Updating particle filters

[ADRIAN PINTO]

Hi,

I created a few stationary particles in my simulations using filters. Now, I want to update them at a later step. In the documentation page, there is an updater called FilterUpdater, but I'm unable to figure out how to use it exactly. I checked for example scripts to help me with the task, but found none.

This is what I am doing.

As an example script, I am initializing two particles. I'm creating two groups particle and stationary with hoomd.filters.Tags. Now, I instantiate filter updater with [stationary] as my parameter. But this doesn't help.

filter_update = hoomd.update.FilterUpdater(trigger = 100, filters = [stationary])

cpu = hoomd.device.CPU()

sim = hoomd.Simulation(cpu, seed = 100)

sim.create_state_from_gsd("lattice.gsd")

sim.operations.integrator = integrator

sim.operations.writers.append(gsd_writer)

# sim.operations.updaters.append(move_action)

sim.operations.updaters.append(filter_update)

Any help would be much appreciated.

Best regards,

Adrian

[Joshua Anderson]

Adrian,

When I run your script, I get `NameError: name 'hoomd' is not defined`. I don't understand what output you get compared to what you expect.

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

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[ADRIAN PINTO]

Hi Joshua,

That was just a snippet of the code. Here is the entire code. I want the stationary particle to get updated since I have used FilterUpdater. In my actual system, I want to update filters dynamically, that's why I have written this example script.

import numpy as np

import hoomd

import gsd.hoomd

L = 200

box_size = [L, L, L, 0, 0, 0]

xpos = np.zeros(2)

ypos = np.zeros(2)

zpos = np.zeros(2)

xpos[0] = 1

xpos[1] = 10

vx = np.zeros(2)

vy = np.zeros(2)

vz = np.zeros(2)

vx[0] = 0.1

vx[1] = -0.1

frame = gsd.hoomd.Frame()

frame.configuration.box = box_size

frame.particles.N = 2

frame.particles.position = list(zip(xpos, ypos, zpos))

frame.particles.velocity = list(zip(vx, vy, vz))

frame.particles.types = ['A']

frame.particles.typeid = [0]*2

particle1 = hoomd.filter.Tags([0])

stationary = hoomd.filter.Tags([1])

# class ExampleAction(hoomd.custom.Action):

# def act(self, timestep):

# self._state.snapshot.particles.position[1] = self._state.snapshot.particles.position[1] + 1

with gsd.hoomd.open(name='lattice.gsd', mode='w') as f:

f.append(frame)

nl = hoomd.md.nlist.Cell(buffer = 1)

nlist = hoomd.md.nlist.Tree(buffer=0.4, exclusions=('bond',), rebuild_check_delay=10, check_dist=True, mesh=None, default_r_cut=3)

fslj = hoomd.md.pair.ForceShiftedLJ(nlist=nlist, default_r_cut=3)

fslj.params[('A', 'A')] = dict(epsilon=1.0, sigma=0.8)

dt = 0.001

MTTK = hoomd.md.methods.thermostats.Berendsen(kT=1.0, tau=dt*100)

nvt = hoomd.md.methods.ConstantVolume(filter=particle1,

thermostat=MTTK)

integrator = hoomd.md.Integrator(dt = 0.001, methods=[nvt], forces = [fslj])

gsd_writer = hoomd.write.GSD(filename='molecular_trajectory_1.gsd',

trigger=hoomd.trigger.Periodic(10),

mode='wb')

class moveAction(hoomd.custom.Action):

def act(self, timestep):

pass

action_custom = moveAction()

# move_action = hoomd.update.CustomUpdater(trigger = 1000, action = action_custom)

filter_update = hoomd.update.FilterUpdater(trigger = 1, filters = [stationary])

cpu = hoomd.device.CPU()

sim = hoomd.Simulation(cpu, seed = 100)

sim.create_state_from_gsd("lattice.gsd")

sim.operations.integrator = integrator

sim.operations.writers.append(gsd_writer)

# sim.operations.updaters.append(move_action)

sim.operations.updaters.append(filter_update)

logger = hoomd.logging.Logger(categories=['scalar', 'string'])

logger.add(sim, quantities= ['timestep', 'tps'])

#table_file = hoomd.write.Table(output=file, trigger = hoomd.trigger.Periodic(period = 100000), logger = logger1)

table = hoomd.write.Table(trigger = hoomd.trigger.Periodic(period = 100000), logger = logger)

sim.operations.writers.append(table)

sim.run(10e5)

Best regards,

Adrian

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[Joshua Anderson]

Adrian,

I executed your script and get the output I expect. Particle 0 moves and particle 1 remains stationary. Particle 0 is selected by the filter `particle1` and integrated by the `nvt` integration method. Particle 1 remains stationary because it is selected by the `particle1` filter, not because it is in the unused `stationary` group.

Use `FilterUpdater` with a a dynamic filter, such as one that selects based on time or particle position, AND use the updated filter in the integration method to define the particles that you wish to be integrated. See `CustomFilter` for details on defining your own filters: https://hoomd-blue.readthedocs.io/en/v4.0.1/module-hoomd-filter.html#hoomd.filter.CustomFilter

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

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