--- name: "sc_Molecule" section: "3" platform: "linux" package: "libsc-doc" version: "2.3.1-22" release: "Debian 12 (Bookworm)" platforms: ["linux"] url: "https://new.carta.tech/sc_Molecule" --- # sc\_Molecule(3) The Molecule class contains information about molecules. ## NAME sc::Molecule - The **Molecule** class contains information about molecules. ## SYNOPSIS `#include ` Inherits **sc::SavableState**. ### Public Member Functions **Molecule** (const **Molecule** &)\ **Molecule** (**StateIn** &)\ **Molecule** (const **Ref**\< **KeyVal** \> &input)\ The **Molecule** **KeyVal** constructor is used to generate a **Molecule** object from the input. **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** ()\ void **throw\_if\_atom\_duplicated** (int begin=0, double tol=1e-3)\ ### 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\_**\ ### Additional Inherited Members ## Detailed Description The **Molecule** class contains information about molecules. 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: ( pdb_file = 'h2o.pdb' ) ``` The following input explicitly gives the atom coordinates, using the **ParsedKeyVal** table notation: ``` 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: ( 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 $C\_{2v}$ symmetry: ``` 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. ## Constructor & Destructor Documentation ### sc::Molecule::Molecule (const Ref\< KeyVal \> & input) The **Molecule** **KeyVal** constructor is used to generate a **Molecule** object from the input. Several examples are given in the **Molecule** class overview. The full list of keywords that are accepted is below. KeywordTypeDefaultDescription `include_q`booleanfalseSome of the atoms can be specified as `Q` and given a customizable charge. Such atoms are a point charge that do not have basis functions. If this option is true, then the `Q` atoms are included when computing the nuclear charge and the electric field due to the nuclear charge. `include_qq`booleanfalseSome of the atoms can be specified as `Q` and given a customizable charge. Such atoms are a point charge that do not have basis functions. If this option is true, then the `Q` atoms are included when computing the nuclear repulsion energy and its derivatives. `atominfo`**AtomInfo**library valuesThis gives information about each atom, such as the symbol, name, and various atomic radii. `symmetry`string\`C1`The Schoenflies symbol of the point group. This is case insensitive. It should be a subgroup of D2h . If it is `auto`, then the appropriate subgroup of D2h will be found. `symmetry_tolerance`double1.0e-4When 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 `symmetry = auto`. `origin`double\[3\]\[0 0 0\]The origin of the symmetry frame. Ignored for `symmetry = auto`. `redundant_atoms`booleanfalseIf true, do not generate symmetry equivalent atoms; they are already given in the input. It should not be necessary to specify this option, since, by default, if a symmetry operation duplicates an atom, the generated atom will not be added to the list of atoms. Ignored for `symmetry = auto`. `pdb_file`stringundefinedThis gives the name of a PDB file, from which the nuclear coordinates will be read. If this is given, the following options will be ignored. `unit`stringbohrThis gives the name of the units used for the geometry. See the **Units** class for information about the known units. This replaces deprecated keywords that are still recognized: `angstrom` and `angstroms`. This is ignored if `pdb_file` is given. `geometry`double\[\]\[3\]noneThis gives the Cartesian coordinates of the molecule. This is ignored if `pdb_file` is given. `atoms`string\[\]noneThis gives the Cartesian coordinates of the molecule. This is ignored if `pdb_file` is given. `ghost`boolean\[\]noneIf true, the atom will be given zero charge. It will still have basis functions, however. This is used to estimate basis set superposition error. This is ignored if `pdb_file` is given. `charge`double\[\]Z for each atomAllows specification of the charge for each atom. This is ignored if `pdb_file` is given. `atom_labels`string\[\]noneThis gives a user defined atom label for each atom. This is ignored if `pdb_file` is given. `mass`double\[\]Taken from **AtomInfo** given by the `atominfo` keyword. This gives a user defined mass for each atom. This is ignored if `pdb_file` is given. ## Member Function Documentation ### int sc::Molecule::atom\_at\_position (double \*, double tol = `0.05`) const Takes an (x, y, z) postion and finds an atom within the given tolerance distance. If no atom is found -1 is returned. ### int sc::Molecule::atom\_label\_to\_index (const char \* label) const Returns the index of the atom with the given label. If the label cannot be found -1 is returned. ### int sc::Molecule::atom\_to\_unique (int iatom) const` [inline]` Converts an atom number to the number of its generating unique atom. The return value is in \[0, nunique). ### int sc::Molecule::atom\_to\_unique\_offset (int iatom) const Converts an atom number to the offset of this atom in the list of generated atoms. The unique atom itself is allows offset 0. \ ### double \* sc::Molecule::charges () const Returns a double\* containing the nuclear charges of the atoms. The caller is responsible for freeing the return value. ### void sc::Molecule::cleanup\_molecule (double tol = `0.1`) 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. ### Ref\< PointGroup \> sc::Molecule::highest\_point\_group (double tol = `1.0e-8`) const 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. ### int sc::Molecule::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. The direction vector must be a unit vector. ### void sc::Molecule::is\_linear\_planar (int & linear, int & planar, double tol = `1.0e-5`) const Sets linear to 1 if the molecular is linear, 0 otherwise. Sets planar to 1 if the molecular is planar, 0 otherwise. ### int sc::Molecule::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. The perpendicular vector must be a unit vector. ### const char \* sc::Molecule::label (int atom) const Returns the label explicitly assigned to atom. If no label has been assigned, then null is returned. ### virtual void sc::Molecule::print (std::ostream & = ExEnv::out0`()`) const` [virtual]` Print information about the molecule. Reimplemented from **sc::DescribedClass**. ### void sc::Molecule::save\_data\_state (StateOut &)` [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**. ### void sc::Molecule::symmetrize (double tol = `0.5`) 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. ## Author Generated automatically by Doxygen for MPQC from the source code.