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