GauXC Molecule API ================== This section provides a reference for the GauXC API related to molecule objects, including C++ class definitions, C bindings, and Fortran bindings. C++ defintions -------------- .. cpp:class:: GauXC::Molecule : public std::Vector A class to represent a collection of atoms in a molecule. .. cpp:function:: inline Molecule(std::vector atoms) Construct a Molecule object from a vector of Atom objects. :param atoms: A vector of Atom objects representing the atoms in the molecule. :returns: A Molecule object initialized with the given atoms. .. cpp:function:: inline size_t natoms() const Get the number of atoms in the molecule. :returns: The number of atoms in the molecule. .. cpp:function:: inline AtomicNumber maxZ() const Get the maximum atomic number among the atoms in the molecule. :returns: The maximum atomic number among the atoms in the molecule. .. cpp:function:: inline bool operator==(const Molecule& other) const Compare this molecule with another molecule for equality. :param other: Another molecule to compare with. :returns: True if this molecule is equal to the other molecule, false otherwise. .. cpp:struct:: GauXC::Atom Representation of an atom in a molecule, containing its atomic number and Cartesian coordinates. .. cpp:member:: AtomicNumber Z The atomic number of the atom. .. cpp:member:: double x The x-coordinate of the atom in Cartesian coordinates. .. cpp:member:: double y The y-coordinate of the atom in Cartesian coordinates. .. cpp:member:: double z The z-coordinate of the atom in Cartesian coordinates. .. cpp:function:: inline Atom(AtomicNumber Z, double x, double y, double z) Construct an Atom object with the given atomic number and coordinates. :param Z: The atomic number of the atom. :param x: The x-coordinate of the atom in Cartesian coordinates. :param y: The y-coordinate of the atom in Cartesian coordinates. :param z: The z-coordinate of the atom in Cartesian coordinates. :returns: An Atom object initialized with the given atomic number and coordinates. .. cpp:type:: GauXC::AtomicNumber = int64_t A type to represent the atomic number of an atom. C bindings ---------- .. c:struct:: GauXCMolecule Opaque struct representing a molecule in the GauXC C API. .. c:function:: GauXCMolecule gauxc_molecule_new(GauXCStatus* status) Create a new GauXCMolecule object. :param status: Pointer to a GauXCStatus variable to store the status of the operation. :returns: A new GauXCMolecule object. .. c:function:: GauXCMolecule gauxc_molecule_new_from_atoms(GauXCStatus* status, const GauXCAtom* atoms, size_t natoms) Create a new GauXCMolecule object from an array of GauXCAtom structs. :param status: Pointer to a GauXCStatus variable to store the status of the operation. :param atoms: Pointer to an array of GauXCAtom structs representing the atoms in the molecule. :param natoms: The number of atoms in the molecule. :returns: A new GauXCMolecule object initialized with the given atoms. .. c:function:: void gauxc_molecule_delete(GauXCStatus* status, GauXCMolecule* molecule) Delete a GauXCMolecule object. :param status: Pointer to a GauXCStatus variable to store the status of the operation. :param molecule: Pointer to the GauXCMolecule object to be deleted. .. c:struct:: GauXCAtom Representation of an atom in a molecule for the GauXC C API, containing its atomic number and Cartesian coordinates. .. c:member:: int64_t Z The atomic number of the atom. .. c:member:: double x The x-coordinate of the atom in Cartesian coordinates. .. c:member:: double y The y-coordinate of the atom in Cartesian coordinates. .. c:member:: double z The z-coordinate of the atom in Cartesian coordinates. Fortran bindings ---------------- .. f:module:: gauxc_molecule :synopsis: Fortran bindings for GauXC molecule objects. .. f:currentmodule:: gauxc_molecule .. f:type:: gauxc_molecule_type Opaque type representing a molecule in the GauXC Fortran API. Available from the module :f:mod:`gauxc_molecule`. .. f:function:: gauxc_molecule_new(status) Create a new gauxc_molecule_type object. :param type(gauxc_status_type) status: A variable to store the status of the operation. :returns type(gauxc_molecule_type): A new gauxc_molecule_type object. .. f:function:: gauxc_molecule_new_from_atoms(status, atoms, natoms) Create a new gauxc_molecule_type object from an array of gauxc_atom_type objects. :param type(gauxc_status_type) status: A variable to store the status of the operation. :param type(gauxc_atom_type) atoms(*): An array of :f:type:`gauxc_atom_type` objects representing the atoms in the molecule. :param integer(c_int64_t) natoms: The number of atoms in the molecule. :returns type(gauxc_molecule_type): A new gauxc_molecule_type object initialized with the given atoms. .. f:function:: gauxc_molecule_delete(status, molecule) Delete a gauxc_molecule_type object. Part of the :f:func:`gauxc_delete` interface. :param type(gauxc_status_type) status: A variable to store the status of the operation. :param type(gauxc_molecule_type) molecule: The gauxc_molecule_type object to be deleted. .. f:currentmodule:: gauxc_atom .. f:type:: gauxc_atom_type A derived type representing an atom in the GauXC Fortran API, containing its atomic number and Cartesian coordinates. :f integer(c_int64_t) Z: The atomic number of the atom. :f real(c_double) x: The x-coordinate of the atom in Cartesian coordinates. :f real(c_double) y: The y-coordinate of the atom in Cartesian coordinates. :f real(c_double) z: The z-coordinate of the atom in Cartesian coordinates. Serialization to HDF5 --------------------- If GauXC has been built with HDF5 support :c:macro:`GAUXC_HAS_HDF5`, the :cpp:class:`GauXC::Molecule` class can be serialized to and deserialized from HDF5 files using the provided HDF5 interface. This allows for easy storage and retrieval of molecular data in a standardized format. .. cpp:function:: void GauXC::write_hdf5_record(const Molecule& molecule, const std::string& filename, const std::string& group_name) Write a Molecule object to an HDF5 file. :param molecule: The Molecule object to be written to the file. :param filename: The name of the HDF5 file to write to. :param group_name: The name of the group in the HDF5 file where the molecule data will be stored. .. cpp:function:: void GauXC::read_hdf5_record(Molecule& molecule, const std::string& filename, const std::string& group_name) Read a Molecule object from an HDF5 file. :param molecule: The Molecule object to be populated with the data read from the file. :param filename: The name of the HDF5 file to read from. :param group_name: The name of the group in the HDF5 file where the molecule data is stored. The same functions are available in the GauXC C API. .. c:function:: void gauxc_molecule_write_hdf5_record(GauXCMolecule molecule, const char* filename, const char* group_name) Write a GauXCMolecule object to an HDF5 file in C. :param molecule: The GauXCMolecule object to be written to the file. :param filename: The name of the HDF5 file to write to. :param group_name: The name of the group in the HDF5 file where the molecule data will be stored. .. c:function:: void gauxc_molecule_read_hdf5_record(GauXCMolecule molecule, const char* filename, const char* group_name) Read a GauXCMolecule object from an HDF5 file in C. :param molecule: The GauXCMolecule object to be populated with the data read from the file. :param filename: The name of the HDF5 file to read from. :param group_name: The name of the group in the HDF5 file where the molecule data is stored. The same functions are also available in the GauXC Fortran API, available from the module :f:mod:`gauxc_external_hdf5`. .. f:module:: gauxc_external_hdf5 :synopsis: HDF5 serialization functions for GauXC molecule objects. .. f:currentmodule:: gauxc_external_hdf5 .. f:subroutine:: gauxc_molecule_write_hdf5_record(molecule, filename, group_name) Write a gauxc_molecule_type object to an HDF5 file in Fortran. :param type(gauxc_molecule_type) molecule: The gauxc_molecule_type object to be written to the file. :param character(len=*) filename: The name of the HDF5 file to write to. :param character(len=*) group_name: The name of the group in the HDF5 file where the molecule data will be stored. .. f:subroutine:: gauxc_molecule_read_hdf5_record(molecule, filename, group_name) Read a gauxc_molecule_type object from an HDF5 file in Fortran. :param type(gauxc_molecule_type) molecule: The gauxc_molecule_type object to be populated with the data read from the file. :param character(len=*) filename: The name of the HDF5 file to read from. :param character(len=*) group_name: The name of the group in the HDF5 file where the molecule data is stored. .. f:currentmodule::