  64 {
  65 template<typename>
  66 class ArrayRef;
  67 }
  68
  69 /*! \libinternal \brief
  70  * Storage of all atom types used during preprocessing of a simulation
  71  * input.
  72  */
  73 class PreprocessingAtomTypes
  74 {
  75 public:
  76     PreprocessingAtomTypes();
  77     //! Move constructor.
  78     PreprocessingAtomTypes(PreprocessingAtomTypes&& old) noexcept;
  79     //! Move assignment constructor.
  80     PreprocessingAtomTypes& operator=(PreprocessingAtomTypes&& old) noexcept;
  81
  82     ~PreprocessingAtomTypes();
  83
  84     /*! \brief
  85      *  Get atom type index for atom type name if present in the database, or NOTSET.
  86      *
  87      *  \todo The code should be changed to instead use a gmx::compat version
  88      *  of std::optional to return an iterator to the element being searched,
  89      *  or an empty optional construct if the entry has not been found.
  90      *
  91      *  \param[in] str Input string to search type for.
  92      *  \returns Atomtype as integer.
  93      */
  94     int atomTypeFromName(const std::string& str) const;
  95
  96     //! Get number of defined atom types.
  97     size_t size() const;
  98
  99     /*! \brief
 100      * Get name of atom from internal atom type number.
 101      *
 102      * \param[in] nt Internal number of atom type.
 103      * \returns The type name.
 104      */
 105     const char* atomNameFromAtomType(int nt) const;
 106
 107     /*! \brief
 108      * Get normal mass of atom from internal atom type number.
 109      *
 110      * \param[in] nt Internal number of atom type.
 111      * \returns The mass for the atom or NOTSET.
 112      */
 113     real atomMassFromAtomType(int nt) const;
 114
 115     /*! \brief
 116      * Get normal charge of atom from internal atom type number.
 117      *
 118      * \param[in] nt Internal number of atom type.
 119      * \returns The charge for the atom or NOTSET.
 120      */
 121     real atomChargeFromAtomType(int nt) const;
 122
 123     /*! \brief
 124      * Get particle type for atom type \p nt
 125      *
 126      * \param[in] nt Internal number of atom type.
 127      * \returns The particle type or NOTSET.
 128      */
 129     int atomParticleTypeFromAtomType(int nt) const;
 130
 131     /*! \brief
 132      * Get bond atom parameter of atom from internal atom type number.
 133      *
 134      * \param[in] nt Internal number of atom type.
 135      * \returns The bond atom parameter or NOTSET.
 136      */
 137     int bondAtomTypeFromAtomType(int nt) const;
 138
 139     /*! \brief
 140      * Get atomic number of atom from internal atom type number.
 141      *
 142      * \param[in] nt Internal number of atom type.
 143      * \returns The atomic number type or NOTSET.
 144      */
 145     int atomNumberFromAtomType(int nt) const;
 146
 147     /*! \brief
 148      * Get the value of \p param of type \p nt.
 149      *
 150      * \param[in] param The parameter value to find.
 151      * \param[in] nt The number of the type.
 152      * \returns The value of the parameter or NOTSET.
 153      */
 154     real atomNonBondedParamFromAtomType(int nt, int param) const;
 155
 156     /*! \brief
 157      * If a value is within the range of the current types or not.
 158      *
 159      * \param[in] nt Value to check.
 160      * \returns True if value is in range.
 161      */
 162     bool isSet(int nt) const;
 163
 164     /*! \brief
 165      * Print data to file.
 166      *
 167      * \param[in] out File pointer.
 168      */
 169     void printTypes(FILE* out);
 170
 171     /*! \brief
 172      * Set the values of an existing atom type \p nt.
 173      *
 174      * \param[in] nt Type that should be set.
 175      * \param[in] tab Symbol table.
 176      * \param[in] a Atom information.
 177      * \param[in] name Atom name.
 178      * \param[in] nb Nonbonded parameters.
 179      * \param[in] bondAtomType What kind of bonded interactions are there.
 180      * \param[in] atomNumber Atomic number of the entry.
 181      * \returns Number of the type set or NOTSET
 182      */
 183     int setType(int                      nt,
 184                 t_symtab*                tab,
 185                 const t_atom&            a,
 186                 const std::string&       name,
 187                 const InteractionOfType& nb,
 188                 int                      bondAtomType,
 189                 int                      atomNumber);
 190
 191     /*! \brief
 192      * Add new atom type to database.
 193      *
 194      * \param[in] tab Symbol table.
 195      * \param[in] a Atom information.
 196      * \param[in] name Atom name.
 197      * \param[in] nb Nonbonded parameters.
 198      * \param[in] bondAtomType What kind of bonded interactions are there.
 199      * \param[in] atomNumber Atomic number of the entry.
 200      * \returns Number of entries in database.
 201      */
 202     int addType(t_symtab*                tab,
 203                 const t_atom&            a,
 204                 const std::string&       name,
 205                 const InteractionOfType& nb,
 206                 int                      bondAtomType,
 207                 int                      atomNumber);
 208
 209     /*! \brief
 210      * Renumber existing atom type entries.
 211      *
 212      * \param[in] plist List of parameters.
 213      * \param[in] mtop Global topology.
 214      * \param[inout] wallAtomType Atom types of wall atoms, which may also be renumbered
 215      * \param[in] verbose If we want to print additional info.
 216      */
 217     void renumberTypes(gmx::ArrayRef<InteractionsOfType> plist, gmx_mtop_t* mtop, int* wallAtomType, bool verbose);
 218
 219     /*! \brief
 220      * Copy information to other structure.
 221      *
 222      * \param[inout] atypes Other datastructure to copy to.
 223      */
 224     void copyTot_atomtypes(t_atomtypes* atypes) const;
 225
 226 private:
 227     class Impl;
 228     //! Pimpl that holds the data.
 229     gmx::PrivateImplPointer<Impl> impl_;
 230 };
 231
 232 #endif