Plugins¶

Plugins are used to add specific data processing or to modify the regular pipeline in certain way. However, the functionality they provide is not considered essential.

If the simulation is started without postprocess part (see Overview), most of the plugins are disabled.

Summary¶

Classes¶

`PinObject`	Contains the special value Unrestricted for unrestricted axes in `createPinObject`.
`PostprocessPlugin`	Base postprocess plugin class
`SimulationPlugin`	Base simulation plugin class

Creation functions¶

`createAddForce`(state, name, pv, force)	This plugin will add constant force \(\mathbf{F}_{extra}\) to each particle of a specific PV every time-step.
`createAddForceField`(args, *kwargs)	Overloaded function.
`createAddFourRollMillForce`(state, name, pv, …)	This plugin will add a force \(\mathbf{f} = (A \sin x \cos y, A \cos x \sin y, 0)\) to each particle of a specific PV every time-step.
`createAddPotentialForce`(args, *kwargs)	Overloaded function.
`createAddReversePoiseuilleForce`(state, name, …)	This plugin will add constant force \(\mathbf{F}_{extra}\) to each particle of a specific PV every time-step.
`createAddSinusoidalForce`(state, name, pv, …)	This plugin will add sinusoidal force \(\mathbf{F}(\mathbf{r}) = A \sin\left( 2\pi k r_y / L_y\right)\) to each particle of a specific PV every time-step, where \(L_y\) is the dimension of the domain along :math`y`.
`createAddTorque`(state, name, ov, torque)	This plugin will add constant torque \(\mathbf{T}_{extra}\) to each object of a specific OV every time-step.
`createAnchorParticles`(state, name, pv, …)	This plugin will set a given particle at a given position and velocity.
`createBerendsenThermostat`(state, name, pvs, …)	Berendsen thermostat.
`createDensityControl`(state, name, file_name, …)	This plugin applies forces to a set of particle vectors in order to get a constant density.
`createDensityOutlet`(state, name, pvs, …)	This plugin removes particles from a set of `ParticleVector` in a given region if the number density is larger than a given target.
`createDumpAverage`(state, name, pvs, …)	This plugin will project certain quantities of the particle vectors on the grid (by simple binning), perform time-averaging of the grid and dump it in XDMF format with HDF5 backend.The quantities of interest are represented as channels associated with particles vectors.Some interactions, integrators, etc.and more notable plug-ins can add to the Particle Vectors per-particles arrays to hold different values.These arrays are called channels.Any such channel may be used in this plug-in, however, user must explicitely specify the type of values that the channel holds.Particle number density is used to correctly average the values, so it will be sampled and written in any case into the field “number_densities”..
`createDumpAverageRelative`(state, name, pvs, …)	This plugin acts just like the regular flow dumper, with one difference.
`createDumpMesh`(state, name, ov, dump_every, path)	This plugin will write the meshes of all the object of the specified Object Vector in a PLY format.
`createDumpObjectStats`(state, name, ov, …)	This plugin will write the coordinates of the centers of mass of the objects of the specified Object Vector.
`createDumpParticles`(state, name, pv, …)	This plugin will dump positions, velocities and optional attached data of all the particles of the specified Particle Vector.
`createDumpParticlesWithMesh`(state, name, ov, …)	This plugin will dump positions, velocities and optional attached data of all the particles of the specified Object Vector, as well as connectivity information.
`createDumpParticlesWithPolylines`(state, …)	This plugin will dump positions, velocities and optional attached data of all the particles of the specified ChainVector, as well as connectivity information representing polylines.
`createDumpXYZ`(state, name, pv, dump_every, path)	This plugin will dump positions of all the particles of the specified Particle Vector in the XYZ format.
`createExchangePVSFluxPlane`(state, name, pv1, …)	This plugin exchanges particles from a particle vector crossing a given plane to another particle vector.
`createExpMovingAverage`(state, name, pv, …)	Compute the exponential moving average (EMA) of the given channel of a `ParticleVector` and stores it in the new channel “ema_channel_name”.
`createExternalMagneticTorque`(state, name, …)	This plugin gives a magnetic moment \(\mathbf{M}\) to every rigid objects in a given `RigidObjectVector`.
`createForceSaver`(state, name, pv)	This plugin creates an extra channel per particle inside the given particle vector named ‘forces’.
`createImposeProfile`(state, name, pv, low, …)	This plugin will set the velocity of each particle inside a given domain to a target velocity with an additive term drawn from Maxwell distribution of the given temperature.
`createImposeVelocity`(state, name, pvs, …)	This plugin will add velocity to all the particles of the target PV in the specified area (rectangle) such that the average velocity equals to desired.
`createMagneticDipoleInteractions`(state, …)	This plugin computes the forces and torques resulting from pairwise dipole-dipole interactions between rigid objects.
`createMembraneExtraForce`(state, name, pv, forces)	This plugin adds a given external force to a given membrane.
`createMsd`(state, name, pv, start_time, …)	This plugin computes the mean square displacement of th particles of a given `ParticleVector`.
`createParticleChannelAverager`(state, name, …)	This plugin averages a channel (per particle data) inside the given particle vector and saves it to a new channel.
`createParticleChannelSaver`(state, name, pv, …)	This plugin creates an extra channel per particle inside the given particle vector with a given name.
`createParticleChecker`(state, name, check_every)	This plugin will check the positions and velocities of all particles in the simulation every given time steps.
`createParticleDisplacement`(state, name, pv, …)	This plugin computes and save the displacement of the particles within a given particle vector.
`createParticleDrag`(state, name, pv, drag)	This plugin will add drag force \(\mathbf{f} = - C_d \mathbf{u}\) to each particle of a specific PV every time-step.
`createPinObject`(state, name, ov, dump_every, …)	This plugin will impose given velocity as the center of mass velocity (by axis) of all the objects of the specified Object Vector.
`createPinRodExtremity`(state, name, rv, …)	This plugin adds a force on a given segment of all the rods in a `RodVector`.
`createPlaneOutlet`(state, name, pvs, plane)	This plugin removes all particles from a set of `ParticleVector` that are on the non-negative side of a given plane.
`createRateOutlet`(state, name, pvs, …)	This plugin removes particles from a set of `ParticleVector` in a given region at a given mass rate.
`createRdf`(state, name, pv, max_dist, nbins, …)	Compute the radial distribution function (RDF) of a given `ParticleVector`.
`createRmacf`(state, name, cv, start_time, …)	This plugin computes the mean Rouse mode autocorrelation over time from a given `ChainVector`.
`createShearField`(state, name, pv, shear, …)	This plugin computes the shear velocity field at every particle’s position and stores it in a channel vector.
`createSinusoidalField`(state, name, pv, …)	This plugin computes a sinusoidal velocity field at every particle’s position and stores it in a channel vector.
`createStats`(state, name, every, pvs, filename)	This plugin will report aggregate quantities of all the particles in the simulation: total number of particles in the simulation, average temperature and momentum, maximum velocity magnutide of a particle and also the mean real time per step in milliseconds.
`createTemperaturize`(state, name, pv, kBT, …)	This plugin changes the velocity of each particles from a given `ParticleVector`.
`createVacf`(state, name, pv, start_time, …)	This plugin computes the mean velocity autocorrelation over time from a given `ParticleVector`.
`createVelocityControl`(state, name, filename, …)	This plugin applies a uniform force to all the particles of the target PVS in the specified area (rectangle).
`createVelocityInlet`(state, name, pv, …)	This plugin inserts particles in a given `ParticleVector`.
`createVirialPressurePlugin`(state, name, pv, …)	This plugin computes the virial pressure from a given `ParticleVector`.
`createWallForceCollector`(state, name, wall, …)	This plugin collects and averages the total force exerted on a given wall.
`createWallRepulsion`(state, name, pv, wall, …)	This plugin will add force on all the particles that are nearby a specified wall.

Details¶

class PinObject¶

Bases: mmirheo.Plugins.SimulationPlugin

Contains the special value Unrestricted for unrestricted axes in createPinObject.

class PostprocessPlugin¶

Bases: object

Base postprocess plugin class

class SimulationPlugin¶

Bases: object

Base simulation plugin class

createAddForce(state: MirState, name: str, pv: ParticleVectors.ParticleVector, force: real3) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will add constant force \(\mathbf{F}_{extra}\) to each particle of a specific PV every time-step. Is is advised to only use it with rigid objects, since Velocity-Verlet integrator with constant pressure can do the same without any performance penalty.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with force – extra force

createAddForceField(*args, **kwargs)¶

Overloaded function.

createAddForceField(state: MirState, name: str, pv: ParticleVectors.ParticleVector, force_field: Callable[[real3], real3], h: real3) -> Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]

Add a force to each particle of a specific PV every time-step.

Args:

name: name of the plugin pv: ParticleVector that we’ll work with force_field: force field h: grid spacing used to discretize the force field
createAddForceField(state: MirState, name: str, pv: ParticleVectors.ParticleVector, force_field_filename: str, h: real3) -> Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]

Add a force to each particle of a specific PV every time-step.

Args:

name: name of the plugin pv: ParticleVector that we’ll work with force_field_filename: file that contains the force field on a cartesian grid. Same format as Sdf for walls but with 4 components per grid point (only the first three are used). h: grid spacing used to discretize the force field

createAddFourRollMillForce(state: MirState, name: str, pv: ParticleVectors.ParticleVector, intensity: float) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will add a force \(\mathbf{f} = (A \sin x \cos y, A \cos x \sin y, 0)\) to each particle of a specific PV every time-step.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with intensity – The intensity of the force

createAddPotentialForce(*args, **kwargs)¶

Overloaded function.

createAddPotentialForce(state: MirState, name: str, pv: ParticleVectors.ParticleVector, potential_field: Callable[[real3], float], h: real3) -> Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]

Add a force \(\mathbf{F}_{extra}\) to each particle of a specific PV every time-step. The force is the negative gradient of a potential field at the particle position.

Args:

name: name of the plugin pv: ParticleVector that we’ll work with potential_field: potential field h: grid spacing used to discretize the potential field
createAddPotentialForce(state: MirState, name: str, pv: ParticleVectors.ParticleVector, potential_field_filename: str, h: real3) -> Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]

Add a force \(\mathbf{F}_{extra}\) to each particle of a specific PV every time-step. The force is the negative gradient of a potential field at the particle position.

Args:

name: name of the plugin pv: ParticleVector that we’ll work with potential_field_filename: file that contains the potential field on a cartesian grid. Same format as Sdf for walls. h: grid spacing used to discretize the potential field

createAddReversePoiseuilleForce(state: MirState, name: str, pv: ParticleVectors.ParticleVector, force: real3, flip_direction: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will add constant force \(\mathbf{F}_{extra}\) to each particle of a specific PV every time-step. The force is flipped if the position is in the upper half along the flip_direction.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with force – extra force flip_direction – either x, y or z. The direction along with the sign of the force changes.

createAddSinusoidalForce(state: MirState, name: str, pv: ParticleVectors.ParticleVector, magnitude: float, wave_number: int) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will add sinusoidal force \(\mathbf{F}(\mathbf{r}) = A \sin\left( 2\pi k r_y / L_y\right)\) to each particle of a specific PV every time-step, where \(L_y\) is the dimension of the domain along :math`y`.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with magnitude – coefficient \(A\) wave_number – mode \(k\) (integer)

createAddTorque(state: MirState, name: str, ov: ParticleVectors.ParticleVector, torque: real3) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will add constant torque \(\mathbf{T}_{extra}\) to each object of a specific OV every time-step.

Parameters:	name – name of the plugin ov – `ObjectVector` that we’ll work with torque – extra torque (per object)

createAnchorParticles(state: MirState, name: str, pv: ParticleVectors.ParticleVector, positions: Callable[[float], List[real3]], velocities: Callable[[float], List[real3]], pids: List[int], report_every: int, path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will set a given particle at a given position and velocity.

Parameters:

name – name of the plugin
pv – ParticleVector that we’ll work with
positions – positions (at given time) of the particles
velocities – velocities (at given time) of the particles
pids – global ids of the particles in the given particle vector
report_every – report the time averaged force acting on the particles every this amount of timesteps
path – folder where to dump the stats

createBerendsenThermostat(state: MirState, name: str, pvs: List[ParticleVectors.ParticleVector], tau: float, kBT: float, increaseIfLower: bool=True) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

Berendsen thermostat.

On each time step the velocities of all particles in given particle vectors are multiplied by the following factor:

\[\lambda = \sqrt{1 + \frac{\Delta t}{\tau} \left( \frac{T_0}{T} - 1 \right)}\]

where \(\Delta t\) is a time step, \(\tau\) relaxation time, \(T\) current temperature, \(T_0\) target temperature.

Reference: Berendsen et al. (1984)

Parameters:	name – name of the plugin pvs – list of `ParticleVector` objects to apply the thermostat to tau – relaxation time \(\tau\) kBT – target thermal energy \(k_B T_0\) increaseIfLower – whether to increase the temperature if it’s lower than the target temperature

createDensityControl(state: MirState, name: str, file_name: str, pvs: List[ParticleVectors.ParticleVector], target_density: float, region: Callable[[real3], float], resolution: real3, level_lo: float, level_hi: float, level_space: float, Kp: float, Ki: float, Kd: float, tune_every: int, dump_every: int, sample_every: int) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin applies forces to a set of particle vectors in order to get a constant density.

Parameters:

name – name of the plugin
file_name – output filename
pvs – list of ParticleVector that we’ll work with
target_density – target number density (used only at boundaries of level sets)
region – a scalar field which describes how to subdivide the domain. It must be continuous and differentiable, as the forces are in the gradient direction of this field
resolution – grid resolution to represent the region field
level_lo – lower level set to apply the controller on
level_hi – highest level set to apply the controller on
level_space – the size of one subregion in terms of level sets
Ki, Kd (Kp,) – pid control parameters
tune_every – update the forces every this amount of time steps
dump_every – dump densities and forces in file filename
sample_every – sample to average densities every this amount of time steps

createDensityOutlet(state: MirState, name: str, pvs: List[ParticleVectors.ParticleVector], number_density: float, region: Callable[[real3], float], resolution: real3) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin removes particles from a set of ParticleVector in a given region if the number density is larger than a given target.

Parameters:	name – name of the plugin pvs – list of `ParticleVector` that we’ll work with number_density – maximum number_density in the region region – a function that is negative in the concerned region and positive outside resolution – grid resolution to represent the region field

createDumpAverage(state: MirState, name: str, pvs: List[ParticleVectors.ParticleVector], sample_every: int, dump_every: int, bin_size: real3=real3(1.0, 1.0, 1.0), channels: List[str], path: str='xdmf/') → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will project certain quantities of the particle vectors on the grid (by simple binning), perform time-averaging of the grid and dump it in XDMF format with HDF5 backend. The quantities of interest are represented as channels associated with particles vectors. Some interactions, integrators, etc. and more notable plug-ins can add to the Particle Vectors per-particles arrays to hold different values. These arrays are called channels. Any such channel may be used in this plug-in, however, user must explicitely specify the type of values that the channel holds. Particle number density is used to correctly average the values, so it will be sampled and written in any case into the field “number_densities”.

Note

This plugin is inactive if postprocess is disabled

Parameters:

name – name of the plugin
pvs – list of ParticleVector that we’ll work with
sample_every – sample quantities every this many time-steps
dump_every – write files every this many time-steps
bin_size – bin size for sampling. The resulting quantities will be cell-centered
path – Path and filename prefix for the dumps. For every dump two files will be created: <path>_NNNNN.xmf and <path>_NNNNN.h5
channels – list of channel names. See Reserved names.

createDumpAverageRelative(state: MirState, name: str, pvs: List[ParticleVectors.ParticleVector], relative_to_ov: ParticleVectors.ObjectVector, relative_to_id: int, sample_every: int, dump_every: int, bin_size: real3=real3(1.0, 1.0, 1.0), channels: List[str], path: str='xdmf/') → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin acts just like the regular flow dumper, with one difference. It will assume a coordinate system attached to the center of mass of a specific object. In other words, velocities and coordinates sampled correspond to the object reference frame.

Note

Note that this plugin needs to allocate memory for the grid in the full domain, not only in the corresponding MPI subdomain. Therefore large domains will lead to running out of memory

Note

This plugin is inactive if postprocess is disabled

The arguments are the same as for createDumpAverage() with a few additions:

Parameters:

name – name of the plugin
pvs – list of ParticleVector that we’ll work with
sample_every – sample quantities every this many time-steps
dump_every – write files every this many time-steps
bin_size – bin size for sampling. The resulting quantities will be cell-centered
path – Path and filename prefix for the dumps. For every dump two files will be created: <path>_NNNNN.xmf and <path>_NNNNN.h5
channels – list of channel names. See Reserved names.
relative_to_ov – take an object governing the frame of reference from this ObjectVector
relative_to_id – take an object governing the frame of reference with the specific ID

createDumpMesh(state: MirState, name: str, ov: ParticleVectors.ObjectVector, dump_every: int, path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will write the meshes of all the object of the specified Object Vector in a PLY format.

Note

This plugin is inactive if postprocess is disabled

Parameters:	name – name of the plugin ov – `ObjectVector` that we’ll work with dump_every – write files every this many time-steps path – the files will look like this: <path>/<ov_name>_NNNNN.ply

createDumpObjectStats(state: MirState, name: str, ov: ParticleVectors.ObjectVector, dump_every: int, filename: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will write the coordinates of the centers of mass of the objects of the specified Object Vector. Instantaneous quantities (COM velocity, angular velocity, force, torque) are also written. If the objects are rigid bodies, also will be written the quaternion describing the rotation. The type id field is also dumped if the objects have this field activated (see MembraneWithTypeId).

The file format is the following:

Note

Note that all the written values are instantaneous

Note

This plugin is inactive if postprocess is disabled

Parameters:	name – Name of the plugin. ov – `ObjectVector` that we’ll work with. dump_every – Write files every this many time-steps. filename – The name of the resulting csv file.

createDumpParticles(state: MirState, name: str, pv: ParticleVectors.ParticleVector, dump_every: int, channel_names: List[str], path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will dump positions, velocities and optional attached data of all the particles of the specified Particle Vector. The data is dumped into hdf5 format. An additional xdfm file is dumped to describe the data and make it readable by visualization tools. If a channel from object data or bisegment data is provided, the data will be scattered to particles before being dumped as normal particle data.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with dump_every – write files every this many time-steps channel_names – list of channel names to be dumped. path – Path and filename prefix for the dumps. For every dump two files will be created: <path>_NNNNN.xmf and <path>_NNNNN.h5

createDumpParticlesWithMesh(state: MirState, name: str, ov: ParticleVectors.ObjectVector, dump_every: int, channel_names: List[str], path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will dump positions, velocities and optional attached data of all the particles of the specified Object Vector, as well as connectivity information. The data is dumped into hdf5 format. An additional xdfm file is dumped to describe the data and make it readable by visualization tools.

Parameters:	name – name of the plugin ov – `ObjectVector` that we’ll work with dump_every – write files every this many time-steps channel_names – list of channel names to be dumped. path – Path and filename prefix for the dumps. For every dump two files will be created: <path>_NNNNN.xmf and <path>_NNNNN.h5

createDumpParticlesWithPolylines(state: MirState, name: str, cv: ParticleVectors.ChainVector, dump_every: int, channel_names: List[str], path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will dump positions, velocities and optional attached data of all the particles of the specified ChainVector, as well as connectivity information representing polylines. The data is dumped into hdf5 format. An additional xdfm file is dumped to describe the data and make it readable by visualization tools.

Parameters:	name – name of the plugin. cv – `ChainVector` to be dumped. dump_every – write files every this many time-steps. channel_names – list of channel names to be dumped. path – Path and filename prefix for the dumps. For every dump two files will be created: <path>_NNNNN.xmf and <path>_NNNNN.h5

createDumpXYZ(state: MirState, name: str, pv: ParticleVectors.ParticleVector, dump_every: int, path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will dump positions of all the particles of the specified Particle Vector in the XYZ format.

Note

This plugin is inactive if postprocess is disabled

Parameters:	name – name of the plugin pvs – list of `ParticleVector` that we’ll work with dump_every – write files every this many time-steps path – the files will look like this: <path>/<pv_name>_NNNNN.xyz

createExchangePVSFluxPlane(state: MirState, name: str, pv1: ParticleVectors.ParticleVector, pv2: ParticleVectors.ParticleVector, plane: real4) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin exchanges particles from a particle vector crossing a given plane to another particle vector. A particle with position x, y, z has crossed the plane if ax + by + cz + d >= 0, where a, b, c and d are the coefficient stored in the ‘plane’ variable

Parameters:	name – name of the plugin pv1 – `ParticleVector` source pv2 – `ParticleVector` destination plane – 4 coefficients for the plane equation ax + by + cz + d >= 0

createExpMovingAverage(state: MirState, name: str, pv: ParticleVectors.ParticleVector, alpha: float, src_channel_name: str, ema_channel_name: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

Compute the exponential moving average (EMA) of the given channel of a ParticleVector and stores it in the new channel “ema_channel_name”.

Parameters:	name – name of the plugin pv – `ParticleVector` source alpha – EMA coefficient. must be in [0, 1]. src_channel_name – The name of the source channel. ema_channel_name – The name of the new EMA channel.

createExternalMagneticTorque(state: MirState, name: str, rov: ParticleVectors.RigidObjectVector, moment: real3, magneticFunction: Callable[[float], real3]) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin gives a magnetic moment \(\mathbf{M}\) to every rigid objects in a given RigidObjectVector. It also models a uniform magnetic field \(\mathbf{B}\) (varying in time) and adds the induced torque to the objects according to:

\[\mathbf{T} = \mathbf{M} \times \mathbf{B}\]

The magnetic field is passed as a function from python. The function must take a real (time) as input and output a tuple of three reals (magnetic field).

Parameters:	name – name of the plugin rov – `RigidObjectVector` with which the magnetic field will interact moment – magnetic moment per object magneticFunction – a function that depends on time and returns a uniform (real3) magnetic field

createForceSaver(state: MirState, name: str, pv: ParticleVectors.ParticleVector) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin creates an extra channel per particle inside the given particle vector named ‘forces’. It copies the total forces at each time step and make it accessible by other plugins. The forces are stored in an array of real3.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with

createImposeProfile(state: MirState, name: str, pv: ParticleVectors.ParticleVector, low: real3, high: real3, velocity: real3, kBT: float) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will set the velocity of each particle inside a given domain to a target velocity with an additive term drawn from Maxwell distribution of the given temperature.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with low – the lower corner of the domain high – the higher corner of the domain velocity – target velocity kBT – temperature in the domain (appropriate Maxwell distribution will be used)

createImposeVelocity(state: MirState, name: str, pvs: List[ParticleVectors.ParticleVector], every: int, low: real3, high: real3, velocity: real3) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will add velocity to all the particles of the target PV in the specified area (rectangle) such that the average velocity equals to desired.

Parameters:	name – name of the plugin pvs – list of `ParticleVector` that we’ll work with every – change the velocities once in every timestep low – the lower corner of the domain high – the higher corner of the domain velocity – target velocity

createMagneticDipoleInteractions(state: MirState, name: str, rov: ParticleVectors.RigidObjectVector, moment: real3, mu0: float, periodic: bool=True) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin computes the forces and torques resulting from pairwise dipole-dipole interactions between rigid objects. All rigid objects are assumed to be the same with a constant magnetic moment in their frame of reference.

Parameters:	name – name of the plugin rov – `RigidObjectVector` with which the magnetic field will interact moment – magnetic moment per object mu0 – magnetic permeability of the medium periodic – if True, compute the interactions from the closest periodic image of each object.

createMembraneExtraForce(state: MirState, name: str, pv: ParticleVectors.ParticleVector, forces: List[real3]) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin adds a given external force to a given membrane. The force is defined vertex wise and does not depend on position. It is the same for all membranes belonging to the same particle vector.

Parameters:	name – name of the plugin pv – `ParticleVector` to which the force should be added forces – array of forces, one force (3 reals) per vertex in a single mesh

createMsd(state: MirState, name: str, pv: ParticleVectors.ParticleVector, start_time: float, end_time: float, dump_every: int, path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin computes the mean square displacement of th particles of a given ParticleVector. The reference position` is that of the given ParticleVector at the given start time.

Parameters:	name – Name of the plugin. pv – Concerned `ParticleVector`. start_time – Simulation time of the reference positions. end_time – End time until which to compute the MSD. dump_every – Report MSD every this many time-steps. path – The folder name in which the file will be dumped.

createParticleChannelAverager(state: MirState, name: str, pv: ParticleVectors.ParticleVector, channelName: str, averageName: str, updateEvery: float) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin averages a channel (per particle data) inside the given particle vector and saves it to a new channel. This new channel (containing the averaged data) is updated every fixed number of time steps.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with channelName – The name of the source channel. averageName – The name of the average channel. updateEvery – reinitialize the averages every this number of steps.

createParticleChannelSaver(state: MirState, name: str, pv: ParticleVectors.ParticleVector, channelName: str, savedName: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin creates an extra channel per particle inside the given particle vector with a given name. It copies the content of an extra channel of pv at each time step and make it accessible by other plugins.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with channelName – the name of the source channel savedName – name of the extra channel

createParticleChecker(state: MirState, name: str, check_every: int) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will check the positions and velocities of all particles in the simulation every given time steps. To be used for debugging purpose.

Parameters:	name – name of the plugin check_every – check every this amount of time steps

createParticleDisplacement(state: MirState, name: str, pv: ParticleVectors.ParticleVector, update_every: int) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin computes and save the displacement of the particles within a given particle vector. The result is stored inside the extra channel “displacements” as an array of real3.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with update_every – displacements are computed between positions separated by this amount of timesteps

createParticleDrag(state: MirState, name: str, pv: ParticleVectors.ParticleVector, drag: float) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will add drag force \(\mathbf{f} = - C_d \mathbf{u}\) to each particle of a specific PV every time-step.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with drag – drag coefficient

createPinObject(state: MirState, name: str, ov: ParticleVectors.ObjectVector, dump_every: int, path: str, velocity: real3, angular_velocity: real3) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will impose given velocity as the center of mass velocity (by axis) of all the objects of the specified Object Vector. If the objects are rigid bodies, rotation may be restricted with this plugin as well. The time-averaged force and/or torque required to impose the velocities and rotations are reported in the dumped file, with the following format:

Note

This plugin is inactive if postprocess is disabled

Parameters:

name – name of the plugin
ov – ObjectVector that we’ll work with
dump_every – write files every this many time-steps
path – the files will look like this: <path>/<ov_name>.csv
velocity – 3 reals, each component is the desired object velocity. If the corresponding component should not be restricted, set this value to PinObject::Unrestricted
angular_velocity – 3 reals, each component is the desired object angular velocity. If the corresponding component should not be restricted, set this value to PinObject::Unrestricted

createPinRodExtremity(state: MirState, name: str, rv: ParticleVectors.RodVector, segment_id: int, f_magn: float, target_direction: real3) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin adds a force on a given segment of all the rods in a RodVector. The force has the form deriving from the potential

\[E = k \left( 1 - \cos \theta \right),\]

where \(\theta\) is the angle between the material frame and a given direction (projected on the concerned segment). Note that the force is applied only on the material frame and not on the center line.

Parameters:	name – name of the plugin rv – `RodVector` that we’ll work with segment_id – the segment to which the plugin is active f_magn – force magnitude target_direction – the direction in which the material frame tends to align

createPlaneOutlet(state: MirState, name: str, pvs: List[ParticleVectors.ParticleVector], plane: real4) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin removes all particles from a set of ParticleVector that are on the non-negative side of a given plane.

Parameters:	name – name of the plugin pvs – list of `ParticleVector` that we’ll work with plane – Tuple (a, b, c, d). Particles are removed if ax + by + cz + d >= 0.

createRateOutlet(state: MirState, name: str, pvs: List[ParticleVectors.ParticleVector], mass_rate: float, region: Callable[[real3], float], resolution: real3) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin removes particles from a set of ParticleVector in a given region at a given mass rate.

Parameters:	name – name of the plugin pvs – list of `ParticleVector` that we’ll work with mass_rate – total outlet mass rate in the region region – a function that is negative in the concerned region and positive outside resolution – grid resolution to represent the region field

createRdf(state: MirState, name: str, pv: ParticleVectors.ParticleVector, max_dist: float, nbins: int, basename: str, every: int) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

Compute the radial distribution function (RDF) of a given ParticleVector. For simplicity, particles that are less that max_dist from the subdomain border are not counted.

Parameters:

name – Name of the plugin.
pv – The ParticleVector that we ant to compute the RDF from.
max_dist – The RDF will be computed on the interval [0, max_dist]. Must be strictly less than half the minimum size of one subdomain.
nbins – The RDF is computed on nbins bins.
basename – Each RDF dump will be dumped in csv format to <basename>-XXXXX.csv.
every – Computes and dump the RDF every this amount of timesteps.

createRmacf(state: MirState, name: str, cv: ParticleVectors.ChainVector, start_time: float, end_time: float, dump_every: int, path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin computes the mean Rouse mode autocorrelation over time from a given ChainVector. The reference modes are that of the ChainVector at the given start time.

Parameters:	name – Name of the plugin. cv – Concerned `ChainVector`. start_time – Simulation time of the reference velocities. end_time – End time until which to compute the RMACF. dump_every – Report the RMACF every this many time-steps. path – The folder name in which the file will be dumped.

createShearField(state: MirState, name: str, pv: ParticleVectors.ParticleVector, shear: List[float[9]], origin: real3, sf_channel_name: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin computes the shear velocity field at every particle’s position and stores it in a channel vector.

Parameters:	name – Name of the plugin. pv – Concerned `ParticleVector`. shear – Shear tensor. origin – Point in space with zero velocity. sf_channel_name – Name of the channel that will contain the shear field.

createSinusoidalField(state: MirState, name: str, pv: ParticleVectors.ParticleVector, magnitude: float, wave_number: int, sf_channel_name: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin computes a sinusoidal velocity field at every particle’s position and stores it in a channel vector.

Parameters:	name – Name of the plugin. pv – Concerned `ParticleVector`. magnitude – Maximum velocity along x. wave_number – Number of periods along y. sf_channel_name – Name of the channel that will contain the sinusoidal field.

createStats(state: MirState, name: str, every: int, pvs: List[ParticleVectors.ParticleVector]=[], filename: str='') → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will report aggregate quantities of all the particles in the simulation: total number of particles in the simulation, average temperature and momentum, maximum velocity magnutide of a particle and also the mean real time per step in milliseconds.

Note

This plugin is inactive if postprocess is disabled

Parameters:	name – Name of the plugin. every – Report to standard output every that many time-steps. pvs – List of pvs to compute statistics from. If empty, will use all the pvs registered in the simulation. filename – The statistics are saved in this csv file. The name should either end with .csv or have no extension, in which case .csv is added.

createTemperaturize(state: MirState, name: str, pv: ParticleVectors.ParticleVector, kBT: float, keepVelocity: bool) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin changes the velocity of each particles from a given ParticleVector. It can operate under two modes: keepVelocity = True, in which case it adds a term drawn from a Maxwell distribution to the current velocity; keepVelocity = False, in which case it sets the velocity to a term drawn from a Maxwell distribution.

Parameters:	name – name of the plugin pv – the concerned `ParticleVector` kBT – the target temperature keepVelocity – True for adding Maxwell distribution to the previous velocity; False to set the velocity to a Maxwell distribution.

createVacf(state: MirState, name: str, pv: ParticleVectors.ParticleVector, start_time: float, end_time: float, dump_every: int, path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin computes the mean velocity autocorrelation over time from a given ParticleVector. The reference velocity v0 is that of the given ParticleVector at the given start time.

Parameters:	name – Name of the plugin. pv – Concerned `ParticleVector`. start_time – Simulation time of the reference velocities. end_time – End time until which to compute the VACF. dump_every – Report the VACF every this many time-steps. path – The folder name in which the file will be dumped.

createVelocityControl(state: MirState, name: str, filename: str, pvs: List[ParticleVectors.ParticleVector], low: real3, high: real3, sample_every: int, tune_every: int, dump_every: int, target_vel: real3, Kp: float, Ki: float, Kd: float) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin applies a uniform force to all the particles of the target PVS in the specified area (rectangle). The force is adapted bvia a PID controller such that the velocity average of the particles matches the target average velocity.

Parameters:

name – Name of the plugin.
filename – Dump file name. Must have a csv extension or no extension at all.
pvs – List of concerned ParticleVector.
high (low,) – boundaries of the domain of interest
sample_every – sample velocity every this many time-steps
tune_every – adapt the force every this many time-steps
dump_every – write files every this many time-steps
target_vel – the target mean velocity of the particles in the domain of interest
Ki, Kd (Kp,) – PID controller coefficients

createVelocityInlet(state: MirState, name: str, pv: ParticleVectors.ParticleVector, implicit_surface_func: Callable[[real3], float], velocity_field: Callable[[real3], real3], resolution: real3, number_density: float, kBT: float) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin inserts particles in a given ParticleVector. The particles are inserted on a given surface with given velocity inlet. The rate of insertion is governed by the velocity and the given number density.

Parameters:

name – name of the plugin
pv – the ParticleVector that we ll work with
implicit_surface_func – a scalar field function that has the required surface as zero level set
velocity_field – vector field that describes the velocity on the inlet (will be evaluated on the surface only)
resolution – grid size used to discretize the surface
number_density – number density of the inserted solvent
kBT – temperature of the inserted solvent

createVirialPressurePlugin(state: MirState, name: str, pv: ParticleVectors.ParticleVector, regionFunc: Callable[[real3], float], h: real3, dump_every: int, path: str) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin computes the virial pressure from a given ParticleVector. Note that the stress computation must be enabled with the corresponding stressName. This returns the total internal virial part only (no temperature term). Note that the volume is not devided in the result, the user is responsible to properly scale the output.

Parameters:	name – name of the plugin pv – concerned `ParticleVector` regionFunc – predicate for the concerned region; positive inside the region and negative outside h – grid size for representing the predicate onto a grid dump_every – report total pressure every this many time-steps path – the folder name in which the file will be dumped

createWallForceCollector(state: MirState, name: str, wall: Walls.Wall, pvFrozen: ParticleVectors.ParticleVector, sample_every: int, dump_every: int, filename: str, detailed_dump: bool=False) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin collects and averages the total force exerted on a given wall. The result has 2 components:

bounce back: force necessary to the momentum change

frozen particles: total interaction force exerted on the frozen particles

Parameters:

name – name of the plugin
wall – The Wall to collect forces from
pvFrozen – corresponding frozen ParticleVector
sample_every – sample every this number of time steps
dump_every – dump every this number of time steps
filename – output filename (csv format)
detailed_dump – if True, will dump separately the bounce contribution and the rest. If False, only the sum is dumped.

createWallRepulsion(state: MirState, name: str, pv: ParticleVectors.ParticleVector, wall: Walls.Wall, C: float, h: float, max_force: float) → Tuple[Plugins.SimulationPlugin, Plugins.PostprocessPlugin]¶

This plugin will add force on all the particles that are nearby a specified wall. The motivation of this plugin is as follows. The particles of regular PVs are prevented from penetrating into the walls by Wall Bouncers. However, using Wall Bouncers with Object Vectors may be undesirable (e.g. in case of a very viscous membrane) or impossible (in case of rigid objects). In these cases one can use either strong repulsive potential between the object and the wall particle or alternatively this plugin. The advantage of the SDF-based repulsion is that small penetrations won’t break the simulation.

The force expression looks as follows:

\[\begin{split}\mathbf{F}(\mathbf{r}) = \mathbf{\nabla}S(\mathbf{r}) \cdot \begin{cases} 0, & S(\mathbf{r}) < -h,\\ \min(F_\text{max}, C (S(\mathbf{r}) + h)), & S(\mathbf{r}) \geqslant -h,\\ \end{cases}\end{split}\]

where \(S\) is the SDF of the wall, \(C\), \(F_\text{max}\) and \(h\) are parameters.

Parameters:	name – name of the plugin pv – `ParticleVector` that we’ll work with wall – `Wall` that defines the repulsion C – \(C\) h – \(h\) max_force – \(F_{max}\)