Data Structures in GMSO
Following data structures are available within GMSO.
Core Classes
A topology. |
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A sub-topology i.e. topology within a topology. |
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An atom represents a single element association in a topology. |
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A 2-partner connection between sites. |
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A 3-partner connection between Atoms. |
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A 4-partner connection between sites. |
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sA 4-partner connection between sites. |
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A description of non-bonded interactions between sites. |
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A descripton of the interaction between 2 bonded partners. |
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A descripton of the interaction between 3 bonded partners. |
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A descripton of the interaction between 4 bonded partners. |
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A description of the interaction between 4 bonded partners. |
Topology
- class gmso.Topology(name='Topology', box=None)[source]
A topology.
A topology represents a chemical structure wherein lie the collection of sites which together form a chemical structure containing connections (gmso.Bond, gmso.Angle and gmso.Dihedral (along with their associated types). A topology is the fundamental data structure in GMSO, from which we can gather various information about the chemical structure and apply a forcefield before converting the structure into a format familiar to various simulation engines.
- Parameters
name (str, optional, default=’Topology’) – A name for the Topology.
box (gmso.Box, optional, default=None) – A gmso.Box object bounding the topology
- Variables
typed (bool) – True if the topology is typed
combining_rule (str, ['lorentz', 'geometric']) – The combining rule for the topology, can be either ‘lorentz’ or ‘geometric’
scaling_factors (dict) – A collection of scaling factors used in the forcefield
n_sites (int) – Number of sites in the topology
n_connections (int) – Number of connections in the topology (Bonds, Angles, Dihedrals, Impropers)
n_bonds (int) – Number of bonds in the topology
n_angles (int) – Number of angles in the topology
n_dihedrals (int) – Number of dihedrals in the topology
n_impropers (int) – Number of impropers in the topology
n_subtops (int) – Number of subtopolgies in the topology
connections (tuple of gmso.Connection objects) – A collection of bonds, angles, dihedrals, and impropers in the topology
bonds (tuple of gmso.Bond objects) – A collection of bonds in the topology
angles (tuple of gmso.Angle objects) – A collection of angles in the topology
dihedrals (tuple of gmso.Dihedral objects) – A collection of dihedrals in the topology
impropers (tuple of gmso.Improper objects) – A collection of impropers in the topology
connection_types (tuple of gmso.Potential objects) – A collection of BondTypes, AngleTypes, DihedralTypes, and ImproperTypes in the topology
atom_types (tuple of gmso.AtomType objects) – A collection of AtomTypes in the topology
bond_types (tuple of gmso.BondType objects) – A collection of BondTypes in the topology
angle_types (tuple of gmso.AngleType objects) – A collection go AngleTypes in the topology
dihedral_types (tuple of gmso.DihedralType objects) – A collection of DihedralTypes in the topology
improper_types (tuple of gmso.ImproperType objects) – A collection of ImproperTypes in the topology
pairpotential_types (tuple of gmso.PairPotentialType objects) – A collection of PairPotentialTypes in the topology
atom_type_expressions (list of gmso.AtomType.expression objects) – A collection of all the expressions for the AtomTypes in topology
connection_type_expressions (list of gmso.Potential.expression objects) – A collection of all the expressions for the Potential objects in the topology that represent a connection type
bond_type_expressions (list of gmso.BondType.expression objects) – A collection of all the expressions for the BondTypes in topology
angle_type_expressions (list of gmso.AngleType.expression objects) – A collection of all the expressions for the AngleTypes in topology
dihedral_type_expressions (list of gmso.DihedralType.expression objects) – A collection of all the expression for the DihedralTypes in the topology
improper_type_expressions (list of gmso.ImproperType.expression objects) – A collection of all the expression for the ImproperTypes in the topology
pairpotential_type_expressions (list of gmso.PairPotentialType.expression objects) – A collection of all the expression for the PairPotentialTypes in the topology
See also
gmso.SubTopology
A topology within a topology
- add_connection(connection, update_types=True)[source]
Add a gmso.Connection object to the topology.
This method will add a gmso.Connection object to the topology, it can be used to generically include any Connection object i.e. Bond or Angle or Dihedral to the topology. According to the type of object added, the equivalent collection in the topology is updated. For example- If you add a Bond, this method will update topology.connections and topology.bonds object. Additionally, if update_types is True (default behavior), it will also update any Potential objects associated with the connection.
- Parameters
connection (one of gmso.Connection, gmso.Bond, gmso.Angle, gmso.Dihedral, or gmso.Improper object)
update_types (bool, default=True) – If True also add any Potential object associated with connection to the topology.
- Returns
The Connection object or equivalent Connection object that is in the topology
- Return type
gmso.Connection
- add_site(site, update_types=True)[source]
Add a site to the topology.
This method will add a site to the existing topology, since sites are stored in an indexed set, adding redundant site will have no effect. If the update_types parameter is set to true (default behavior), this method will also check if there is an gmso.AtomType associated with the site and it to the topology’s AtomTypes collection.
- Parameters
site (gmso.core.Site) – Site to be added to this topology
update_types ((bool), default=True) – If true, add this site’s atom type to the topology’s set of AtomTypes
SubTopology
- class gmso.SubTopology(name='Sub-Topology', parent=None)[source]
A sub-topology i.e. topology within a topology.
This class provides a hierarchical topological representation to the topology as it imperative with many chemical structures to have separation of layers/ boundaries. A sub-topology can be added to a gmso.Topology object which will be the parent of the sub-topology.
- Parameters
name (str, optional, default=’Sub-Topology’) – Name of the sub-topology
parent (gmso.Topology, optional, default=None) – The parent topology of this SubTopology
- Variables
sites (IndexedSet of gmso.Site objects) – Collection of sites within this sub-topology
n_sites (int) – Number of sites withing this sub-topology
- add_site(site, update_types=True)[source]
Add a site to this sub-topology.
This method adds a site to the sub-topology. If the sub-topology has a parent, the site will also be added to the parent topology. If the update_types parameter is set to true (default behavior), this method will also check if there is an gmso.AtomType associated with the site and it to the sub-topology’s AtomTypes collection.
- Parameters
site (gmso.Atom) – The site to be added to this sub-topology
update_types ((bool), default=True) – If true, add this site’s atom type to the sub-topology’s set of AtomTypes
- Raises
TypeError – If the parameter site is not of type topology.Site
- property n_sites
Return the number of sites associated with the sub-topology.
- property name
Return the name of the sub-topology.
- property parent
Return the parent of the sub-topology.
- property sites
Return the sites associated with the sub-topology.
Atom
- class gmso.Atom(name="''", label="''", residue_number=None, residue_name=None, position=None, charge=None, mass=None, element=None, atom_type=None)[source]
An atom represents a single element association in a topology.
Atoms are the representation of an element within gmso that describes any general atom in a molecular simulation. Atoms also contain information that are unique to elements vs other types of interaction sites in molecular simulations. For example, charge, mass, and periodic table information.
- Parameters
name (str, default=’’) – Name of the atom, defaults to class name
label (str, default=’’) – Label to be assigned to the atom
residue_number (<class ‘pydantic.types.StrictInt’>, default=None) – Residue number for the atom
residue_name (StrictStr, default=None) – Residue label for the atom
position (Union[Sequence[float], numpy.ndarray, unyt.array.unyt_array], default=None) – The 3D Cartesian coordinates of the position of the atom
charge (Union[unyt.array.unyt_quantity, float, NoneType], default=None) – Charge of the atom
mass (Union[unyt.array.unyt_quantity, float, NoneType], default=None) – Mass of the atom
element (<class ‘gmso.core.element.Element’>, default=None) – Element associated with the atom
atom_type (<class ‘gmso.core.atom_type.AtomType’>, default=None) – AtomType associated with the atom
Notes
Atoms have all the attributes inherited from the base Site class, The order of precedence when attaining properties charge and mass is:
atom.charge > atom.atom_type.charge
atom.mass > atom.atom_type.mass
Examples
>>> from gmso.core.atom import Atom >>> atom1 = Atom(name='lithium')See also
gmso.abc.AbstractSite
An Abstract Base class for implementing site objects in GMSO. The class Atom bases from the gmso.abc.abstract site class
- property atom_type: Optional[gmso.core.atom_type.AtomType]
Return the atom_type associated with the atom.
- property charge: Optional[unyt.array.unyt_quantity]
Return the charge of the atom.
- property element: Optional[gmso.core.element.Element]
Return the element associated with the atom.
- property mass: Optional[unyt.array.unyt_quantity]
Return the mass of the atom.
Bond
- class gmso.Bond(name="''", connection_members=None, bond_type=None)[source]
A 2-partner connection between sites.
This is a subclass of the gmso.abc.Connection superclass. This class has strictly 2 members in its connection_members. The connection_type in this class corresponds to gmso.BondType.
- Parameters
name (str, default=’’) – Name of the bond. Defaults to class name
bond_members (Tuple[gmso.core.atom.Atom, gmso.core.atom.Atom], default=None) – The 2 atoms involved in the bond.
bond_type (<class ‘gmso.core.bond_type.BondType’>, default=None) – BondType of this bond.
Notes
- Inherits some methods from Connection:
__eq__, __repr__, _validate methods.
Additional _validate methods are presented.
- property bond_type
Return parameters of the potential type.
- property connection_type
Return parameters of the potential type.
Angle
- class gmso.Angle(name="''", connection_members=None, angle_type=None)[source]
A 3-partner connection between Atoms.
This is a subclass of the gmso.Connection superclass. This class has strictly 3 members in its connection members. The connection_type in this class corresponds to gmso.AngleType.
- Parameters
name (str, default=’’) – Name of the angle. Defaults to class name
angle_members (Tuple[gmso.core.atom.Atom, gmso.core.atom.Atom, gmso.core.atom.Atom], default=None) – The 3 atoms involved in the angle.
angle_type (<class ‘gmso.core.angle_type.AngleType’>, default=None) – AngleType of this angle.
Notes
- Inherits some methods from Connection:
__eq__, __repr__, _validate methods
Additional _validate methods are presented
- property angle_type
Return the angle type if the angle is parametrized.
- property connection_type
Return the angle type if the angle is parametrized.
Dihedral
- class gmso.Dihedral(name="''", connection_members=None, dihedral_type=None)[source]
A 4-partner connection between sites.
This is a subclass of the gmso.Connection superclass. This class has strictly 4 members in its connection_members. The connection_type in this class corresponds to gmso.DihedralType. The connectivity of a dihedral is:
m1–m2–m3–m4
where m1, m2, m3, and m4 are connection members 1-4, respectively.
- Parameters
name (str, default=’’) – Name of the dihedral. Defaults to class name
dihedral_members (Tuple[gmso.core.atom.Atom, gmso.core.atom.Atom, gmso.core.atom.Atom, gmso.core.atom.Atom], default=None) – The 4 atoms involved in the dihedral.
dihedral_type (<class ‘gmso.core.dihedral_type.DihedralType’>, default=None) – DihedralType of this dihedral.
Notes
- Inherits some methods from Connection:
__eq__, __repr__, _validate methods
Additional _validate methods are presented
Improper
- class gmso.Improper(name="''", connection_members=None, improper_type=None)[source]
sA 4-partner connection between sites.
This is a subclass of the gmso.Connection superclass. This class has strictly 4 members in its connection_members. The connection_type in this class corresponds to gmso.ImproperType The connectivity of an improper is:
m2 | m1 / m3 m4
where m1, m2, m3, and m4 are connection members 1-4, respectively.
- Parameters
name (str, default=’’) – Name of the improper. Defaults to class name
improper_members (Tuple[gmso.core.atom.Atom, gmso.core.atom.Atom, gmso.core.atom.Atom, gmso.core.atom.Atom], default=None) – The 4 atoms of this improper. Central atom first, then the three atoms connected to the central site.
improper_type (<class ‘gmso.core.improper_type.ImproperType’>, default=None) – ImproperType of this improper.
Notes
- Inherits some methods from Connection:
__eq__, __repr__, _validate methods
Additional _validate methods are presented
- property connection_type
Return Potential object for this connection if it exists.
- equivalent_members()[source]
Get a set of the equivalent connection member tuples.
- Returns
A unique set of tuples of equivalent connection members
- Return type
Notes
For an improper:
i, j, k, l == i, k, j, l
where i, j, k, and l are the connection members.
- property improper_type
Return Potential object for this connection if it exists.
Potential Classes
AtomType
- class gmso.AtomType(name='AtomType', mass=unyt_quantity(0., 'g/mol'), charge=unyt_quantity(0., 'C'), expression=None, parameters=None, potential_expression=None, independent_variables=None, atomclass='', doi='', overrides=None, definition='', description='', tags=None, topology=None)[source]
A description of non-bonded interactions between sites.
- Parameters
name (str, default=’’) – The name of the potential. Defaults to class name
potential_expression (_PotentialExpression, default=<PotentialExpression, expression: a*x + b, 1 independent variables>) – The mathematical expression for the potential
tags (Any, default={}) – Tags associated with the potential
topology (Any, default=None) – the topology of which this potential is a part of
mass (unyt_array, default=0.0 g/mol) – The mass of the atom type
charge (unyt_array, default=0.0 C) – The charge of the atom type
atomclass (str, default=’’) – The class of the atomtype
doi (str, default=’’) – Digital Object Identifier of publication where this atom type was introduced
overrides (str, default=set()) – Set of other atom types that this atom type overrides
definition (str, default=’’) – SMARTS string defining this atom type
description (str, default=’’) – Description for the AtomType
expression (Optional[Union[str, sympy.Expr]], default=None) – The mathematical expression of the functional form of the potential.
parameters (Optional[dict], default=None) – The parameters of the Potential expression and their corresponding values, as unyt quantities
independent_variables (Optional[Union[set, str]], default=None) – The independent variables in the Potential’s expression.
- property atomclass
Return the atomclass of the atom_type.
- property charge
Return the charge of the atom_type.
- property definition
Return the SMARTS string of the atom_type.
- property description
Return the description of the atom_type.
- property doi
Return the doi of the atom_type.
- property mass
Return the mass of the atom_type.
- property overrides
Return the overrides of the atom_type.
BondType
- class gmso.BondType(name='BondType', expression=None, parameters=None, independent_variables=None, potential_expression=None, member_types=None, member_classes=None, topology=None, tags=None)[source]
A descripton of the interaction between 2 bonded partners.
This is a subclass of the gmso.core.Potential superclass. BondType represents a bond type and includes the functional form describing its interactions. The functional form of the potential is stored as a sympy expression and the parameters, with units, are stored explicitly. The AtomTypes that are used to define the bond type are stored as member_types.
- Parameters
name (str, default=’’) – The name of the potential. Defaults to class name
potential_expression (_PotentialExpression, default=<PotentialExpression, expression: a*x + b, 1 independent variables>) – The mathematical expression for the potential
tags (Any, default={}) – Tags associated with the potential
topology (Any, default=None) – the topology of which this potential is a part of
member_types (Tuple[str, str], default=None) – List-like of of gmso.AtomType.name defining the members of this bond type
member_classes (Tuple[str, str], default=None) – List-like of of gmso.AtomType.atomclass defining the members of this bond type
expression (Optional[Union[str, sympy.Expr]], default=None) – The mathematical expression of the functional form of the potential.
parameters (Optional[dict], default=None) – The parameters of the Potential expression and their corresponding values, as unyt quantities
independent_variables (Optional[Union[set, str]], default=None) – The independent variables in the Potential’s expression.
Notes
- Inherits many functions from gmso.ParametricPotential:
__eq__, _validate functions
- property member_types
Return the members involved in this bondtype.
AngleType
- class gmso.AngleType(name='AngleType', expression=None, parameters=None, independent_variables=None, potential_expression=None, member_types=None, member_classes=None, topology=None, tags=None)[source]
A descripton of the interaction between 3 bonded partners.
This is a subclass of the gmso.core.Potential superclass. AngleType represents an angle type and includes the functional form describing its interactions. The functional form of the potential is stored as a sympy expression and the parameters, with units, are stored explicitly. The AtomTypes that are used to define the angle type are stored as member_types.
- Parameters
name (str, default=’’) – The name of the potential. Defaults to class name
potential_expression (_PotentialExpression, default=<PotentialExpression, expression: a*x + b, 1 independent variables>) – The mathematical expression for the potential
tags (Any, default={}) – Tags associated with the potential
topology (Any, default=None) – the topology of which this potential is a part of
member_types (Tuple[str, str, str], default=None) – List-like of gmso.AtomType.name defining the members of this angle type
member_classes (Tuple[str, str, str], default=None) – List-like of gmso.AtomType.atomclass defining the members of this angle type
expression (Optional[Union[str, sympy.Expr]], default=None) – The mathematical expression of the functional form of the potential.
parameters (Optional[dict], default=None) – The parameters of the Potential expression and their corresponding values, as unyt quantities
independent_variables (Optional[Union[set, str]], default=None) – The independent variables in the Potential’s expression.
Notes
- Inherits many functions from gmso.ParametricPotential:
__eq__, _validate functions
DihedralType
- class gmso.DihedralType(name='DihedralType', expression=None, parameters=None, independent_variables=None, potential_expression=None, member_types=None, member_classes=None, topology=None, tags=None)[source]
A descripton of the interaction between 4 bonded partners.
This is a subclass of the gmso.core.Potential superclass. DihedralType represents a dihedral type and includes the functional form describing its interactions. The functional form of the potential is stored as a sympy expression and the parameters, with units, are stored explicitly. The AtomTypes that are used to define the dihedral type are stored as member_types. The connectivity of a dihedral is:
m1–m2–m3–m4
where m1, m2, m3, and m4 are connection members 1-4, respectively.
- Parameters
name (str, default=’’) – The name of the potential. Defaults to class name
potential_expression (_PotentialExpression, default=<PotentialExpression, expression: a*x + b, 1 independent variables>) – The mathematical expression for the potential
tags (Any, default={}) – Tags associated with the potential
topology (Any, default=None) – the topology of which this potential is a part of
member_types (Tuple[str, str, str, str], default=None) – List-like of of gmso.AtomType.name defining the members of this dihedral type
member_classes (Tuple[str, str, str, str], default=None) – List-like of of gmso.AtomType.atomclass defining the members of this dihedral type
expression (Optional[Union[str, sympy.Expr]], default=None) – The mathematical expression of the functional form of the potential.
parameters (Optional[dict], default=None) – The parameters of the Potential expression and their corresponding values, as unyt quantities
independent_variables (Optional[Union[set, str]], default=None) – The independent variables in the Potential’s expression.
Notes
- Inherits many functions from gmso.ParametricPotential:
__eq__, _validate functions
ImproperType
- class gmso.ImproperType(name='ImproperType', expression=None, parameters=None, independent_variables=None, potential_expression=None, member_types=None, member_classes=None, topology=None, tags=None)[source]
A description of the interaction between 4 bonded partners.
This is a subclass of the gmso.core.Potential superclass. ImproperType represents a improper type and includes the functional form describing its interactions. The functional form of the potential is stored as a sympy expression and the parameters, with units, are stored explicitly. The AtomTypes that are used to define the improper type are stored as member_types. The connectivity of an improper is:
m2 | m1 / m3 m4
where m1, m2, m3, and m4 are connection members 1-4, respectively.
- Parameters
name (str, default=’’) – The name of the potential. Defaults to class name
potential_expression (_PotentialExpression, default=<PotentialExpression, expression: a*x + b, 1 independent variables>) – The mathematical expression for the potential
tags (Any, default={}) – Tags associated with the potential
topology (Any, default=None) – the topology of which this potential is a part of
member_types (Tuple[str, str, str, str], default=None) – List-like of gmso.AtomType.name defining the members of this improper type
member_classes (Tuple[str, str, str, str], default=None) – List-like of gmso.AtomType.atomclass defining the members of this improper type
expression (Optional[Union[str, sympy.Expr]], default=None) – The mathematical expression of the functional form of the potential.
parameters (Optional[dict], default=None) – The parameters of the Potential expression and their corresponding values, as unyt quantities
independent_variables (Optional[Union[set, str]], default=None) – The independent variables in the Potential’s expression.
Notes
- Inherits many functions from gmso.ParametricPotential:
__eq__, _validate functions
- property member_types
Return member information for this ImproperType.
PairPotentialType
- class gmso.PairPotentialType(name='PairPotentialType', expression=None, parameters=None, independent_variables=None, potential_expression=None, member_types=None, topology=None, tags=None)[source]
A description of custom pairwise potential between 2 AtomTypes that does not follow combination rule.
This is a subclass of the gmso.core.ParametricPotential superclass. PairPotentialType represents a type of pairwise potential between two Atomtypes that does not follow a specific combination rule, and includes the functional form describing its interactions. The functional form of the potential is stored as a sympy expression and the parameters, with units, are stored explicitly. The AtomTypes that are used to define the dihedral type are stored as member_types.
- Parameters
name (str, default=’’) – The name of the potential. Defaults to class name
potential_expression (_PotentialExpression, default=<PotentialExpression, expression: a*x + b, 1 independent variables>) – The mathematical expression for the potential
tags (Any, default={}) – Tags associated with the potential
topology (Any, default=None) – the topology of which this potential is a part of
member_types (Tuple[str, str], default=None) – List-like of strs, referring to gmso.Atomtype.name or gmso.Atomtype.atomclass, defining the members of this pair potential type
expression (Optional[Union[str, sympy.Expr]], default=None) – The mathematical expression of the functional form of the potential.
parameters (Optional[dict], default=None) – The parameters of the Potential expression and their corresponding values, as unyt quantities
independent_variables (Optional[Union[set, str]], default=None) – The independent variables in the Potential’s expression.
Notes
- Inherits many functions from gmso.ParametricPotential:
__eq__, _validate functions
ForceField
- class gmso.ForceField(xml_loc=None, strict=True, greedy=True)[source]
A generic implementation of the forcefield class.
The ForceField class is one of the core data structures in gmso, which is used to hold a collection of gmso.core.Potential subclass objects along with some metadata to represent a forcefield. The forcefield object can be applied to any gmso.Topology which has effects on its Sites, Bonds, Angles and Dihedrals.
- Parameters
name (str) – Name of the forcefield, default ‘ForceField’
version (str) – a cannonical semantic version of the forcefield, default 1.0.0
strict (bool, default=True) – If true, perform a strict validation of the forcefield XML file
greedy (bool, default=True) – If True, when using strict mode, fail on the first error/mismatch
- Variables
name (str) – Name of the forcefield
version (str) – Version of the forcefield
atom_types (dict) – A collection of atom types in the forcefield
bond_types (dict) – A collection of bond types in the forcefield
angle_types (dict) – A collection of angle types in the forcefield
dihedral_types (dict) – A collection of dihedral types in the forcefield
units (dict) – A collection of unyt.Unit objects used in the forcefield
scaling_factors (dict) – A collection of scaling factors used in the forcefield
See also
gmso.ForceField.from_xml
A class method to create forcefield object from XML files
gmso.utils.ff_utils.validate
Function to validate the gmso XML file
- property atom_class_groups
Return a dictionary of atomClasses in the Forcefield.
- classmethod from_xml(xmls_or_etrees, strict=True, greedy=True)[source]
Create a gmso.Forcefield object from XML File(s).
This class method creates a ForceField object from the reference XML file. This method takes in a single or collection of XML files with information about gmso.AtomTypes, gmso.BondTypes, gmso.AngleTypes , gmso.PairPotentialTypes and gmso.DihedralTypes to create the ForceField object.
- Parameters
xmls_or_etrees (Union[str, Iterable[str], etree._ElementTree, Iterable[etree._ElementTree]]) – The forcefield XML locations or XML Element Trees
strict (bool, default=True) – If true, perform a strict validation of the forcefield XML file
greedy (bool, default=True) – If True, when using strict mode, fail on the first error/mismatch
- Returns
forcefield – A gmso.Forcefield object with a collection of Potential objects created using the information in the XML file
- Return type
- get_parameters(group, key, warn=False, copy=False)[source]
Return parameters for a specific potential by key in this ForceField.
This function uses the get_potential function to get Parameters
See also
gmso.ForceField.get_potential
Get specific potential/parameters from a forcefield potential group by key
- get_potential(group, key, warn=False)[source]
Return a specific potential by key in this ForceField.
- Parameters
group ({‘atom_types’, ‘bond_types’, ‘angle_types’, ‘dihedral_types’, ‘improper_types’}) – The potential group to perform this search on
key (str or list of str) – The key to lookup for this potential group
warn (bool, default=False) – If true, raise a warning instead of Error if no match found
- Returns
The parametric potential requested
- Return type
gmso.ParametricPotential
- Raises
MissingPotentialError – When the potential specified by key is not found in the ForceField potential group group
- group_angle_types_by_expression()[source]
Return all AngleTypes in this ForceField with grouped by expression.
See also
_group_by_expression
Groups a dictionary of gmso.ParametricPotentials by their expression
- Returns
A dictionary where the key, value -> expression, list of AngleTypes with that expression
- Return type
- group_atom_types_by_expression()[source]
Return all AtomTypes in this ForceField with grouped by expression.
See also
_group_by_expression
Groups a dictionary of gmso.ParametricPotentials by their expression
- Returns
A dictionary where the key, value -> expression, list of atom_types with that expression
- Return type
- group_bond_types_by_expression()[source]
Return all BondTypes in this ForceField with grouped by expression.
See also
_group_by_expression
Groups a dictionary of gmso.ParametricPotentials by their expression
- Returns
A dictionary where the key, value -> expression, list of BondTypes with that expression
- Return type
- group_dihedral_types_by_expression()[source]
Return all DihedralTypes in this ForceField with grouped by expression.
See also
_group_by_expression
Groups a dictionary of gmso.ParametricPotentials by their expression
- Returns
A dictionary where the key, value -> expression, list of DihedralTypes with that expression
- Return type
- group_improper_types_by_expression()[source]
Return all ImproperTypes in this ForceField with grouped by expression.
See also
_group_by_expression
Groups a dictionary of gmso.ParametricPotentials by their expression
- Returns
A dictionary where the key, value -> expression, list of ImproperTypes with that expression
- Return type
- group_pairpotential_types_by_expression()[source]
Return all PairPotentialTypes in this ForceField with grouped by expression
See also
_group_by_expression
Groups a dictionary of gmso.ParametricPotentials by their expression
- Returns
A dictionary where the key, value -> expression, list of PairPotentialTypes with that expression
- Return type