#include <cstdio>
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
struct gmx_mtop_t;
-struct gpp_atomtype;
struct t_atom;
struct t_atomtypes;
struct t_param;
struct InteractionTypeParameters;
struct t_symtab;
-int get_atomtype_type(const char *str, gpp_atomtype *at);
-/* Return atomtype corresponding to case-insensitive str
- or NOTSET if not found */
-
-int get_atomtype_ntypes(gpp_atomtype *at);
-/* Return number of atomtypes */
-
-char *get_atomtype_name(int nt, gpp_atomtype *at);
-/* Return name corresponding to atomtype nt, or NULL if not found */
-
-real get_atomtype_massA(int nt, gpp_atomtype *at);
-real get_atomtype_massB(int nt, gpp_atomtype *at);
-real get_atomtype_qA(int nt, gpp_atomtype *at);
-real get_atomtype_qB(int nt, gpp_atomtype *at);
-int get_atomtype_ptype(int nt, gpp_atomtype *at);
-int get_atomtype_batype(int nt, const gpp_atomtype* at);
-int get_atomtype_atomnumber(int nt, gpp_atomtype *at);
-
-/* Return the above variable for atomtype nt, or NOTSET if not found */
-
-real get_atomtype_nbparam(int nt, int param, gpp_atomtype *at);
-/* Similar to the previous but returns the paramth parameter or NOTSET */
-
-gpp_atomtype *init_atomtype();
-/* Return a new atomtype structure */
-
-void done_atomtype(gpp_atomtype *at);
-/* Free the memory in the structure */
-
-int set_atomtype(int nt, gpp_atomtype *at, t_symtab *tab,
- t_atom *a, const char *name, t_param *nb,
- int bondatomtype, int atomnumber);
-/* Set the values of an existing atom type nt. Returns nt on success or
- NOTSET on error. */
-
-int add_atomtype(gpp_atomtype *at, t_symtab *tab,
- t_atom *a, const char *name, t_param *nb,
- int bondatomtype, int atomnumber);
-/* Add a complete new atom type to an existing atomtype structure. Returns
- the number of the atom type. */
-
-void print_at (FILE * out, gpp_atomtype *at);
-/* Print an atomtype record to a text file */
-
-void renum_atype(gmx::ArrayRef<InteractionTypeParameters> plist, gmx_mtop_t *mtop,
- int *wall_atomtype,
- gpp_atomtype *at, bool bVerbose);
-
-void copy_atomtype_atomtypes(gpp_atomtype *atype, t_atomtypes *atypes);
-/* Copy from one structure to another */
+/*! \libinternal \brief
+ * Storage of all atom types used during preprocessing of a simulation
+ * input.
+ */
+class PreprocessingAtomTypes
+{
+ public:
+ PreprocessingAtomTypes();
+ //! Move constructor.
+ PreprocessingAtomTypes(PreprocessingAtomTypes &&old) noexcept;
+ //! Move assignment constructor.
+ PreprocessingAtomTypes &operator=(PreprocessingAtomTypes &&old) noexcept;
+
+ ~PreprocessingAtomTypes();
+
+ /*! \brief
+ * Get atom type index for atom type name if present in the database, or NOTSET.
+ *
+ * \todo The code should be changed to instead use a gmx::compat version
+ * of std::optional to return an iterator to the element being searched,
+ * or an empty optional construct if the entry has not been found.
+ *
+ * \param[in] str Input string to search type for.
+ * \returns Atomtype as integer.
+ */
+ int atomTypeFromName(const std::string &str) const;
+
+ //! Get number of defined atom types.
+ size_t size() const;
+
+ /*! \brief
+ * Get name of atom from internal atom type number.
+ *
+ * \param[in] nt Internal number of atom type.
+ * \returns The type name.
+ */
+ const char *atomNameFromAtomType(int nt) const;
+
+ /*! \brief
+ * Get normal mass of atom from internal atom type number.
+ *
+ * \param[in] nt Internal number of atom type.
+ * \returns The mass for the atom in state A or NOTSET.
+ */
+ real atomMassAFromAtomType(int nt) const;
+
+ /*! \brief
+ * Get mass for B state of atom from internal atom type number.
+ *
+ * \param[in] nt Internal number of atom type.
+ * \returns The mass for the atom in state B or NOTSET.
+ */
+ real atomMassBFromAtomType(int nt) const;
+
+ /*! \brief
+ * Get normal charge of atom from internal atom type number.
+ *
+ * \param[in] nt Internal number of atom type.
+ * \returns The charge for the atom in state A or NOTSET.
+ */
+ real atomChargeAFromAtomType(int nt) const;
+
+ /*! \brief
+ * Get charge for B state of atom from internal atom type number.
+ *
+ * \param[in] nt Internal number of atom type.
+ * \returns The charge for the atom in state B or NOTSET.
+ */
+ real atomChargeBFromAtomType(int nt) const;
+
+ /*! \brief
+ * Get particle type for atom type \p nt
+ *
+ * \param[in] nt Internal number of atom type.
+ * \returns The particle type or NOTSET.
+ */
+ int atomParticleTypeFromAtomType(int nt) const;
+
+ /*! \brief
+ * Get bond atom parameter of atom from internal atom type number.
+ *
+ * \param[in] nt Internal number of atom type.
+ * \returns The bond atom parameter or NOTSET.
+ */
+ int bondAtomTypeFromAtomType(int nt) const;
+
+ /*! \brief
+ * Get atomic number of atom from internal atom type number.
+ *
+ * \param[in] nt Internal number of atom type.
+ * \returns The atomic number type or NOTSET.
+ */
+ int atomNumberFromAtomType(int nt) const;
+
+ /*! \brief
+ * Get the value of \p param of type \p nt.
+ *
+ * \param[in] param The parameter value to find.
+ * \param[in] nt The number of the type.
+ * \returns The value of the parameter or NOTSET.
+ */
+ real atomNonBondedParamFromAtomType(int nt, int param) const;
+
+ /*! \brief
+ * If a value is within the range of the current types or not.
+ *
+ * \param[in] nt Value to check.
+ * \returns True if value is in range.
+ */
+ bool isSet(int nt) const;
+
+ /*! \brief
+ * Print data to file.
+ *
+ * \param[in] out File pointer.
+ */
+ void printTypes(FILE *out);
+
+ /*! \brief
+ * Set the values of an existing atom type \p nt.
+ *
+ * \param[in] nt Type that should be set.
+ * \param[in] tab Symbol table.
+ * \param[in] a Atom information.
+ * \param[in] name Atom name.
+ * \param[in] nb Nonbonded parameters.
+ * \param[in] bondAtomType What kind of bonded interactions are there.
+ * \param[in] atomNumber Atomic number of the entry.
+ * \returns Number of the type set or NOTSET
+ */
+ int setType(int nt,
+ t_symtab *tab,
+ const t_atom &a,
+ const char *name,
+ const t_param *nb,
+ int bondAtomType,
+ int atomNumber);
+
+ /*! \brief
+ * Add new atom type to database.
+ *
+ * \param[in] tab Symbol table.
+ * \param[in] a Atom information.
+ * \param[in] name Atom name.
+ * \param[in] nb Nonbonded parameters.
+ * \param[in] bondAtomType What kind of bonded interactions are there.
+ * \param[in] atomNumber Atomic number of the entry.
+ * \returns Number of entries in database.
+ */
+ int addType(t_symtab *tab,
+ const t_atom &a,
+ const char *name,
+ const t_param *nb,
+ int bondAtomType,
+ int atomNumber);
+
+ /*! \brief
+ * Renumber existing atom type entries.
+ *
+ * \param[in] plist List of parameters.
+ * \param[in] mtop Global topology.
+ * \param[inout] wallAtomType Atom types of wall atoms, which may also be renumbered
+ * \param[in] verbose If we want to print additional info.
+ */
+ void renumberTypes(gmx::ArrayRef<InteractionTypeParameters> plist,
+ gmx_mtop_t *mtop,
+ int *wallAtomType,
+ bool verbose);
+
+ /*! \brief
+ * Copy information to other structure.
+ *
+ * \param[inout] atypes Other datastructure to copy to.
+ */
+ void copyTot_atomtypes(t_atomtypes *atypes) const;
+ private:
+ class Impl;
+ gmx::PrivateImplPointer<Impl> impl_;
+};
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff