Initial conditions

Initial conditions create the distribution of the particles or objects at the beginning of any simulation. Several variants include random placement, reading ICs from Python or restarting from the previous state

Summary

FromArray()	Set particles according to given position and velocity arrays.
InitialConditions()	Base class for initial conditions
Membrane()	Can only be used with Membrane Object Vector, see Initial conditions.
MembraneWithTypeId()	Same as Membrane with an additional type id field which distinguish membranes with different properties.
RandomChains()	Creates chains of particles with random shapes at prescribed positions.
Restart()	Read the state of the particle vector from restart files.
Rigid()	Can only be used with Rigid Object Vector or Rigid Ellipsoid, see Initial conditions.
Rod()	Can only be used with Rod Vector.
StraightChains()	Creates chains of particles of the same orientations and lengths at prescribed positions.
Uniform()	The particles will be generated with the desired number density uniformly at random in all the domain.
UniformFiltered()	The particles will be generated with the desired number density uniformly at random in all the domain and then filtered out by the given filter.
UniformSphere()	The particles will be generated with the desired number density uniformly at random inside or outside a given sphere.
UniformWithPolChain()	The particles will be generated with the desired number density uniformly at random in all the domain.

Details

class FromArray

Bases: mmirheo.InitialConditions.InitialConditions

Set particles according to given position and velocity arrays.

__init__(pos: List[real3], vel: List[real3]) → None

Parameters:

• pos – array of positions
• vel – array of velocities

class InitialConditions

Bases: object

Base class for initial conditions

__init__()

Initialize self. See help(type(self)) for accurate signature.

class Membrane

Bases: mmirheo.InitialConditions.InitialConditions

Can only be used with Membrane Object Vector, see Initial conditions. These IC will initialize the particles of each object according to the mesh associated with Membrane, and then the objects will be translated/rotated according to the provided initial conditions.

__init__(com_q: List[ComQ], global_scale: float=1.0) → None

Parameters:

• com_q – List describing location and rotation of the created objects. One entry in the list corresponds to one object created. Each entry consist of 7 reals: <com_x> <com_y> <com_z> <q_x> <q_y> <q_z> <q_w>, where com is the center of mass of the object, q is the quaternion of its rotation, not necessarily normalized
• global_scale – All the membranes will be scaled by that value. Useful to implement membranes growth so that they can fill the space with high volume fraction

class MembraneWithTypeId

Bases: mmirheo.InitialConditions.Membrane

Same as Membrane with an additional type id field which distinguish membranes with different properties. This is may be used with MembraneForces with the corresponding filter.

__init__(com_q: List[ComQ], type_ids: List[int], global_scale: float=1.0) → None

Parameters:

• com_q – List describing location and rotation of the created objects. One entry in the list corresponds to one object created. Each entry consist of 7 reals: <com_x> <com_y> <com_z> <q_x> <q_y> <q_z> <q_w>, where com is the center of mass of the object, q is the quaternion of its rotation, not necessarily normalized
• type_ids – list of type ids. Each entry corresponds to the id of the group to which the corresponding membrane belongs.
• global_scale – All the membranes will be scaled by that value. Useful to implement membranes growth so that they can fill the space with high volume fraction

class RandomChains

Bases: mmirheo.InitialConditions.InitialConditions

Creates chains of particles with random shapes at prescribed positions. Each chain is generated by a random walk with a constant step size.

__init__(positions: List[real3], length: float) → None

Parameters:

• positions – center of mass of each chain
• length – length of the chains.

class Restart

Bases: mmirheo.InitialConditions.InitialConditions

Read the state of the particle vector from restart files.

__init__(path: str='restart/') → None

Parameters:path – folder where the restart files reside.

class Rigid

Bases: mmirheo.InitialConditions.InitialConditions

Can only be used with Rigid Object Vector or Rigid Ellipsoid, see Initial conditions. These IC will initialize the particles of each object according to the template .xyz file and then the objects will be translated/rotated according to the provided initial conditions.

__init__(*args, **kwargs)

Overloaded function.

1. __init__(com_q: List[ComQ], xyz_filename: str) -> None

   Args:

   com_q:

   List describing location and rotation of the created objects. One entry in the list corresponds to one object created. Each entry consist of 7 reals: <com_x> <com_y> <com_z> <q_x> <q_y> <q_z> <q_w>, where com is the center of mass of the object, q is the quaternion of its rotation, not necessarily normalized

   xyz_filename:

   Template that describes the positions of the body particles before translation or rotation is applied. Standard .xyz file format is used with first line being the number of particles, second comment, third and onwards - particle coordinates. The number of particles in the file must be the same as in number of particles per object in the corresponding PV

2. __init__(com_q: List[ComQ], coords: List[real3]) -> None

   Args:

   com_q:

   List describing location and rotation of the created objects. One entry in the list corresponds to one object created. Each entry consist of 7 reals: <com_x> <com_y> <com_z> <q_x> <q_y> <q_z> <q_w>, where com is the center of mass of the object, q is the quaternion of its rotation, not necessarily normalized

   coords:

   Template that describes the positions of the body particles before translation or rotation is applied. The number of coordinates must be the same as in number of particles per object in the corresponding PV

3. __init__(com_q: List[ComQ], coords: List[real3], init_vels: List[real3]) -> None

   Args:

   com_q:

   List describing location and rotation of the created objects. One entry in the list corresponds to one object created. Each entry consist of 7 reals: <com_x> <com_y> <com_z> <q_x> <q_y> <q_z> <q_w>, where com is the center of mass of the object, q is the quaternion of its rotation, not necessarily normalized

   coords:

   Template that describes the positions of the body particles before translation or rotation is applied. The number of coordinates must be the same as in number of particles per object in the corresponding PV

   com_q:

   List specifying initial Center-Of-Mass velocities of the bodies. One entry (list of 3 reals) in the list corresponds to one object

class Rod

Bases: mmirheo.InitialConditions.InitialConditions

Can only be used with Rod Vector. These IC will initialize the particles of each rod according to the the given explicit center-line position aand torsion mapping and then the objects will be translated/rotated according to the provided initial conditions.

__init__(com_q: List[ComQ], center_line: Callable[[float], real3], torsion: Callable[[float], float], a: float, initial_frame: real3=real3(inf, inf, inf)) → None

Parameters:

• com_q – List describing location and rotation of the created objects. One entry in the list corresponds to one object created. Each entry consist of 7 reals: <com_x> <com_y> <com_z> <q_x> <q_y> <q_z> <q_w>, where com is the center of mass of the object, q is the quaternion of its rotation, not necessarily normalized
• center_line – explicit mapping \(\mathbf{r} : [0,1] \rightarrow R^3\). Assume \(|r'(s)|\) is constant for all \(s \in [0,1]\).
• torsion – explicit mapping \(\tau : [0,1] \rightarrow R\).
• a – width of the rod
• initial_frame – Orientation of the initial frame (optional) By default, will come up with any orthogonal frame to the rod at origin

class StraightChains

Bases: mmirheo.InitialConditions.InitialConditions

Creates chains of particles of the same orientations and lengths at prescribed positions.

__init__(positions: List[real3], orientations: List[real3], length: float) → None

Parameters:

• positions – center of mass of each chain
• orientations – array of unit vectors indicating the orientation of the chains
• length – length of the chains.

class Uniform

Bases: mmirheo.InitialConditions.InitialConditions

The particles will be generated with the desired number density uniformly at random in all the domain. These IC may be used with any Particle Vector, but only make sense for regular PV.

__init__(number_density: float) → None

Parameters:number_density – target number density

class UniformFiltered

Bases: mmirheo.InitialConditions.InitialConditions

The particles will be generated with the desired number density uniformly at random in all the domain and then filtered out by the given filter. These IC may be used with any Particle Vector, but only make sense for regular PV.

__init__(number_density: float, filter: Callable[[real3], bool]) → None

Parameters:

• number_density – target number density
• filter – given position, returns True if the particle should be kept

class UniformSphere

Bases: mmirheo.InitialConditions.InitialConditions

The particles will be generated with the desired number density uniformly at random inside or outside a given sphere. These IC may be used with any Particle Vector, but only make sense for regular PV.

__init__(number_density: float, center: real3, radius: float, inside: bool) → None

Parameters:

• number_density – target number density
• center – center of the sphere
• radius – radius of the sphere
• inside – whether the particles should be inside or outside the sphere

class UniformWithPolChain

Bases: mmirheo.InitialConditions.InitialConditions

The particles will be generated with the desired number density uniformly at random in all the domain. In addition, will provide an additional channel containing polymeric chain end to end vectors.

__init__(number_density: float, q0: float=0.0) → None

Parameters:

• number_density – target number density
• q0 – average length of the q vector