Build¶

Overview

`hoobas.Build.Builder`	General building methods of Hoobas.
`hoobas.Build.HOOMDBuilder`	Building methods specialized for the HOOMD package
`hoobas.Build.ESPResSOppBuilder`	Building methods specialized for ESPResSO++ simulation package.
`hoobas.Build.openMMBuilder`	Building methods specialized for the openMM simulation package
`hoobas.Build.CrossBuilder`	This class provides functionality for cross MD package functionalities.
`hoobas.Build.Bias`	Object to manage adding biases to the system in the form of bonds, e.g.
`hoobas.Build.Electrostatics`	Class dealing with charge normalization in the system and permittivity values.
`hoobas.Build.FileWriter`	Handles file writing from builder objects

Details

class hoobas.Build.Bias(parent)[source]¶

Object to manage adding biases to the system in the form of bonds, e.g. for umbrella sampling or thermodynamic integration

add_bonds_colloids(bond_name=None, colloid_test=None)[source]¶

Add bonds between every center of colloid objects in the domain

Parameters

bond_name – Name of the bond type created
colloid_test (dict) – Dictionary of properties the colloid must satisfy

Returns

add_einstein_crystal_lattice(additional_offsets=None, beadopts=None, bond_name=None, colloid_test=None)[source]¶

Creates additional beads on each center of the colloids. Default type is ‘EC’ with a default mass of 1.0. Bonds are appended between this particle and the colloid center for thermodynamic integration. Bond name is ‘EC-bond’ by default. Additional points to append can be supplied by additional_offsets, which are offsets from the center of the colloid by index.

Conditions to evaluate on the properties of the colloid can be specified by a colloid dict.

Parameters

additional_offsets – additional points where to add beads
beadopts – options to be passed to the bead constructor
bond_name – name of the bond to append
colloid_test – dict of properties that has to be specified

Returns

None

class hoobas.Build.Builder(domain, **kwargs)[source]¶

General building methods of Hoobas. This class only assembles the system and related commands. It is composed with the following classes for specialized post-processing:

Electrostatics: charge normalization (permittivity)

Bias: adding biasing potentials in the form of bonds, fixed Einstein lattices, etc.

FileWriter: writing simulation information to files

Args:: domain: Simulation domain used

add_N_ext_obj(ext_obj, N)[source]¶

Adds N composite objects to the system positioned at random locations, with random rotation

Parameters

ext_obj (CompositeObject) – external object to be copied.
N (int) – number of objects

Return type

None

Returns

add_ions(N, qtype='ion', ion_mass=1.0, q=1.0, ion_diam=1.0)[source]¶

Adds N ions in the simulation, randomly positioned

Parameters

N (int) – Number of ions
qtype (str) – ion beadtype
ion_mass (float) – mass of ions
q (float) – charge of ions
ion_diam (float) – diameter of ions

Returns

None

add_layer(multilayer, midplane=0.0, displace_elements=True)[source]¶

Adds a 2D object in the simulation box. It is automatically added in the (001) plane, crossing the z=0 plane. For most simulation boxes, this is a flat plane laying in the XY plane. By default, the box size is increased and the simulation contents that would had overlapped are pushed away. This behavior is controlled by displace_elements

Parameters

multilayer (Layers.Multilayer) – 2D layer to add
midplane (float) – location of the plane
displace_elements (bool) – whether to displace existing contents away from the layer

Return type

None

Returns

None

add_rho_molar_ions(rho, qtype='ion', ion_mass=1.0, q=1.0, ion_diam=1.0)[source]¶

Adds a volumetric density of rho ions to the simulation domain

Parameters

rho (float) – molar density (mol / L)
qtype (basestring) – beadtype for added ions
q (float) – charge of the ions
ion_mass (float) – mass of added ions
ion_diam (float) – size of ions

Return type

None

Returns

None

property bead_types¶

Beadtypes in the simulation

Returns: beadtypes
Return type: list

property center_tags¶

Tags of the center of rigid bodies in the simulation

Returns: tags
Return type: list

property center_types¶

Beadtypes of centers of rigid bodies in the simulation

Returns: beadtypes
Return type: list

property charge_list¶

Returns the list of charged beadtypes in the simulation

Returns: charged beadtypes
Return type: list

copy_ext_obj(ext_obj)[source]¶

Directly imports a composite object into the simulation domain without performing any changes

Parameters: ext_obj (CompositeObject) – object to import
Return type: None
Returns

enforce_PBC(z_box_multi=None)[source]¶

enforces periodic boundary conditions on particles. The last vector length can be multiplied by a constant to create empty space

Parameters: z_box_multi (float) – z multiplier for PBC
Return type: None
Returns

enforce_XYPBC()[source]¶

Enforces a special 2D periodic conditions in the XY plane while leaving Z free. (x,y) components of the last box vectors are assumed to be zero, while the z components of the first two vectors are assumed to be zero. This is called when making crystal slabs.

Return type: None
Returns: None

fix_remaining_charge(ptype='ion', ntype='ion', pion_mass=1.0, nion_mass=1.0, qp=1.0, qn=-1.0, pion_diam=1.0, nion_diam=1.0, isrerun=False)[source]¶

Enforces electroneutrality of the system

Parameters

ptype (str) – type name of cation
ntype (str) – type name of anion
pion_mass (float) – mass of cation
nion_mass (float) – mass of anion
qp (float) – charge of cation
qn (float) – charge of anion
pion_diam (float) – diameter of cation
nion_diam (float) – diameter of anion
isrerun (bool) – internal parameter; should not be used from outside

Return type

None

Returns

None

property num_beads¶

Number of beads in the simulation

Returns: number of beads
Return type: int

property obj_end_index¶

Queries the list of last indexes of each object added to the simulation. This can be used to create groups in HOOMD-blue, when used in conjunction with the starting indexes

Returns: Ending indexes
Return type: list

property obj_start_index¶

Queries the list of starting indexes of each object added to the simulation. This can be used to create groups in HOOMD-blue for instance, in conjunction with ending indexes

Returns: Starting indexes
Return type: list

set_rotation_function(mode=None, key_search=None)[source]¶

Sets the rotation of rigid bodies in the domain. Note that all rigid bodies will be rotated according to their orientations, which includes rigid objects that are grafted on other objects. For these cases, the key_search option must be employed.

Parameters

mode (Optional[str]) – (string, None), either ‘none’ or ‘random’
key_search (Union[None, str, dict]) – (string, dict), used for random list of properties the rigid body must have in order to be rotated.

Returns

shift_pos(displacement)[source]¶: shift positions of all beads by a constant displacement :type displacement: ndarray :param displacement: Displacement to apply to all beads :rtype: None :return:

property surface_types¶

Tags of the surfaces of rigid bodies in the simulation

Returns: tags
Return type: list

property sys_box¶

Queries the simulation domain of the builder

Returns: box
Return type: iterable

class hoobas.Build.CrossBuilder(domain, **kwargs)[source]¶

This class provides functionality for cross MD package functionalities. This inherits from all the classes defined in MetaBuilder.BuilderTypes and also copies all class methods in another namespace, such that if a class MD_Build has a method called read, it located in CrossBuilder.read and CrossBuilder.MD_Build.read. This is meant to avoid overriden methods by external builders added to BuilderTypes.

Args:: domain: Simulation domain passed to Builder units(default = None): units of simulation. Defaults to reduced units

class hoobas.Build.ESPResSOppBuilder(domain, **kwargs)[source]¶

Building methods specialized for ESPResSO++ simulation package. Imports yield mangled names as the simulation package has no internal string representation for bonded types.

Args:: domain (SimulationDomain.Domain): domain to build units (SimulationUnits): units to use

pairlist_by_type(bondtype)[source]¶

In espresso++, a pairlist represents a bond interaction type. This returns all bonds corresponding to the supplied bondtype argument

Parameters: bondtype (str) – builder bondtype representation
Returns: bonds
Return type: list[Composite.Bond]

quadruplelist_by_type(dihedral_type)[source]¶

In espresso++, a triple list represents an angle interaction type. This returns all angles corresponding to the supplied angletype argument

Parameters: dihedral_type (str) – builder dihedral representation
Returns: dihedrals
Return type: list[Composite.Dihedral]

read(system)[source]¶

Reads an espresso++ system into the builder object. Bonded force-field names obtained are mangled

Parameters: system (espressopp.system) – espresso++ system
Returns: None

triplelist_by_type(angletype)[source]¶

In espresso++, a triple list represents an angle interaction type. This returns all angles corresponding to the supplied angletype argument

Parameters: angletype (str) – builder angletype representation
Returns: angles
Return type: list[Composite.Angle]

write(system, espressopp)[source]¶

Writes the contents of ESPResSOppBuilder to an espresso++ system. The package itself is an argument to this method

Parameters

system (espressopp.system) – espresso++ system to set
espressopp – espresso++ package

Returns

None

class hoobas.Build.Electrostatics(beads, units)[source]¶

Class dealing with charge normalization in the system and permittivity values.

Args:: beads: list of beads for which charge is managed units: units to which beads correspond

denormalize()[source]¶

Removes the normalization of charges in the system

Return type: None
Returns: None

get_type_charge_product(typeA, typeB)[source]¶

returns the charge product of two types of beads in the lists. Will not return correct values if multiple beads of a given type can have different charges

Parameters

typeA (str) – first beadtype
typeB (str) – second beadtype

Returns

charge product

Return type

float

property normalization¶

The normalization constant of charges in the system. This is equivalent to \(\epsilon^{1/2} / \mathcal{q}\), where \(\epsilon\) is the permittivity and \(\mathcal{q}\) the charge unit

Getter: returns the normalization constant
Setter: sets the normalization constant
Type: float
Return type: float

normalize()[source]¶

Normalizes the charges in the simulation. Normally, this should be done automatically by builders

Return type: None
Returns: None

property permittivity¶

Defines the relative permittivity of the system. For atomistic simulations, this value should be 1. For CG systems, this depends on the force-field. For Martini, this is 10.0.

Getter: Returns the permittivity value
Setter: Sets the permittivity value
Type: float
Return type: float

set_eps_salt_water(salt_concentration)[source]¶

Sets the permittivity of the simulation to known values for water-NaCl mixtures at a given ion concentration. These values are taken from: J.-W. Shen, C. Li, N. F. A. Vegt, C. Peter, “Transferability of coarse-grained potentials: implicit solver models for hydrated ions”, J. Chem. Th. and Comp., 2011

Parameters: salt_concentration (float) – Salt concentration in water (M)
Return type: None
Returns: None

set_eps_water_temperature(temperature)[source]¶: Sets the permittivity of the simulation to known values for water at different temperatures. Fit is taken from D. M. Hinckley, J. J. De Pablo, “Coarse-grained Ions for Nucleic Acid Modeling”, J. Chem. Th. Comp. 2015, with data from D. P. Fernandez et al. “A formulation for the static permittivity of water and steam at temperatures from 238K to 873K at pressures up to 1200 MPa including derivatives and Debye-Huckel coefficients”, J. Phys. and Chem. Ref. Data, 1997 :type temperature: float :param temperature: temperature (K) :type temperature: float :rtype: None :return:

class hoobas.Build.FileWriter(parent)[source]¶

Handles file writing from builder objects

This is automatically made by the builder class and methods can be accessed by builder.FileWriter.method

Args:: parent: Parent builder object

export_pdb(file_path)[source]¶

Writes a very short pdb file

Parameters: file_path (str) – file path to write to
Returns: None

class hoobas.Build.HOOMDBuilder(domain, **kwargs)[source]¶

Building methods specialized for the HOOMD package

Args:: domain (SimulationDomain.Domain): simulation domain used by the builder shapes (list of GenShape objects): list of shapes to build colloids with
kwargs:: units (SimulationUnits): units used by the builder

aggregate_rigid_tuples()[source]¶

Provides a method to obtain arguments for constrain.rigid(). This is required for rigid body dynamics

Returns: parameters to pass to hoomd
Return type: list[tuple]

charge_to_types_per_rigid_body(types)[source]¶

Sets a charge to every bead listed in types. This charge only depends on the rigid body number. This was used in O’Brien et al., “Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle self-assembly”, PNAS 2016

Parameters: types – beadtypes to apply charge on
Returns: None

correct_pnum_body_lists()[source]¶

Fixes the body attribute of beads to their particle tag number to fit HOOMD blue standards

Returns: None

import_snapshot(snapshot)[source]¶

Imports a hoomd snapshot as a HOOMDBuilder object.

Parameters: snapshot (hoomd.data.snapshot) – snapshot to import
Returns: None

match_hoomd_box_conventions()[source]¶

Shifts the base vectors used in the build to hoomd standards

Returns: None

set_snapshot(snapshot, PBC=True)[source]¶

Sets a given HOOMD snapshots to match the contents of the HOOMDBuilder object

Parameters

snapshot (hoomd.data.snapshot) – empty snapshot
PBC (bool) – Whether to enforce PBC conditions

Returns

None

class hoobas.Build.MetaBuilder[source]¶: Syntaxic sugar to have the CrossBuilder class inherits from all classes defined in BuilderTypes

class hoobas.Build.openMMBuilder(domain, **kwargs)[source]¶

Building methods specialized for the openMM simulation package

Args:: domain (SimulationDomain.Domain): domain to build kwargs: units to build this

match_box_conventions()[source]¶

shifts the base vectors used in the build to openMM standards

Returns: None

write(topology)[source]¶

Write the openMMBuilder contents to a openMM topology class

Parameters: topology – openMM topology object
Returns: None