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)

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)

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)

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)

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)

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

Parameters:

• ext_obj – external object to be copied.
• N – number of objects

Returns:

add_ions(N, qtype='ion', ion_mass=1.0, q=1.0, ion_diam=1.0)

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)

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

Returns:

None

add_rho_molar_ions(rho, qtype='ion', ion_mass=1.0, q=1.0, ion_diam=1.0)

Adds a volumetric density of rho ions to the simulation domain

Parameters:

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

Returns:

None

bead_types

Beadtypes in the simulation

Returns:beadtypes Return type:list

center_tags

Tags of the center of rigid bodies in the simulation

Returns:tags Return type:list

center_types

Beadtypes of centers of rigid bodies in the simulation

Returns:beadtypes Return type:list

charge_list

Returns the list of charged beadtypes in the simulation

Returns:charged beadtypes Return type:list

copy_ext_obj(ext_obj)

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

Parameters:ext_obj – object to import Returns:

enforce_PBC(z_box_multi=None)

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 Returns:

enforce_XYPBC()

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.

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)

Enforces electroneutrality of the system

Parameters:

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

Returns:

None

num_beads

Number of beads in the simulation

Returns:number of beads Return type:int

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

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)

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

Returns:

shift_pos(displacement)

shift positions of all beads by a constant displacement :param displacement: Displacement to apply to all beads :return:

surface_types

Tags of the surfaces of rigid bodies in the simulation

Returns:tags Return type:list

sys_box

Queries the simulation domain of the builder

Returns:box Return type:iterable

class hoobas.Build.CrossBuilder(domain, **kwargs)

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)

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)

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)

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)

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)

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)

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)

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()

Removes the normalization of charges in the system

Returns:None

get_type_charge_product(typeA, typeB)

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

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

normalize()

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

Returns:None

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

set_eps_to_salt_CPeter(salt_concentration)

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) Returns:None

class hoobas.Build.FileWriter(parent)

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)

Writes a very short pdb file

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

class hoobas.Build.HOOMDBuilder(domain, **kwargs)

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()

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)

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()

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

Returns:None

import_snapshot(snapshot)

Imports a hoomd snapshot as a HOOMDBuilder object.

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

match_hoomd_box_conventions()

Shifts the base vectors used in the build to hoomd standards

Returns:None

set_snapshot(snapshot, PBC=True)

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

Syntaxic sugar to have the CrossBuilder class inherits from all classes defined in BuilderTypes

class hoobas.Build.openMMBuilder(domain, **kwargs)

Building methods specialized for the openMM simulation package

Args:

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

match_box_conventions()

shifts the base vectors used in the build to openMM standards

Returns:None

write(topology)

Write the openMMBuilder contents to a openMM topology class

Parameters:topology – openMM topology object Returns:None