rigid body

Yulin Luo

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Aug 16, 2021, 11:57:53 PM8/16/21

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Hi , Dear HOMMD-blue users, I am trying to use hoomd.group.rigid() to simulate my systems,

my script looks like this:

import sys

import os

import hoomd, hoomd.md as md

from hoomd import *

from hoomd import deprecated

context.initialize("");

deprecated.init.read_xml("1-rigid.xml");

#WCA

nl = hoomd.md.nlist.cell()

lj = hoomd.md.pair.lj(r_cut=2**(1.0/10), nlist=nl);

lj.pair_coeff.set('A', 'A', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('A', 'B', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('A', 'C', epsilon=1, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('A', 'D', epsilon=1, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('A', 'R', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('B', 'B', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('B', 'C', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('B', 'D', epsilon=0, sigma=0.75, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('B', 'R', epsilon=0, sigma=0.75, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('C', 'C', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('C', 'D', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('C', 'R', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('D', 'D', epsilon=1, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('D', 'R', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.pair_coeff.set('R', 'R', epsilon=0, sigma=1, r_cut=2**(1.0/10), r_on=2.0);

lj.set_params(mode="xplor")

harmonic=hoomd.md.bond.harmonic();

harmonic.bond_coeff.set('C-C',k=30,r0=1.0)

harmonic.bond_coeff.set('C-D',k=30,r0=1.0)

nl.reset_exclusions(exclusions = []);

rigid = hoomd.group.rigid_center()

nonrigid = hoomd.group.nonrigid()

all = hoomd.group.all()

hoomd.md.integrate.mode_standard(dt=0.01);

nvt = hoomd.md.integrate.langevin(group=nonrigid, kT=0.2, seed=42)

lg1 = hoomd.md.integrate.langevin(group=rigid, kT=2.0, seed=42)

lg1.set_gamma('A', gamma=0.5)

lg1.set_gamma('B', gamma=0.5)

lg1.set_gamma('R', gamma=0.5)

hoomd.md.update.zero_momentum()

zeroer= hoomd.md.update.zero_momentum(period=500)

hoomd.analyze.log(filename="thermo.log",

quantities=['potential_energy'],

period=100,

overwrite=True)

hoomd.dump.gsd("trajectory.gsd",

period=100,

group=all,

overwrite=True)

hoomd.run(10000)

My initial configuration is obtained through “read_xml”, it includes a rigid sphere and two polymer chains.But the trajectory.gsd is very strange(see test.gif or gif below).

As you can see from the gif, the rigid sphere is not moving, only a blue particle is moving. Hoomd regards the blue particle as the rigid_center, but the blue particle does not move with the rigid sphere as a whole.

I guess it may be due to the rigid_center settings, when I use the "read_xml" method to set the initial configuration, how should I use the "rigid = hoomd.group.rigid_center()"?

In other words, do I still need to specify the position of the rigid_center?

Could you please help me with this issue? Thanks in advance.

Best,

Yulin Luo

test.gif

Joshua Anderson

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Aug 23, 2021, 8:01:05 AM8/23/21

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Yulin,

Your script is missing the hoomd.md.constrain.rigid object: https://hoomd-blue.readthedocs.io/en/v2.9.7/module-md-constrain.html#hoomd.md.constrain.rigid
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan

> My initial configuration is obtained through “read_xml”, it includes a rigid sphere and two polymer chains.But the trajectory.gsd is very strange(see test.gif or gif below).<test.gif>

> As you can see from the gif, the rigid sphere is not moving, only a blue particle is moving. Hoomd regards the blue particle as the rigid_center, but the blue particle does not move with the rigid sphere as a whole.
>
> I guess it may be due to the rigid_center settings, when I use the "read_xml" method to set the initial configuration, how should I use the "rigid = hoomd.group.rigid_center()"?
> In other words, do I still need to specify the position of the rigid_center?
>
> Could you please help me with this issue? Thanks in advance.
>
> Best,
>
> Yulin Luo
>

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> <test.gif><test.gif>

Yulin Luo

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Aug 23, 2021, 10:09:24 AM8/23/21

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Anderson:

Hi ！Thanks for your suggestion!

As you suggested, I added “hoomd.md.constrain.rigid ” to my script, my script looks like this:

import numpy as np

import pandas as pd

import hoomd, hoomd.md as md

from hoomd import *

from hoomd import deprecated

context.initialize("");

system = deprecated.init.read_xml("1-rigid_with_R.xml");

system.particles[24].moment_inertia = [1, 1, 1]

system.particles[157].moment_inertia = [1, 1, 1]

num_particle = 2

par_pos =[]

for i in range(133*num_particle):

par_pos.append(system.particles[i+24].position)

par_type =[]

for i in range(133*num_particle):

par_type.append(system.particles[i+24].type)

rigid = hoomd.md.constrain.rigid();

for i in range(num_particle-1):

rigid.set_param('R',

types=par_type[1:133*(i+1)],

positions=par_pos[1:133*(i+1)])

rigid.create_bodies()