#include <molecule.h>
Inheritance diagram for sc::Molecule:
Public Member Functions | |
Molecule (const Molecule &) | |
Molecule (StateIn &) | |
Molecule (const Ref< KeyVal > &input) | |
The KeyVal constructor. | |
Molecule & | operator= (const Molecule &) |
void | add_atom (int Z, double x, double y, double z, const char *=0, double mass=0.0, int have_charge=0, double charge=0.0) |
Add an AtomicCenter to the Molecule. | |
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 |
int | natom () const |
Returns the number of atoms in the molcule. | |
int | Z (int atom) const |
double & | r (int atom, int xyz) |
const double & | r (int atom, int xyz) const |
double * | r (int atom) |
const double * | r (int atom) const |
double | mass (int atom) const |
const char * | label (int atom) const |
Returns the label explicitly assigned to atom. | |
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. | |
int | atom_label_to_index (const char *label) const |
Returns the index of the atom with the given label. | |
double * | charges () const |
Returns a double* containing the nuclear charges of the atoms. | |
double | charge (int iatom) const |
Return the charge of the atom. | |
double | nuclear_charge () const |
Returns the total nuclear charge. | |
void | set_point_group (const Ref< PointGroup > &, double tol=1.0e-7) |
Sets the PointGroup of the molecule. | |
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). | |
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. | |
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. | |
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. | |
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. | |
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. | |
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_pdb (std::ostream &=ExEnv::out0(), char *title=0) const |
void | read_pdb (const char *filename) |
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. | |
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. | |
int | atom_to_unique_offset (int iatom) const |
Converts an atom number to the offset of this atom in the list of generated atoms. | |
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. | |
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. | |
Protected Member Functions | |
void | init_symmetry_info (double tol=0.5) |
void | clear_symmetry_info () |
void | clear () |
Protected Attributes | |
int | natoms_ |
Ref< AtomInfo > | atominfo_ |
Ref< PointGroup > | pg_ |
Ref< Units > | geometry_units_ |
double ** | r_ |
int * | Z_ |
double * | charges_ |
int | nuniq_ |
int * | nequiv_ |
int ** | equiv_ |
int * | atom_to_uniq_ |
double * | mass_ |
char ** | labels_ |
int | q_Z_ |
bool | include_q_ |
bool | include_qq_ |
std::vector< int > | q_atoms_ |
std::vector< int > | non_q_atoms_ |
It has a KeyVal constructor that can create a new molecule from either a PDB file or from a list of Cartesian coordinates.
The following ParsedKeyVal input reads from the PDB file h2o.pdb
:
molecule<Molecule>: ( pdb_file = "h2o.pdb" )
The following input explicitly gives the atom coordinates, using the ParsedKeyVal table notation:
molecule<Molecule>: ( unit=angstrom { atom_labels atoms geometry } = { O1 O [ 0.000000000 0 0.369372944 ] H1 H [ 0.783975899 0 -0.184686472 ] H2 H [-0.783975899 0 -0.184686472 ] } ) )The default units are Bohr which can be overridden with
unit=angstrom
. The atom_labels
array can be omitted. The atoms
and geometry
arrays are required.
As a special case, an atom can be given with the symbol Q
or the name charge
. Such centers are treated as point charges and not given basis functions. The values of the charges must be specified with a charge
vector in the Molecule input. Since the charge vector assign charges to all centers, including atoms, it is easiest to place all point charge centers first in the geometry, and then give a charge vector with a number of elements equal to the number of point charges. The following example shows a water molecule interacting with a point charge having value 0.1:
molecule<Molecule>: ( unit=angstrom charge = [ 0.1 ] { atom_labels atoms geometry } = { Q1 Q [ 0.0 0 10.0 ] O1 O [ 0.000000000 0 0.369372944 ] H1 H [ 0.783975899 0 -0.184686472 ] H2 H [-0.783975899 0 -0.184686472 ] } ) )
This feature is designed for doing QM/MM calculations, so, by default, methods will not include interactions between the Q
centers when computing the energy or the gradient. To include these interactions, set include_qq=1
.
The Molecule class has a PointGroup member object, which also has a KeyVal constructor that is called when a Molecule is made. The following example constructs a molecule with symmetry:
molecule<Molecule>: ( symmetry=c2v unit=angstrom { atoms geometry } = { O [0.000000000 0 0.369372944 ] H [0.783975899 0 -0.184686472 ] } ) )Only the symmetry unique atoms need to be specified. Nonunique atoms can be given too, however, numerical errors in the geometry specification can result in the generation of extra atoms so be careful.
|
Takes an (x, y, z) postion and finds an atom within the given tolerance distance. If no atom is found -1 is returned. |
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Returns the index of the atom with the given label. If the label cannot be found -1 is returned. |
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Converts an atom number to the number of its generating unique atom. The return value is in [0, nunique). |
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Converts an atom number to the offset of this atom in the list of generated atoms. The unique atom itself is allows offset 0. |
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Returns a double* containing the nuclear charges of the atoms. The caller is responsible for freeing the return value. |
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This will try to carefully correct symmetry errors in molecules. If any atom is out of place by more then tol, abort will be called. |
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Find this molecules true point group (limited to abelian groups). If the point group of this molecule is set to the highest point group, then the origin must first be set to the center of mass. |
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Return 1 if this given axis is a symmetry element for the molecule. The direction vector must be a unit vector. |
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Sets linear to 1 if the molecular is linear, 0 otherwise. Sets planar to 1 if the molecular is planar, 0 otherwise. |
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Return 1 if the given plane is a symmetry element for the molecule. The perpendicular vector must be a unit vector. |
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Returns the label explicitly assigned to atom. If no label has been assigned, then null is returned. |
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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. |
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If the molecule contains only symmetry unique atoms, this function will generate the other, redundant atoms. The redundant atom will only be generated if there is no other atoms within a distance of tol. If the is another atom and it is not identical, then abort will be called. |