Data Structures in GMSO

Following data structures are available within GMSO.

Core Classes

gmso.Topology

A topology.

gmso.SubTopology

A sub-topology i.e. topology within a topology.

gmso.Atom

An atom represents a single element association in a topology.

gmso.Bond

A 2-partner connection between sites.

gmso.Angle

A 3-partner connection between Atoms.

gmso.Dihedral

A 4-partner connection between sites.

gmso.Improper

sA 4-partner connection between sites.

gmso.AtomType

A description of non-bonded interactions between sites.

gmso.BondType

A descripton of the interaction between 2 bonded partners.

gmso.AngleType

A descripton of the interaction between 3 bonded partners.

gmso.DihedralType

A descripton of the interaction between 4 bonded partners.

gmso.ImproperType

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

update_topology()[source]

Update the entire topology.

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

json_dict()[source]

Return a json serializable dictionary of this subtopology.

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="''", 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

  • 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:

  1. atom.charge > atom.atom_type.charge

  2. 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

class Config[source]

Pydantic configuration for the atom 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.

classmethod is_valid_charge(charge)[source]

Ensure that the charge is physically meaningful.

classmethod is_valid_mass(mass)[source]

Ensure that the mass is physically meaningful.

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.

class Config[source]

Pydantic configuration for Bond.

property bond_type

Return parameters of the potential type.

property connection_type

Return parameters of the potential type.

equivalent_members()[source]

Get a set of the equivalent connection member tuples.

Returns

A unique set of tuples of equivalent connection members

Return type

frozenset

Notes

For a bond:

i, j == j, i

where i and j are the connection members.

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

class Config[source]

Support pydantic configuration for attributes and behavior.

property angle_type

Return the angle type if the angle is parametrized.

property connection_type

Return the angle type if the angle is parametrized.

equivalent_members()[source]

Return a set of the equivalent connection member tuples.

Returns

A unique set of tuples of equivalent connection members

Return type

frozenset

Notes

For an angle:

i, j, k == k, j, i

where i, j and k are the connection members.

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

equivalent_members()[source]

Get a set of the equivalent connection member tuples

Returns

A unique set of tuples of equivalent connection members

Return type

frozenset

Notes

For a dihedral:

i, j, k, l == l, k, j, i

where i, j, k, and l are the connection members.

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

class Config[source]

Pydantic configuration to link fields to their public attribute.

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

frozenset

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
  • tags (Any, default={}) – Tags associated with the metadata

  • 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

  • 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.

class Config[source]

Pydantic configuration of the attributes for an atom_type.

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.

classmethod validate_charge(charge)[source]

Check to see that a charge is a unyt array of the right dimension.

classmethod validate_mass(mass)[source]

Check to see that a mass is a unyt array of the right dimension.

BondType

class gmso.BondType(name='BondType', expression=None, parameters=None, independent_variables=None, potential_expression=None, member_types=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
  • tags (Any, default={}) – Tags associated with the metadata

  • 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

  • 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 or 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

class Config[source]

Pydantic configuration for class attributes.

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, 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
  • tags (Any, default={}) – Tags associated with the metadata

  • 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

  • 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 or 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, 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
  • tags (Any, default={}) – Tags associated with the metadata

  • 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

  • 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 or 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, 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
  • tags (Any, default={}) – Tags associated with the metadata

  • 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

  • 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 or 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

class Config[source]

Pydantic configuration for attributes.

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
  • tags (Any, default={}) – Tags associated with the metadata

  • 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

  • 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

gmso.ForceField

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

dict

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

dict

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

dict

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

dict

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

dict

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

dict