232 lines
13 KiB
Plaintext
232 lines
13 KiB
Plaintext
---
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title: Molecule
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description: API reference for qiskit.chemistry.drivers.Molecule
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in_page_toc_min_heading_level: 1
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python_api_type: class
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python_api_name: qiskit.chemistry.drivers.Molecule
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---
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# qiskit.chemistry.drivers.Molecule
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<Class id="qiskit.chemistry.drivers.Molecule" isDedicatedPage={true} github="https://github.com/qiskit-community/qiskit-aqua/tree/stable/0.9/qiskit/chemistry/drivers/molecule.py" signature="Molecule(geometry, multiplicity=1, charge=0, degrees_of_freedom=None, masses=None)" modifiers="class">
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Driver-independent Molecule definition.
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This module implements an interface for a driver-independent, i.e. generic molecule definition. It defines the composing atoms (with properties like masses), and allows for changing the molecular geometry through given degrees of freedom (e.g. bond-stretching, angle-bending, etc.). The geometry as provided in the constructor can be affected, through setting perturbations, and it is this perturbed geometry that is supplied by the geometry getter. Setting perturbations to None will cause the original geometry to be returned, and there is a getter to get this value directly if its needed.
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**Parameters**
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* **geometry** (`List`\[`Tuple`\[`str`, `List`\[`float`]]]) – A list of atoms defining a given molecule where each item in the list is an atom name together with a list of 3 floats representing the x,y and z Cartesian coordinates of the atom’s position in units of **Angstrom**.
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* **multiplicity** (`int`) – Multiplicity (2S+1) of the molecule
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* **charge** (`int`) – Charge on the molecule
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* **degrees\_of\_freedom** (`Optional`\[`List`\[`Callable`]]) – List of functions taking a perturbation value and geometry and returns a perturbed geometry. Helper functions for typical perturbations are provided and can be used by the form itertools.partial(Molecule.stretching\_potential,\{‘atom\_pair’: (1, 2)) to specify the desired degree of freedom.
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* **masses** (`Optional`\[`List`\[`float`]]) – Mass of each atom the molecule may optionally be provided.
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**Raises**
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**ValueError** – Length of masses must match length of geometries.
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### \_\_init\_\_
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<Function id="qiskit.chemistry.drivers.Molecule.__init__" signature="__init__(geometry, multiplicity=1, charge=0, degrees_of_freedom=None, masses=None)">
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**Parameters**
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* **geometry** (`List`\[`Tuple`\[`str`, `List`\[`float`]]]) – A list of atoms defining a given molecule where each item in the list is an atom name together with a list of 3 floats representing the x,y and z Cartesian coordinates of the atom’s position in units of **Angstrom**.
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* **multiplicity** (`int`) – Multiplicity (2S+1) of the molecule
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* **charge** (`int`) – Charge on the molecule
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* **degrees\_of\_freedom** (`Optional`\[`List`\[`Callable`]]) – List of functions taking a perturbation value and geometry and returns a perturbed geometry. Helper functions for typical perturbations are provided and can be used by the form itertools.partial(Molecule.stretching\_potential,\{‘atom\_pair’: (1, 2)) to specify the desired degree of freedom.
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* **masses** (`Optional`\[`List`\[`float`]]) – Mass of each atom the molecule may optionally be provided.
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**Raises**
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**ValueError** – Length of masses must match length of geometries.
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</Function>
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## Methods
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| ------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------- |
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| [`__init__`](#qiskit.chemistry.drivers.Molecule.__init__ "qiskit.chemistry.drivers.Molecule.__init__")(geometry\[, multiplicity, charge, …]) | **type geometry**`List`\[`Tuple`\[`str`, `List`\[`float`]]] |
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| [`absolute_angle`](#qiskit.chemistry.drivers.Molecule.absolute_angle "qiskit.chemistry.drivers.Molecule.absolute_angle")(angle, geometry, atom\_trio) | **type angle**`float` |
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| [`absolute_bending`](#qiskit.chemistry.drivers.Molecule.absolute_bending "qiskit.chemistry.drivers.Molecule.absolute_bending")(bend, geometry, atom\_trio) | **type bend**`float` |
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| [`absolute_distance`](#qiskit.chemistry.drivers.Molecule.absolute_distance "qiskit.chemistry.drivers.Molecule.absolute_distance")(distance, geometry, atom\_pair) | **type distance**`float` |
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| [`absolute_stretching`](#qiskit.chemistry.drivers.Molecule.absolute_stretching "qiskit.chemistry.drivers.Molecule.absolute_stretching")(perturbation, geometry, …) | **type perturbation**`float` |
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| [`relative_bending`](#qiskit.chemistry.drivers.Molecule.relative_bending "qiskit.chemistry.drivers.Molecule.relative_bending")(bend, geometry, atom\_trio) | **type bend**`float` |
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| [`relative_stretching`](#qiskit.chemistry.drivers.Molecule.relative_stretching "qiskit.chemistry.drivers.Molecule.relative_stretching")(perturbation, geometry, …) | **type perturbation**`float` |
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## Attributes
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| --------------------------------------------------------------------------------------------------------------------- | --------------------------------------------- |
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| [`charge`](#qiskit.chemistry.drivers.Molecule.charge "qiskit.chemistry.drivers.Molecule.charge") | Get charge |
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| [`geometry`](#qiskit.chemistry.drivers.Molecule.geometry "qiskit.chemistry.drivers.Molecule.geometry") | Get geometry accounting for any perturbations |
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| [`masses`](#qiskit.chemistry.drivers.Molecule.masses "qiskit.chemistry.drivers.Molecule.masses") | Get masses |
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| [`multiplicity`](#qiskit.chemistry.drivers.Molecule.multiplicity "qiskit.chemistry.drivers.Molecule.multiplicity") | Get multiplicity |
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| [`perturbations`](#qiskit.chemistry.drivers.Molecule.perturbations "qiskit.chemistry.drivers.Molecule.perturbations") | Get perturbations |
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| [`units`](#qiskit.chemistry.drivers.Molecule.units "qiskit.chemistry.drivers.Molecule.units") | The geometry coordinate units |
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### absolute\_angle
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<Function id="qiskit.chemistry.drivers.Molecule.absolute_angle" signature="absolute_angle(angle, geometry, atom_trio)" modifiers="classmethod">
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**Parameters**
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* **angle** (`float`) – The magnitude of the perturbation in **radians**. **Positive bend is always in the direction toward Atom3.** the direction of increasing the starting angle.\*\*
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* **geometry** (`List`\[`Tuple`\[`str`, `List`\[`float`]]]) – The initial geometry to perturb.
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* **atom\_trio** (`Tuple`\[`int`, `int`, `int`]) – A tuple with three integers, indexing which atoms from the starting geometry should be bent apart. **Atom1 is bent \*away\* from Atom3 by an angle whose vertex is Atom2 and equal to \*\*angle**, while Atom2 and Atom3 remain stationary.\*\*
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**Return type**
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`List`\[`Tuple`\[`str`, `List`\[`float`]]]
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**Returns**
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end geometry
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</Function>
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### absolute\_bending
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<Function id="qiskit.chemistry.drivers.Molecule.absolute_bending" signature="absolute_bending(bend, geometry, atom_trio)" modifiers="classmethod">
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**Parameters**
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* **bend** (`float`) – The magnitude of the perturbation in **radians**. **Positive bend is always in the direction toward Atom3.** the direction of increasing the starting angle.\*\*
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* **geometry** (`List`\[`Tuple`\[`str`, `List`\[`float`]]]) – The initial geometry to perturb.
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* **atom\_trio** (`Tuple`\[`int`, `int`, `int`]) – A tuple with three integers, indexing which atoms from the starting geometry should be bent apart. **Atom1 is bent \*away\* from Atom3 by an angle whose vertex is Atom2 and equal to the initial angle \*\*plus** bend, while Atom2 and Atom3 remain stationary.\*\*
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**Return type**
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`List`\[`Tuple`\[`str`, `List`\[`float`]]]
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**Returns**
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end geometry
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</Function>
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### absolute\_distance
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<Function id="qiskit.chemistry.drivers.Molecule.absolute_distance" signature="absolute_distance(distance, geometry, atom_pair)" modifiers="classmethod">
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**Parameters**
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* **distance** (`float`) – The (new) distance between the two atoms.
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* **geometry** (`List`\[`Tuple`\[`str`, `List`\[`float`]]]) – The initial geometry to perturb.
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* **atom\_pair** (`Tuple`\[`int`, `int`]) – A tuple with two integers, indexing which atoms from the starting geometry should be moved apart. **Atom1 is moved away (at the given distance) from Atom2, while Atom2 remains stationary.**
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**Return type**
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`List`\[`Tuple`\[`str`, `List`\[`float`]]]
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**Returns**
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end geometry
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</Function>
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### absolute\_stretching
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<Function id="qiskit.chemistry.drivers.Molecule.absolute_stretching" signature="absolute_stretching(perturbation, geometry, atom_pair)" modifiers="classmethod">
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**Parameters**
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* **perturbation** (`float`) – The magnitude of the stretch. (New distance = stretch + old distance)
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* **geometry** (`List`\[`Tuple`\[`str`, `List`\[`float`]]]) – The initial geometry to perturb.
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* **atom\_pair** (`Tuple`\[`int`, `int`]) – A tuple with two integers, indexing which atoms from the starting geometry should be stretched apart. **Atom1 is stretched away from Atom2, while Atom2 remains stationary.**
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**Return type**
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`List`\[`Tuple`\[`str`, `List`\[`float`]]]
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**Returns**
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end geometry
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</Function>
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### charge
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<Attribute id="qiskit.chemistry.drivers.Molecule.charge">
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Get charge
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**Return type**
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`int`
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</Attribute>
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### geometry
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<Attribute id="qiskit.chemistry.drivers.Molecule.geometry">
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Get geometry accounting for any perturbations
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**Return type**
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`List`\[`Tuple`\[`str`, `List`\[`float`]]]
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</Attribute>
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### masses
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<Attribute id="qiskit.chemistry.drivers.Molecule.masses">
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Get masses
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**Return type**
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`Optional`\[`List`\[`float`]]
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</Attribute>
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### multiplicity
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<Attribute id="qiskit.chemistry.drivers.Molecule.multiplicity">
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Get multiplicity
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**Return type**
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`int`
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</Attribute>
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### perturbations
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<Attribute id="qiskit.chemistry.drivers.Molecule.perturbations">
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Get perturbations
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**Return type**
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`Optional`\[`List`\[`float`]]
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</Attribute>
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### relative\_bending
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<Function id="qiskit.chemistry.drivers.Molecule.relative_bending" signature="relative_bending(bend, geometry, atom_trio)" modifiers="classmethod">
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**Parameters**
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* **bend** (`float`) – The magnitude of the perturbation in **radians**. **Positive bend is always in the direction toward Atom3.** the direction of increasing the starting angle.\*\*
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* **geometry** (`List`\[`Tuple`\[`str`, `List`\[`float`]]]) – The initial geometry to perturb.
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* **atom\_trio** (`Tuple`\[`int`, `int`, `int`]) – A tuple with three integers, indexing which atoms from the starting geometry should be bent apart. **Atom1 is bent \*away\* from Atom3 by an angle whose vertex is Atom2 and equal to the initial angle \*\*times** bend, while Atom2 and Atom3 remain stationary.\*\*
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**Return type**
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`List`\[`Tuple`\[`str`, `List`\[`float`]]]
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**Returns**
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end geometry
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</Function>
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### relative\_stretching
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<Function id="qiskit.chemistry.drivers.Molecule.relative_stretching" signature="relative_stretching(perturbation, geometry, atom_pair)" modifiers="classmethod">
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**Parameters**
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* **perturbation** (`float`) – The magnitude of the stretch. (New distance = stretch \* old distance)
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* **geometry** (`List`\[`Tuple`\[`str`, `List`\[`float`]]]) – The initial geometry to perturb.
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* **atom\_pair** (`Tuple`\[`int`, `int`]) – A tuple with two integers, indexing which atoms from the starting geometry should be stretched apart. **Atom1 is stretched away from Atom2, while Atom2 remains stationary.**
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**Return type**
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`List`\[`Tuple`\[`str`, `List`\[`float`]]]
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**Returns**
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end geometry
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</Function>
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### units
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<Attribute id="qiskit.chemistry.drivers.Molecule.units">
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The geometry coordinate units
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</Attribute>
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</Class>
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