sc::MolecularFragment Class Reference
MolecularFragment is a Molecule that is a fragment of another Molecule object. More...
#include <chemistry/molecule/frag.h>
Inheritance diagram for sc::MolecularFragment:
Public Member Functions | |
| MolecularFragment (const Ref< KeyVal > &kv) | |
| A KeyVal constructor is used to generate a MolecularFragment object from the input. More... | |
| MolecularFragment (StateIn &) | |
| void | save_data_state (StateOut &) |
| Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. More... | |
 Public Member Functions inherited from sc::Molecule | |
| Molecule (const Molecule &) | |
| Molecule (StateIn &) | |
| Molecule (const Ref< KeyVal > &input) | |
| The Molecule KeyVal constructor is used to generate a Molecule object from the input. More... | |
| Molecule & | operator= (const Molecule &) |
| void | add_atom (int Z, double x, double y, double z, const std::string &label="", double mass=0.0, int have_charge=0, double charge=0.0, int have_fragment=0, int fragment=0) |
| Add an AtomicCenter to the Molecule. | |
| const Atom & | atom (size_t i) const |
| const std::vector< Atom > & | atoms () const |
| virtual void | print (std::ostream &=ExEnv::out0()) const |
| Print information about the molecule. | |
| virtual void | print_parsedkeyval (std::ostream &=ExEnv::out0(), int print_pg=1, int print_unit=1, int number_atoms=1) const |
| Ref< Units > | geometry_units () const |
| in which units Molecule was specified and in which units it will be reported | |
| size_t | natom () const |
| Returns the number of atoms in the molecule. | |
| int | Z (int atom) const |
| double & | r (int atom, int xyz) |
| const double & | r (int atom, int xyz) const |
| const double * | r (int atom) const |
| double | mass (int atom) const |
| const char * | label (int atom) const |
| Returns the label explicitly assigned to atom. More... | |
| int | fragment (int atom) const |
| returns the fragment to which atom belongs to | |
| int | atom_at_position (double *, double tol=0.05) const |
| Takes an (x, y, z) postion and finds an atom within the given tolerance distance. More... | |
| int | atom_label_to_index (const std::string &label) const |
| Returns the index of the atom with the given label. More... | |
| std::vector< double > | charges () const |
| Returns a vector of the nuclear charges of the atoms. | |
| double | charge (int iatom) const |
| Return the charge of the atom. | |
| bool | is_Q (int iatom) const |
| Return true if iatom is a simple point charge. | |
| double | total_charge () const |
| Returns the total nuclear charge. More... | |
| int | total_Z () const |
| Returns the sum of atomic numbers of nuclei. | |
| void | set_point_group (const Ref< PointGroup > &, double tol=1.0e-7) |
| Sets the PointGroup of the molecule. | |
| const Ref< PointGroup > & | point_group () const |
| Returns the PointGroup of the molecule. | |
| Ref< PointGroup > | highest_point_group (double tol=1.0e-8) const |
| Find this molecules true point group (limited to abelian groups). More... | |
| int | is_axis (SCVector3 &origin, SCVector3 &udirection, int order, double tol=1.0e-8) const |
| Return 1 if this given axis is a symmetry element for the molecule. More... | |
| int | is_plane (SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const |
| Return 1 if the given plane is a symmetry element for the molecule. More... | |
| int | has_inversion (SCVector3 &origin, double tol=1.0e-8) const |
| Return 1 if the molecule has an inversion center. | |
| int | is_linear (double tolerance=1.0e-5) const |
| Returns 1 if the molecule is linear, 0 otherwise. | |
| int | is_planar (double tolerance=1.0e-5) const |
| Returns 1 if the molecule is planar, 0 otherwise. | |
| void | is_linear_planar (int &linear, int &planar, double tol=1.0e-5) const |
| Sets linear to 1 if the molecular is linear, 0 otherwise. More... | |
| SCVector3 | center_of_mass () const |
| Returns a SCVector3 containing the cartesian coordinates of the center of mass for the molecule. | |
| double | nuclear_repulsion_energy () |
| Returns the nuclear repulsion energy for the molecule. | |
| void | nuclear_repulsion_1der (int center, double xyz[3]) |
| Compute the nuclear repulsion energy first derivative with respect to the given center. | |
| void | nuclear_efield (const double *position, double *efield) |
| Compute the electric field due to the nuclei at the given point. | |
| void | nuclear_charge_efield (const double *charges, const double *position, double *efield) |
| Compute the electric field due to the given charges at the positions of the nuclei at the given point. | |
| void | symmetrize (double tol=0.5) |
| If the molecule contains only symmetry unique atoms, this function will generate the other, redundant atoms. More... | |
| void | symmetrize (const Ref< PointGroup > &pg, double tol=0.5) |
| Set the point group and then symmetrize. | |
| void | cleanup_molecule (double tol=0.1) |
| This will try to carefully correct symmetry errors in molecules. More... | |
| void | translate (const double *r) |
| void | move_to_com () |
| void | transform_to_principal_axes (int trans_frame=1) |
| void | transform_to_symmetry_frame () |
| void | print_xyz (std::ostream &=ExEnv::out0(), const char *title=0) const |
| void | principal_moments_of_inertia (double *evals, double **evecs=0) const |
| Compute the principal moments of inertia and, possibly, the principal axes. | |
| int | nunique () const |
| Return information about symmetry unique and equivalent atoms. More... | |
| int | unique (int iuniq) const |
| Returns the overall number of the iuniq'th unique atom. | |
| int | nequivalent (int iuniq) const |
| Returns the number of atoms equivalent to iuniq. | |
| int | equivalent (int iuniq, int j) const |
| Returns the j'th atom equivalent to iuniq. | |
| int | atom_to_unique (int iatom) const |
| Converts an atom number to the number of its generating unique atom. More... | |
| int | atom_to_unique_offset (int iatom) const |
| Converts an atom number to the offset of this atom in the list of generated atoms. More... | |
| int | n_core_electrons () |
| Return the number of core electrons. | |
| int | max_z () |
| Return the maximum atomic number. | |
| Ref< AtomInfo > | atominfo () const |
| Return the molecule's AtomInfo object. | |
| std::string | atom_name (int iatom) const |
| Returns the element name of the atom. | |
| std::string | atom_symbol (int iatom) const |
| Returns the element symbol of the atom. | |
| void | set_include_q (bool iq) |
| If include_q is true, then include the "Q" atoms in the charge and efield routines. | |
| bool | include_q () const |
| Returns include_q. See set_include_q. | |
| void | set_include_qq (bool iqq) |
| If include_qq is true, include the coupling between pairs of "Q" atoms when computing nuclear repulsion energy and gradients. | |
| bool | include_qq () const |
| Returns include_qq. See set_include_qq. | |
| int | n_q_atom () const |
| Retrieve the number of "Q" atoms. | |
| int | q_atom (int i) const |
| Retrieve the "Q" atoms. | |
| int | n_non_q_atom () const |
| Retrieve the number of non-"Q" atoms. | |
| int | non_q_atom (int i) const |
| Retrieve the of non-"Q" atoms. | |
| bool | any_atom_has_charge () const |
| Determine if any of the atoms have non-standard charge. | |
| bool | any_atom_has_fragment () const |
| Determine if any of the atoms have a fragment label. | |
| bool | any_atom_has_label () const |
| Determine if any of the atoms have a user defined label. | |
| SCVector3 | ref_origin () const |
| returns the origin of the reference coordinate system (the system in which atoms were specified before the center-of-mass shift | |
| void | save_data_state (StateOut &) |
| Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. More... | |
| Public Member Functions inherited from sc::SavableState | |
| SavableState & | operator= (const SavableState &) |
| void | save_state (StateOut &) |
| Save the state of the object as specified by the StateOut object. More... | |
| void | save_object_state (StateOut &) |
| This can be used for saving state when the exact type of the object is known for both the save and the restore. More... | |
| virtual void | save_vbase_state (StateOut &) |
| Save the virtual bases for the object. More... | |
| Public Member Functions inherited from sc::DescribedClass | |
| DescribedClass (const DescribedClass &) | |
| DescribedClass & | operator= (const DescribedClass &) |
| ClassDesc * | class_desc () const MPQC__NOEXCEPT |
| This returns the unique pointer to the ClassDesc corresponding to the given type_info object. More... | |
| const char * | class_name () const |
| Return the name of the object's exact type. | |
| int | class_version () const |
| Return the version of the class. | |
| Ref< DescribedClass > | ref () |
| Return this object wrapped up in a Ref smart pointer. More... | |
| Public Member Functions inherited from sc::RefCount | |
| size_t | identifier () const |
| Return the unique identifier for this object that can be compared for different objects of different types. More... | |
| int | lock_ptr () const |
| Lock this object. | |
| int | unlock_ptr () const |
| Unlock this object. | |
| void | use_locks (bool inVal) |
| start and stop using locks on this object | |
| refcount_t | nreference () const |
| Return the reference count. | |
| refcount_t | reference () |
| Increment the reference count and return the new count. | |
| refcount_t | dereference () |
| Decrement the reference count and return the new count. | |
| int | managed () const |
| void | unmanage () |
| Turn off the reference counting mechanism for this object. More... | |
Additional Inherited Members | |
| Static Public Member Functions inherited from sc::SavableState | |
| static void | save_state (SavableState *s, StateOut &) |
| static SavableState * | restore_state (StateIn &si) |
| Restores objects saved with save_state. More... | |
| static SavableState * | key_restore_state (StateIn &si, const char *keyword) |
| Like restore_state, but keyword is used to override values while restoring. | |
| static SavableState * | dir_restore_state (StateIn &si, const char *objectname, const char *keyword=0) |
| Protected Member Functions inherited from sc::Molecule | |
| void | init_symmetry_info (double tol=0.5) |
| void | clear_symmetry_info () |
| void | clear () |
| void | throw_if_atom_duplicated (int begin=0, double tol=1e-3) |
| Protected Member Functions inherited from sc::SavableState | |
| SavableState (const SavableState &) | |
| SavableState (StateIn &) | |
| Each derived class StateIn CTOR handles the restore corresponding to calling save_object_state, save_vbase_state, and save_data_state listed above. More... | |
| Protected Member Functions inherited from sc::RefCount | |
| RefCount (const RefCount &) | |
| RefCount & | operator= (const RefCount &) |
| Protected Attributes inherited from sc::Molecule | |
| std::vector< Atom > | atoms_ |
| Ref< AtomInfo > | atominfo_ |
| Ref< PointGroup > | pg_ |
| Ref< Units > | geometry_units_ |
| double | ref_origin_ [3] |
| int | nuniq_ |
| int * | nequiv_ |
| int ** | equiv_ |
| int * | atom_to_uniq_ |
| int | q_Z_ |
| bool | include_q_ |
| bool | include_qq_ |
| std::vector< int > | q_atoms_ |
| std::vector< int > | non_q_atoms_ |
Detailed Description
MolecularFragment is a Molecule that is a fragment of another Molecule object.
Constructor & Destructor Documentation
◆ MolecularFragment()
A KeyVal constructor is used to generate a MolecularFragment object from the input.
The full list of keywords that are accepted is below.
| Keyword | Type | Default | Description |
molecule | Molecule | none | the Molecule object that this molecule is part of (proto-molecule). |
fragment | integer | 0 | Specifies atoms of which fragment defined in the proto-molecule object will be considered for including into this molecule (see Molecule KeyVal documentation). By default, all atoms will be considered. |
includes_atoms | integer[] | none<td>(optional) only atoms connected by "normal" chemical bonds to the atoms specified by this keyword will be considered (atomic indices are 0-based). The normal chemical bonds are generated for the proto-molecule object using the same distance criterion as that used by IntCoorGen object to generate bonds (see IntCoorGen documentation). | |
excludes_atoms | integer[] | none<td>(optional) only atoms NOT connected by "normal" chemical bonds to the atoms specified by this keyword will be considered. See documentation for | |
symmetry | string | auto | The Schoenflies symbol of the point group. This is case insensitive. It should be a subgroup of D2h. If it is |
symmetry_tolerance | double | 1.0e-4 | When a molecule has symmetry, some atoms may be related by symmetry operations. The distance between given atoms and atoms generated by symmetry operations is compared to this threshold to determine if they are the same. If they are the same, then the coordinates are cleaned up to make them exactly symmetry equivalent. If the given molecule was produced by a optimization that started in C1 symmetry, but produced a roughly symmetric structure and you would like to begin using symmetry, then this may need to be increased a bit to properly symmetrize the molecule. |
symmetry_frame | double[3][3] | [[1 0 0][0 1 0][0 0 1]] | The symmetry frame. Ignored for |
origin | double[3] | [0 0 0] | The origin of the symmetry frame. Specified in the same units as used by proto-molecule. Ignored for |
add_ghosts | boolean | false | If true, the atoms in proto-molecule that are not of this fragment will be included as ghosts (zero-charge atoms that carry basis functions; see documentation for |
Note that although MolecularFragment is derived from Molecule, its KeyVal constructor does not accept all Molecule keywords.
Member Function Documentation
◆ save_data_state()
|
virtual |
Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them.
This must be implemented by the derived class if the class has data.
Reimplemented from sc::SavableState.
The documentation for this class was generated from the following file:
- src/lib/chemistry/molecule/frag.h